File: hisat_bp.cpp

package info (click to toggle)
hisat2 2.1.0-2
  • links: PTS, VCS
  • area: main
  • in suites: bullseye, buster, sid
  • size: 13,756 kB
  • sloc: cpp: 86,309; python: 12,230; sh: 2,171; perl: 936; makefile: 375
file content (3885 lines) | stat: -rw-r--r-- 154,914 bytes parent folder | download | duplicates (2)
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
1001
1002
1003
1004
1005
1006
1007
1008
1009
1010
1011
1012
1013
1014
1015
1016
1017
1018
1019
1020
1021
1022
1023
1024
1025
1026
1027
1028
1029
1030
1031
1032
1033
1034
1035
1036
1037
1038
1039
1040
1041
1042
1043
1044
1045
1046
1047
1048
1049
1050
1051
1052
1053
1054
1055
1056
1057
1058
1059
1060
1061
1062
1063
1064
1065
1066
1067
1068
1069
1070
1071
1072
1073
1074
1075
1076
1077
1078
1079
1080
1081
1082
1083
1084
1085
1086
1087
1088
1089
1090
1091
1092
1093
1094
1095
1096
1097
1098
1099
1100
1101
1102
1103
1104
1105
1106
1107
1108
1109
1110
1111
1112
1113
1114
1115
1116
1117
1118
1119
1120
1121
1122
1123
1124
1125
1126
1127
1128
1129
1130
1131
1132
1133
1134
1135
1136
1137
1138
1139
1140
1141
1142
1143
1144
1145
1146
1147
1148
1149
1150
1151
1152
1153
1154
1155
1156
1157
1158
1159
1160
1161
1162
1163
1164
1165
1166
1167
1168
1169
1170
1171
1172
1173
1174
1175
1176
1177
1178
1179
1180
1181
1182
1183
1184
1185
1186
1187
1188
1189
1190
1191
1192
1193
1194
1195
1196
1197
1198
1199
1200
1201
1202
1203
1204
1205
1206
1207
1208
1209
1210
1211
1212
1213
1214
1215
1216
1217
1218
1219
1220
1221
1222
1223
1224
1225
1226
1227
1228
1229
1230
1231
1232
1233
1234
1235
1236
1237
1238
1239
1240
1241
1242
1243
1244
1245
1246
1247
1248
1249
1250
1251
1252
1253
1254
1255
1256
1257
1258
1259
1260
1261
1262
1263
1264
1265
1266
1267
1268
1269
1270
1271
1272
1273
1274
1275
1276
1277
1278
1279
1280
1281
1282
1283
1284
1285
1286
1287
1288
1289
1290
1291
1292
1293
1294
1295
1296
1297
1298
1299
1300
1301
1302
1303
1304
1305
1306
1307
1308
1309
1310
1311
1312
1313
1314
1315
1316
1317
1318
1319
1320
1321
1322
1323
1324
1325
1326
1327
1328
1329
1330
1331
1332
1333
1334
1335
1336
1337
1338
1339
1340
1341
1342
1343
1344
1345
1346
1347
1348
1349
1350
1351
1352
1353
1354
1355
1356
1357
1358
1359
1360
1361
1362
1363
1364
1365
1366
1367
1368
1369
1370
1371
1372
1373
1374
1375
1376
1377
1378
1379
1380
1381
1382
1383
1384
1385
1386
1387
1388
1389
1390
1391
1392
1393
1394
1395
1396
1397
1398
1399
1400
1401
1402
1403
1404
1405
1406
1407
1408
1409
1410
1411
1412
1413
1414
1415
1416
1417
1418
1419
1420
1421
1422
1423
1424
1425
1426
1427
1428
1429
1430
1431
1432
1433
1434
1435
1436
1437
1438
1439
1440
1441
1442
1443
1444
1445
1446
1447
1448
1449
1450
1451
1452
1453
1454
1455
1456
1457
1458
1459
1460
1461
1462
1463
1464
1465
1466
1467
1468
1469
1470
1471
1472
1473
1474
1475
1476
1477
1478
1479
1480
1481
1482
1483
1484
1485
1486
1487
1488
1489
1490
1491
1492
1493
1494
1495
1496
1497
1498
1499
1500
1501
1502
1503
1504
1505
1506
1507
1508
1509
1510
1511
1512
1513
1514
1515
1516
1517
1518
1519
1520
1521
1522
1523
1524
1525
1526
1527
1528
1529
1530
1531
1532
1533
1534
1535
1536
1537
1538
1539
1540
1541
1542
1543
1544
1545
1546
1547
1548
1549
1550
1551
1552
1553
1554
1555
1556
1557
1558
1559
1560
1561
1562
1563
1564
1565
1566
1567
1568
1569
1570
1571
1572
1573
1574
1575
1576
1577
1578
1579
1580
1581
1582
1583
1584
1585
1586
1587
1588
1589
1590
1591
1592
1593
1594
1595
1596
1597
1598
1599
1600
1601
1602
1603
1604
1605
1606
1607
1608
1609
1610
1611
1612
1613
1614
1615
1616
1617
1618
1619
1620
1621
1622
1623
1624
1625
1626
1627
1628
1629
1630
1631
1632
1633
1634
1635
1636
1637
1638
1639
1640
1641
1642
1643
1644
1645
1646
1647
1648
1649
1650
1651
1652
1653
1654
1655
1656
1657
1658
1659
1660
1661
1662
1663
1664
1665
1666
1667
1668
1669
1670
1671
1672
1673
1674
1675
1676
1677
1678
1679
1680
1681
1682
1683
1684
1685
1686
1687
1688
1689
1690
1691
1692
1693
1694
1695
1696
1697
1698
1699
1700
1701
1702
1703
1704
1705
1706
1707
1708
1709
1710
1711
1712
1713
1714
1715
1716
1717
1718
1719
1720
1721
1722
1723
1724
1725
1726
1727
1728
1729
1730
1731
1732
1733
1734
1735
1736
1737
1738
1739
1740
1741
1742
1743
1744
1745
1746
1747
1748
1749
1750
1751
1752
1753
1754
1755
1756
1757
1758
1759
1760
1761
1762
1763
1764
1765
1766
1767
1768
1769
1770
1771
1772
1773
1774
1775
1776
1777
1778
1779
1780
1781
1782
1783
1784
1785
1786
1787
1788
1789
1790
1791
1792
1793
1794
1795
1796
1797
1798
1799
1800
1801
1802
1803
1804
1805
1806
1807
1808
1809
1810
1811
1812
1813
1814
1815
1816
1817
1818
1819
1820
1821
1822
1823
1824
1825
1826
1827
1828
1829
1830
1831
1832
1833
1834
1835
1836
1837
1838
1839
1840
1841
1842
1843
1844
1845
1846
1847
1848
1849
1850
1851
1852
1853
1854
1855
1856
1857
1858
1859
1860
1861
1862
1863
1864
1865
1866
1867
1868
1869
1870
1871
1872
1873
1874
1875
1876
1877
1878
1879
1880
1881
1882
1883
1884
1885
1886
1887
1888
1889
1890
1891
1892
1893
1894
1895
1896
1897
1898
1899
1900
1901
1902
1903
1904
1905
1906
1907
1908
1909
1910
1911
1912
1913
1914
1915
1916
1917
1918
1919
1920
1921
1922
1923
1924
1925
1926
1927
1928
1929
1930
1931
1932
1933
1934
1935
1936
1937
1938
1939
1940
1941
1942
1943
1944
1945
1946
1947
1948
1949
1950
1951
1952
1953
1954
1955
1956
1957
1958
1959
1960
1961
1962
1963
1964
1965
1966
1967
1968
1969
1970
1971
1972
1973
1974
1975
1976
1977
1978
1979
1980
1981
1982
1983
1984
1985
1986
1987
1988
1989
1990
1991
1992
1993
1994
1995
1996
1997
1998
1999
2000
2001
2002
2003
2004
2005
2006
2007
2008
2009
2010
2011
2012
2013
2014
2015
2016
2017
2018
2019
2020
2021
2022
2023
2024
2025
2026
2027
2028
2029
2030
2031
2032
2033
2034
2035
2036
2037
2038
2039
2040
2041
2042
2043
2044
2045
2046
2047
2048
2049
2050
2051
2052
2053
2054
2055
2056
2057
2058
2059
2060
2061
2062
2063
2064
2065
2066
2067
2068
2069
2070
2071
2072
2073
2074
2075
2076
2077
2078
2079
2080
2081
2082
2083
2084
2085
2086
2087
2088
2089
2090
2091
2092
2093
2094
2095
2096
2097
2098
2099
2100
2101
2102
2103
2104
2105
2106
2107
2108
2109
2110
2111
2112
2113
2114
2115
2116
2117
2118
2119
2120
2121
2122
2123
2124
2125
2126
2127
2128
2129
2130
2131
2132
2133
2134
2135
2136
2137
2138
2139
2140
2141
2142
2143
2144
2145
2146
2147
2148
2149
2150
2151
2152
2153
2154
2155
2156
2157
2158
2159
2160
2161
2162
2163
2164
2165
2166
2167
2168
2169
2170
2171
2172
2173
2174
2175
2176
2177
2178
2179
2180
2181
2182
2183
2184
2185
2186
2187
2188
2189
2190
2191
2192
2193
2194
2195
2196
2197
2198
2199
2200
2201
2202
2203
2204
2205
2206
2207
2208
2209
2210
2211
2212
2213
2214
2215
2216
2217
2218
2219
2220
2221
2222
2223
2224
2225
2226
2227
2228
2229
2230
2231
2232
2233
2234
2235
2236
2237
2238
2239
2240
2241
2242
2243
2244
2245
2246
2247
2248
2249
2250
2251
2252
2253
2254
2255
2256
2257
2258
2259
2260
2261
2262
2263
2264
2265
2266
2267
2268
2269
2270
2271
2272
2273
2274
2275
2276
2277
2278
2279
2280
2281
2282
2283
2284
2285
2286
2287
2288
2289
2290
2291
2292
2293
2294
2295
2296
2297
2298
2299
2300
2301
2302
2303
2304
2305
2306
2307
2308
2309
2310
2311
2312
2313
2314
2315
2316
2317
2318
2319
2320
2321
2322
2323
2324
2325
2326
2327
2328
2329
2330
2331
2332
2333
2334
2335
2336
2337
2338
2339
2340
2341
2342
2343
2344
2345
2346
2347
2348
2349
2350
2351
2352
2353
2354
2355
2356
2357
2358
2359
2360
2361
2362
2363
2364
2365
2366
2367
2368
2369
2370
2371
2372
2373
2374
2375
2376
2377
2378
2379
2380
2381
2382
2383
2384
2385
2386
2387
2388
2389
2390
2391
2392
2393
2394
2395
2396
2397
2398
2399
2400
2401
2402
2403
2404
2405
2406
2407
2408
2409
2410
2411
2412
2413
2414
2415
2416
2417
2418
2419
2420
2421
2422
2423
2424
2425
2426
2427
2428
2429
2430
2431
2432
2433
2434
2435
2436
2437
2438
2439
2440
2441
2442
2443
2444
2445
2446
2447
2448
2449
2450
2451
2452
2453
2454
2455
2456
2457
2458
2459
2460
2461
2462
2463
2464
2465
2466
2467
2468
2469
2470
2471
2472
2473
2474
2475
2476
2477
2478
2479
2480
2481
2482
2483
2484
2485
2486
2487
2488
2489
2490
2491
2492
2493
2494
2495
2496
2497
2498
2499
2500
2501
2502
2503
2504
2505
2506
2507
2508
2509
2510
2511
2512
2513
2514
2515
2516
2517
2518
2519
2520
2521
2522
2523
2524
2525
2526
2527
2528
2529
2530
2531
2532
2533
2534
2535
2536
2537
2538
2539
2540
2541
2542
2543
2544
2545
2546
2547
2548
2549
2550
2551
2552
2553
2554
2555
2556
2557
2558
2559
2560
2561
2562
2563
2564
2565
2566
2567
2568
2569
2570
2571
2572
2573
2574
2575
2576
2577
2578
2579
2580
2581
2582
2583
2584
2585
2586
2587
2588
2589
2590
2591
2592
2593
2594
2595
2596
2597
2598
2599
2600
2601
2602
2603
2604
2605
2606
2607
2608
2609
2610
2611
2612
2613
2614
2615
2616
2617
2618
2619
2620
2621
2622
2623
2624
2625
2626
2627
2628
2629
2630
2631
2632
2633
2634
2635
2636
2637
2638
2639
2640
2641
2642
2643
2644
2645
2646
2647
2648
2649
2650
2651
2652
2653
2654
2655
2656
2657
2658
2659
2660
2661
2662
2663
2664
2665
2666
2667
2668
2669
2670
2671
2672
2673
2674
2675
2676
2677
2678
2679
2680
2681
2682
2683
2684
2685
2686
2687
2688
2689
2690
2691
2692
2693
2694
2695
2696
2697
2698
2699
2700
2701
2702
2703
2704
2705
2706
2707
2708
2709
2710
2711
2712
2713
2714
2715
2716
2717
2718
2719
2720
2721
2722
2723
2724
2725
2726
2727
2728
2729
2730
2731
2732
2733
2734
2735
2736
2737
2738
2739
2740
2741
2742
2743
2744
2745
2746
2747
2748
2749
2750
2751
2752
2753
2754
2755
2756
2757
2758
2759
2760
2761
2762
2763
2764
2765
2766
2767
2768
2769
2770
2771
2772
2773
2774
2775
2776
2777
2778
2779
2780
2781
2782
2783
2784
2785
2786
2787
2788
2789
2790
2791
2792
2793
2794
2795
2796
2797
2798
2799
2800
2801
2802
2803
2804
2805
2806
2807
2808
2809
2810
2811
2812
2813
2814
2815
2816
2817
2818
2819
2820
2821
2822
2823
2824
2825
2826
2827
2828
2829
2830
2831
2832
2833
2834
2835
2836
2837
2838
2839
2840
2841
2842
2843
2844
2845
2846
2847
2848
2849
2850
2851
2852
2853
2854
2855
2856
2857
2858
2859
2860
2861
2862
2863
2864
2865
2866
2867
2868
2869
2870
2871
2872
2873
2874
2875
2876
2877
2878
2879
2880
2881
2882
2883
2884
2885
2886
2887
2888
2889
2890
2891
2892
2893
2894
2895
2896
2897
2898
2899
2900
2901
2902
2903
2904
2905
2906
2907
2908
2909
2910
2911
2912
2913
2914
2915
2916
2917
2918
2919
2920
2921
2922
2923
2924
2925
2926
2927
2928
2929
2930
2931
2932
2933
2934
2935
2936
2937
2938
2939
2940
2941
2942
2943
2944
2945
2946
2947
2948
2949
2950
2951
2952
2953
2954
2955
2956
2957
2958
2959
2960
2961
2962
2963
2964
2965
2966
2967
2968
2969
2970
2971
2972
2973
2974
2975
2976
2977
2978
2979
2980
2981
2982
2983
2984
2985
2986
2987
2988
2989
2990
2991
2992
2993
2994
2995
2996
2997
2998
2999
3000
3001
3002
3003
3004
3005
3006
3007
3008
3009
3010
3011
3012
3013
3014
3015
3016
3017
3018
3019
3020
3021
3022
3023
3024
3025
3026
3027
3028
3029
3030
3031
3032
3033
3034
3035
3036
3037
3038
3039
3040
3041
3042
3043
3044
3045
3046
3047
3048
3049
3050
3051
3052
3053
3054
3055
3056
3057
3058
3059
3060
3061
3062
3063
3064
3065
3066
3067
3068
3069
3070
3071
3072
3073
3074
3075
3076
3077
3078
3079
3080
3081
3082
3083
3084
3085
3086
3087
3088
3089
3090
3091
3092
3093
3094
3095
3096
3097
3098
3099
3100
3101
3102
3103
3104
3105
3106
3107
3108
3109
3110
3111
3112
3113
3114
3115
3116
3117
3118
3119
3120
3121
3122
3123
3124
3125
3126
3127
3128
3129
3130
3131
3132
3133
3134
3135
3136
3137
3138
3139
3140
3141
3142
3143
3144
3145
3146
3147
3148
3149
3150
3151
3152
3153
3154
3155
3156
3157
3158
3159
3160
3161
3162
3163
3164
3165
3166
3167
3168
3169
3170
3171
3172
3173
3174
3175
3176
3177
3178
3179
3180
3181
3182
3183
3184
3185
3186
3187
3188
3189
3190
3191
3192
3193
3194
3195
3196
3197
3198
3199
3200
3201
3202
3203
3204
3205
3206
3207
3208
3209
3210
3211
3212
3213
3214
3215
3216
3217
3218
3219
3220
3221
3222
3223
3224
3225
3226
3227
3228
3229
3230
3231
3232
3233
3234
3235
3236
3237
3238
3239
3240
3241
3242
3243
3244
3245
3246
3247
3248
3249
3250
3251
3252
3253
3254
3255
3256
3257
3258
3259
3260
3261
3262
3263
3264
3265
3266
3267
3268
3269
3270
3271
3272
3273
3274
3275
3276
3277
3278
3279
3280
3281
3282
3283
3284
3285
3286
3287
3288
3289
3290
3291
3292
3293
3294
3295
3296
3297
3298
3299
3300
3301
3302
3303
3304
3305
3306
3307
3308
3309
3310
3311
3312
3313
3314
3315
3316
3317
3318
3319
3320
3321
3322
3323
3324
3325
3326
3327
3328
3329
3330
3331
3332
3333
3334
3335
3336
3337
3338
3339
3340
3341
3342
3343
3344
3345
3346
3347
3348
3349
3350
3351
3352
3353
3354
3355
3356
3357
3358
3359
3360
3361
3362
3363
3364
3365
3366
3367
3368
3369
3370
3371
3372
3373
3374
3375
3376
3377
3378
3379
3380
3381
3382
3383
3384
3385
3386
3387
3388
3389
3390
3391
3392
3393
3394
3395
3396
3397
3398
3399
3400
3401
3402
3403
3404
3405
3406
3407
3408
3409
3410
3411
3412
3413
3414
3415
3416
3417
3418
3419
3420
3421
3422
3423
3424
3425
3426
3427
3428
3429
3430
3431
3432
3433
3434
3435
3436
3437
3438
3439
3440
3441
3442
3443
3444
3445
3446
3447
3448
3449
3450
3451
3452
3453
3454
3455
3456
3457
3458
3459
3460
3461
3462
3463
3464
3465
3466
3467
3468
3469
3470
3471
3472
3473
3474
3475
3476
3477
3478
3479
3480
3481
3482
3483
3484
3485
3486
3487
3488
3489
3490
3491
3492
3493
3494
3495
3496
3497
3498
3499
3500
3501
3502
3503
3504
3505
3506
3507
3508
3509
3510
3511
3512
3513
3514
3515
3516
3517
3518
3519
3520
3521
3522
3523
3524
3525
3526
3527
3528
3529
3530
3531
3532
3533
3534
3535
3536
3537
3538
3539
3540
3541
3542
3543
3544
3545
3546
3547
3548
3549
3550
3551
3552
3553
3554
3555
3556
3557
3558
3559
3560
3561
3562
3563
3564
3565
3566
3567
3568
3569
3570
3571
3572
3573
3574
3575
3576
3577
3578
3579
3580
3581
3582
3583
3584
3585
3586
3587
3588
3589
3590
3591
3592
3593
3594
3595
3596
3597
3598
3599
3600
3601
3602
3603
3604
3605
3606
3607
3608
3609
3610
3611
3612
3613
3614
3615
3616
3617
3618
3619
3620
3621
3622
3623
3624
3625
3626
3627
3628
3629
3630
3631
3632
3633
3634
3635
3636
3637
3638
3639
3640
3641
3642
3643
3644
3645
3646
3647
3648
3649
3650
3651
3652
3653
3654
3655
3656
3657
3658
3659
3660
3661
3662
3663
3664
3665
3666
3667
3668
3669
3670
3671
3672
3673
3674
3675
3676
3677
3678
3679
3680
3681
3682
3683
3684
3685
3686
3687
3688
3689
3690
3691
3692
3693
3694
3695
3696
3697
3698
3699
3700
3701
3702
3703
3704
3705
3706
3707
3708
3709
3710
3711
3712
3713
3714
3715
3716
3717
3718
3719
3720
3721
3722
3723
3724
3725
3726
3727
3728
3729
3730
3731
3732
3733
3734
3735
3736
3737
3738
3739
3740
3741
3742
3743
3744
3745
3746
3747
3748
3749
3750
3751
3752
3753
3754
3755
3756
3757
3758
3759
3760
3761
3762
3763
3764
3765
3766
3767
3768
3769
3770
3771
3772
3773
3774
3775
3776
3777
3778
3779
3780
3781
3782
3783
3784
3785
3786
3787
3788
3789
3790
3791
3792
3793
3794
3795
3796
3797
3798
3799
3800
3801
3802
3803
3804
3805
3806
3807
3808
3809
3810
3811
3812
3813
3814
3815
3816
3817
3818
3819
3820
3821
3822
3823
3824
3825
3826
3827
3828
3829
3830
3831
3832
3833
3834
3835
3836
3837
3838
3839
3840
3841
3842
3843
3844
3845
3846
3847
3848
3849
3850
3851
3852
3853
3854
3855
3856
3857
3858
3859
3860
3861
3862
3863
3864
3865
3866
3867
3868
3869
3870
3871
3872
3873
3874
3875
3876
3877
3878
3879
3880
3881
3882
3883
3884
3885
/*
 * Copyright 2014, Daehwan Kim <infphilo@gmail.com>
 *
 * This file is part of HISAT.
 *
 * HISAT is free software: you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation, either version 3 of the License, or
 * (at your option) any later version.
 *
 * HISAT is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with HISAT.  If not, see <http://www.gnu.org/licenses/>.
 */

#include <stdlib.h>
#include <iostream>
#include <fstream>
#include <string>
#include <cassert>
#include <stdexcept>
#include <getopt.h>
#include <math.h>
#include <utility>
#include <limits>
#include "alphabet.h"
#include "assert_helpers.h"
#include "endian_swap.h"
#include "bt2_idx.h"
#include "bt2_io.h"
#include "bt2_util.h"
#include "hier_idx.h"
#include "formats.h"
#include "sequence_io.h"
#include "tokenize.h"
#include "aln_sink.h"
#include "pat.h"
#include "threading.h"
#include "ds.h"
#include "aligner_metrics.h"
#include "sam.h"
#include "aligner_seed.h"
#include "splice_site.h"
#include "bp_aligner.h"
#include "aligner_seed_policy.h"
#include "aligner_driver.h"
#include "aligner_sw.h"
#include "aligner_sw_driver.h"
#include "aligner_cache.h"
#include "util.h"
#include "pe.h"
#include "simple_func.h"
#include "presets.h"
#include "opts.h"
#include "outq.h"
#include "aligner_seed2.h"

using namespace std;

static EList<string> mates1;  // mated reads (first mate)
static EList<string> mates2;  // mated reads (second mate)
static EList<string> mates12; // mated reads (1st/2nd interleaved in 1 file)
static string adjIdxBase;
bool gColor;              // colorspace (not supported)
int gVerbose;             // be talkative
static bool startVerbose; // be talkative at startup
int gQuiet;               // print nothing but the alignments
static int sanityCheck;   // enable expensive sanity checks
static int format;        // default read format is FASTQ
static string origString; // reference text, or filename(s)
static int seed;          // srandom() seed
static int timing;        // whether to report basic timing data
static int metricsIval;   // interval between alignment metrics messages (0 = no messages)
static string metricsFile;// output file to put alignment metrics in
static bool metricsStderr;// output file to put alignment metrics in
static bool metricsPerRead; // report a metrics tuple for every read
static bool allHits;      // for multihits, report just one
static bool showVersion;  // just print version and quit?
static int ipause;        // pause before maching?
static uint32_t qUpto;    // max # of queries to read
int gTrim5;               // amount to trim from 5' end
int gTrim3;               // amount to trim from 3' end
static int offRate;       // keep default offRate
static bool solexaQuals;  // quality strings are solexa quals, not phred, and subtract 64 (not 33)
static bool phred64Quals; // quality chars are phred, but must subtract 64 (not 33)
static bool integerQuals; // quality strings are space-separated strings of integers, not ASCII
static int nthreads;      // number of pthreads operating concurrently
static int outType;       // style of output
static bool noRefNames;   // true -> print reference indexes; not names
static uint32_t khits;    // number of hits per read; >1 is much slower
static uint32_t mhits;    // don't report any hits if there are > mhits
static int partitionSz;   // output a partitioning key in first field
static bool useSpinlock;  // false -> don't use of spinlocks even if they're #defines
static bool fileParallel; // separate threads read separate input files in parallel
static bool useShmem;     // use shared memory to hold the index
static bool useMm;        // use memory-mapped files to hold the index
static bool mmSweep;      // sweep through memory-mapped files immediately after mapping
int gMinInsert;           // minimum insert size
int gMaxInsert;           // maximum insert size
bool gMate1fw;            // -1 mate aligns in fw orientation on fw strand
bool gMate2fw;            // -2 mate aligns in rc orientation on fw strand
bool gFlippedMatesOK;     // allow mates to be in wrong order
bool gDovetailMatesOK;    // allow one mate to extend off the end of the other
bool gContainMatesOK;     // allow one mate to contain the other in PE alignment
bool gOlapMatesOK;        // allow mates to overlap in PE alignment
bool gExpandToFrag;       // incr max frag length to =larger mate len if necessary
bool gReportDiscordant;   // find and report discordant paired-end alignments
bool gReportMixed;        // find and report unpaired alignments for paired reads
static uint32_t cacheLimit;      // ranges w/ size > limit will be cached
static uint32_t cacheSize;       // # words per range cache
static uint32_t skipReads;       // # reads/read pairs to skip
bool gNofw; // don't align fw orientation of read
bool gNorc; // don't align rc orientation of read
static uint32_t fastaContLen;
static uint32_t fastaContFreq;
static bool hadoopOut; // print Hadoop status and summary messages
static bool fuzzy;
static bool fullRef;
static bool samTruncQname; // whether to truncate QNAME to 255 chars
static bool samOmitSecSeqQual; // omit SEQ/QUAL for 2ndary alignments?
static bool samNoUnal; // don't print records for unaligned reads
static bool samNoHead; // don't print any header lines in SAM output
static bool samNoSQ;   // don't print @SQ header lines
static bool sam_print_as;
static bool sam_print_xs;  // XS:i
static bool sam_print_xss; // Xs:i and Ys:i
static bool sam_print_yn;  // YN:i and Yn:i
static bool sam_print_xn;
static bool sam_print_cs;
static bool sam_print_cq;
static bool sam_print_x0;
static bool sam_print_x1;
static bool sam_print_xm;
static bool sam_print_xo;
static bool sam_print_xg;
static bool sam_print_nm;
static bool sam_print_md;
static bool sam_print_yf;
static bool sam_print_yi;
static bool sam_print_ym;
static bool sam_print_yp;
static bool sam_print_yt;
static bool sam_print_ys;
static bool sam_print_zs;
static bool sam_print_xr;
static bool sam_print_xt;
static bool sam_print_xd;
static bool sam_print_xu;
static bool sam_print_yl;
static bool sam_print_ye;
static bool sam_print_yu;
static bool sam_print_xp;
static bool sam_print_yr;
static bool sam_print_zb;
static bool sam_print_zr;
static bool sam_print_zf;
static bool sam_print_zm;
static bool sam_print_zi;
static bool sam_print_zp;
static bool sam_print_zu;
static bool sam_print_xs_a;
static bool bwaSwLike;
static float bwaSwLikeC;
static float bwaSwLikeT;
static bool qcFilter;
static bool sortByScore;      // prioritize alignments to report by score?
bool gReportOverhangs;        // false -> filter out alignments that fall off the end of a reference sequence
static string rgid;           // ID: setting for @RG header line
static string rgs;            // SAM outputs for @RG header line
static string rgs_optflag;    // SAM optional flag to add corresponding to @RG ID
static bool msample;          // whether to report a random alignment when maxed-out via -m/-M
int      gGapBarrier;         // # diags on top/bot only to be entered diagonally
static EList<string> qualities;
static EList<string> qualities1;
static EList<string> qualities2;
static string polstr;         // temporary holder for policy string
static bool  msNoCache;       // true -> disable local cache
static int   bonusMatchType;  // how to reward matches
static int   bonusMatch;      // constant reward if bonusMatchType=constant
static int   penMmcType;      // how to penalize mismatches
static int   penMmcMax;       // max mm penalty
static int   penMmcMin;       // min mm penalty
static int   penNType;        // how to penalize Ns in the read
static int   penN;            // constant if N pelanty is a constant
static bool  penNCatPair;     // concatenate mates before N filtering?
static bool  localAlign;      // do local alignment in DP steps
static bool  noisyHpolymer;   // set to true if gap penalties should be reduced to be consistent with a sequencer that under- and overcalls homopolymers
static int   penRdGapConst;   // constant cost of extending a gap in the read
static int   penRfGapConst;   // constant cost of extending a gap in the reference
static int   penRdGapLinear;  // coeff of linear term for cost of gap extension in read
static int   penRfGapLinear;  // coeff of linear term for cost of gap extension in ref
static SimpleFunc scoreMin;   // minimum valid score as function of read len
static SimpleFunc nCeil;      // max # Ns allowed as function of read len
static SimpleFunc msIval;     // interval between seeds as function of read len
static double descConsExp;    // how to adjust score minimum as we descent further into index-assisted alignment
static size_t descentLanding; // don't place a search root if it's within this many positions of end
static SimpleFunc descentTotSz;    // maximum space a DescentDriver can use in bytes
static SimpleFunc descentTotFmops; // maximum # FM ops a DescentDriver can perform
static int    multiseedMms;   // mismatches permitted in a multiseed seed
static int    multiseedLen;   // length of multiseed seeds
static size_t multiseedOff;   // offset to begin extracting seeds
static uint32_t seedCacheLocalMB;   // # MB to use for non-shared seed alignment cacheing
static uint32_t seedCacheCurrentMB; // # MB to use for current-read seed hit cacheing
static uint32_t exactCacheCurrentMB; // # MB to use for current-read seed hit cacheing
static size_t maxhalf;        // max width on one side of DP table
static bool seedSumm;         // print summary information about seed hits, not alignments
static bool doUngapped;       // do ungapped alignment
static size_t maxIters;       // stop after this many extend loop iterations
static size_t maxUg;          // stop after this many ungap extends
static size_t maxDp;          // stop after this many DPs
static size_t maxItersIncr;   // amt to add to maxIters for each -k > 1
static size_t maxEeStreak;    // stop after this many end-to-end fails in a row
static size_t maxUgStreak;    // stop after this many ungap fails in a row
static size_t maxDpStreak;    // stop after this many dp fails in a row
static size_t maxStreakIncr;  // amt to add to streak for each -k > 1
static size_t maxMateStreak;  // stop seed range after this many mate-find fails
static bool doExtend;         // extend seed hits
static bool enable8;          // use 8-bit SSE where possible?
static size_t cminlen;        // longer reads use checkpointing
static size_t cpow2;          // checkpoint interval log2
static bool doTri;            // do triangular mini-fills?
static string defaultPreset;  // default preset; applied immediately
static bool ignoreQuals;      // all mms incur same penalty, regardless of qual
static string wrapper;        // type of wrapper script, so we can print correct usage
static EList<string> queries; // list of query files
static string outfile;        // write SAM output to this file
static int mapqv;             // MAPQ calculation version
static int tighten;           // -M tighten mode (0=none, 1=best, 2=secbest+1)
static bool doExactUpFront;   // do exact search up front if seeds seem good enough
static bool do1mmUpFront;     // do 1mm search up front if seeds seem good enough
static size_t do1mmMinLen;    // length below which we disable 1mm e2e search
static int seedBoostThresh;   // if average non-zero position has more than this many elements
static size_t nSeedRounds;    // # seed rounds
static bool reorder;          // true -> reorder SAM recs in -p mode
static float sampleFrac;      // only align random fraction of input reads
static bool arbitraryRandom;  // pseudo-randoms no longer a function of read properties
static bool bowtie2p5;
static bool useTempSpliceSite;
static int penCanSplice;
static int penNoncanSplice;
static SimpleFunc penIntronLen;
static string knownSpliceSiteInfile;  //
static string novelSpliceSiteInfile;  //
static string novelSpliceSiteOutfile; //
static bool no_spliced_alignment;
static int rna_strandness; //

static string bt2index;      // read Bowtie 2 index from files with this prefix
static EList<pair<int, string> > extra_opts;
static size_t extra_opts_cur;

static EList<uint64_t> thread_rids;
static MUTEX_T         thread_rids_mutex;
static uint64_t        thread_rids_mindist;

#define DMAX std::numeric_limits<double>::max()

static void resetOptions() {
	mates1.clear();
	mates2.clear();
	mates12.clear();
	adjIdxBase	            = "";
	gColor                  = false;
	gVerbose                = 0;
	startVerbose			= 0;
	gQuiet					= false;
	sanityCheck				= 0;  // enable expensive sanity checks
	format					= FASTQ; // default read format is FASTQ
	origString				= ""; // reference text, or filename(s)
	seed					= 0; // srandom() seed
	timing					= 0; // whether to report basic timing data
	metricsIval				= 1; // interval between alignment metrics messages (0 = no messages)
	metricsFile             = ""; // output file to put alignment metrics in
	metricsStderr           = false; // print metrics to stderr (in addition to --metrics-file if it's specified
	metricsPerRead          = false; // report a metrics tuple for every read?
	allHits					= false; // for multihits, report just one
	showVersion				= false; // just print version and quit?
	ipause					= 0; // pause before maching?
	qUpto					= 0xffffffff; // max # of queries to read
	gTrim5					= 0; // amount to trim from 5' end
	gTrim3					= 0; // amount to trim from 3' end
	offRate					= -1; // keep default offRate
	solexaQuals				= false; // quality strings are solexa quals, not phred, and subtract 64 (not 33)
	phred64Quals			= false; // quality chars are phred, but must subtract 64 (not 33)
	integerQuals			= false; // quality strings are space-separated strings of integers, not ASCII
	nthreads				= 1;     // number of pthreads operating concurrently
	outType					= OUTPUT_SAM;  // style of output
	noRefNames				= false; // true -> print reference indexes; not names
	khits					= 5;     // number of hits per read; >1 is much slower
	mhits					= 0;     // stop after finding this many alignments+1
	partitionSz				= 0;     // output a partitioning key in first field
	useSpinlock				= true;  // false -> don't use of spinlocks even if they're #defines
	fileParallel			= false; // separate threads read separate input files in parallel
	useShmem				= false; // use shared memory to hold the index
	useMm					= false; // use memory-mapped files to hold the index
	mmSweep					= false; // sweep through memory-mapped files immediately after mapping
	gMinInsert				= 0;     // minimum insert size
	gMaxInsert				= 500;   // maximum insert size
	gMate1fw				= true;  // -1 mate aligns in fw orientation on fw strand
	gMate2fw				= false; // -2 mate aligns in rc orientation on fw strand
	gFlippedMatesOK         = false; // allow mates to be in wrong order
	gDovetailMatesOK        = false; // allow one mate to extend off the end of the other
	gContainMatesOK         = true;  // allow one mate to contain the other in PE alignment
	gOlapMatesOK            = true;  // allow mates to overlap in PE alignment
	gExpandToFrag           = true;  // incr max frag length to =larger mate len if necessary
	gReportDiscordant       = true;  // find and report discordant paired-end alignments
	gReportMixed            = true;  // find and report unpaired alignments for paired reads

	cacheLimit				= 5;     // ranges w/ size > limit will be cached
	cacheSize				= 0;     // # words per range cache
	skipReads				= 0;     // # reads/read pairs to skip
	gNofw					= false; // don't align fw orientation of read
	gNorc					= false; // don't align rc orientation of read
	fastaContLen			= 0;
	fastaContFreq			= 0;
	hadoopOut				= false; // print Hadoop status and summary messages
	fuzzy					= false; // reads will have alternate basecalls w/ qualities
	fullRef					= false; // print entire reference name instead of just up to 1st space
	samTruncQname           = true;  // whether to truncate QNAME to 255 chars
	samOmitSecSeqQual       = false; // omit SEQ/QUAL for 2ndary alignments?
	samNoUnal               = false; // omit SAM records for unaligned reads
	samNoHead				= false; // don't print any header lines in SAM output
	samNoSQ					= false; // don't print @SQ header lines
	sam_print_as            = true;
	sam_print_xs            = true;
	sam_print_xss           = false; // Xs:i and Ys:i
	sam_print_yn            = false; // YN:i and Yn:i
	sam_print_xn            = true;
	sam_print_cs            = false;
	sam_print_cq            = false;
	sam_print_x0            = true;
	sam_print_x1            = true;
	sam_print_xm            = true;
	sam_print_xo            = true;
	sam_print_xg            = true;
	sam_print_nm            = true;
	sam_print_md            = true;
	sam_print_yf            = true;
	sam_print_yi            = false;
	sam_print_ym            = false;
	sam_print_yp            = false;
	sam_print_yt            = true;
	sam_print_ys            = true;
	sam_print_zs            = false;
	sam_print_xr            = false;
	sam_print_xt            = false;
	sam_print_xd            = false;
	sam_print_xu            = false;
	sam_print_yl            = false;
	sam_print_ye            = false;
	sam_print_yu            = false;
	sam_print_xp            = false;
	sam_print_yr            = false;
	sam_print_zb            = false;
	sam_print_zr            = false;
	sam_print_zf            = false;
	sam_print_zm            = false;
	sam_print_zi            = false;
	sam_print_zp            = false;
	sam_print_zu            = false;
    sam_print_xs_a          = true;
	bwaSwLike               = false;
	bwaSwLikeC              = 5.5f;
	bwaSwLikeT              = 20.0f;
	qcFilter                = false; // don't believe upstream qc by default
	sortByScore             = true;  // prioritize alignments to report by score?
	rgid					= "";    // SAM outputs for @RG header line
	rgs						= "";    // SAM outputs for @RG header line
	rgs_optflag				= "";    // SAM optional flag to add corresponding to @RG ID
	msample				    = true;
	gGapBarrier				= 4;     // disallow gaps within this many chars of either end of alignment
	qualities.clear();
	qualities1.clear();
	qualities2.clear();
	polstr.clear();
	msNoCache       = true; // true -> disable local cache
	bonusMatchType  = DEFAULT_MATCH_BONUS_TYPE;
	bonusMatch      = DEFAULT_MATCH_BONUS;
	penMmcType      = DEFAULT_MM_PENALTY_TYPE;
	penMmcMax       = DEFAULT_MM_PENALTY_MAX;
	penMmcMin       = DEFAULT_MM_PENALTY_MIN;
	penNType        = DEFAULT_N_PENALTY_TYPE;
	penN            = DEFAULT_N_PENALTY;
	penNCatPair     = DEFAULT_N_CAT_PAIR; // concatenate mates before N filtering?
	localAlign      = false;     // do local alignment in DP steps
	noisyHpolymer   = false;
	penRdGapConst   = DEFAULT_READ_GAP_CONST;
	penRfGapConst   = DEFAULT_REF_GAP_CONST;
	penRdGapLinear  = DEFAULT_READ_GAP_LINEAR;
	penRfGapLinear  = DEFAULT_REF_GAP_LINEAR;
	// scoreMin.init  (SIMPLE_FUNC_LINEAR, DEFAULT_MIN_CONST,   DEFAULT_MIN_LINEAR);
    scoreMin.init  (SIMPLE_FUNC_CONST, -18, 0);
	nCeil.init     (SIMPLE_FUNC_LINEAR, 0.0f, DMAX, 2.0f, 0.1f);
	msIval.init    (SIMPLE_FUNC_LINEAR, 1.0f, DMAX, DEFAULT_IVAL_B, DEFAULT_IVAL_A);
	descConsExp     = 2.0;
	descentLanding  = 20;
	descentTotSz.init(SIMPLE_FUNC_LINEAR, 1024.0, DMAX, 0.0, 1024.0);
	descentTotFmops.init(SIMPLE_FUNC_LINEAR, 100.0, DMAX, 0.0, 10.0);
	multiseedMms    = DEFAULT_SEEDMMS;
	multiseedLen    = DEFAULT_SEEDLEN;
	multiseedOff    = 0;
	seedCacheLocalMB   = 32; // # MB to use for non-shared seed alignment cacheing
	seedCacheCurrentMB = 20; // # MB to use for current-read seed hit cacheing
	exactCacheCurrentMB = 20; // # MB to use for current-read seed hit cacheing
	maxhalf            = 15; // max width on one side of DP table
	seedSumm           = false; // print summary information about seed hits, not alignments
	doUngapped         = true;  // do ungapped alignment
	maxIters           = 400;   // max iterations of extend loop
	maxUg              = 300;   // stop after this many ungap extends
	maxDp              = 300;   // stop after this many dp extends
	maxItersIncr       = 20;    // amt to add to maxIters for each -k > 1
	maxEeStreak        = 15;    // stop after this many end-to-end fails in a row
	maxUgStreak        = 15;    // stop after this many ungap fails in a row
	maxDpStreak        = 15;    // stop after this many dp fails in a row
	maxStreakIncr      = 10;    // amt to add to streak for each -k > 1
	maxMateStreak      = 10;    // in PE: abort seed range after N mate-find fails
	doExtend           = true;  // do seed extensions
	enable8            = true;  // use 8-bit SSE where possible?
	cminlen            = 2000;  // longer reads use checkpointing
	cpow2              = 4;     // checkpoint interval log2
	doTri              = false; // do triangular mini-fills?
	defaultPreset      = "sensitive%LOCAL%"; // default preset; applied immediately
	extra_opts.clear();
	extra_opts_cur = 0;
	bt2index.clear();        // read Bowtie 2 index from files with this prefix
	ignoreQuals = false;     // all mms incur same penalty, regardless of qual
	wrapper.clear();         // type of wrapper script, so we can print correct usage
	queries.clear();         // list of query files
	outfile.clear();         // write SAM output to this file
	mapqv = 2;               // MAPQ calculation version
	tighten = 3;             // -M tightening mode
	doExactUpFront = true;   // do exact search up front if seeds seem good enough
	do1mmUpFront = true;     // do 1mm search up front if seeds seem good enough
	seedBoostThresh = 300;   // if average non-zero position has more than this many elements
	nSeedRounds = 2;         // # rounds of seed searches to do for repetitive reads
	do1mmMinLen = 60;        // length below which we disable 1mm search
	reorder = false;         // reorder SAM records with -p > 1
	sampleFrac = 1.1f;       // align all reads
	arbitraryRandom = false; // let pseudo-random seeds be a function of read properties
	bowtie2p5 = false;
    useTempSpliceSite = true;
    penCanSplice = 0;
    penNoncanSplice = 3;
    penIntronLen.init(SIMPLE_FUNC_LOG, -8, 1);
    knownSpliceSiteInfile = "";
    novelSpliceSiteInfile = "";
    novelSpliceSiteOutfile = "";
    no_spliced_alignment = false;
    rna_strandness = RNA_STRANDNESS_UNKNOWN;
}

static const char *short_options = "fF:qbzhcu:rv:s:aP:t3:5:w:p:k:M:1:2:I:X:CQ:N:i:L:U:x:S:g:O:D:R:";

static struct option long_options[] = {
	{(char*)"verbose",      no_argument,       0,            ARG_VERBOSE},
	{(char*)"startverbose", no_argument,       0,            ARG_STARTVERBOSE},
	{(char*)"quiet",        no_argument,       0,            ARG_QUIET},
	{(char*)"sanity",       no_argument,       0,            ARG_SANITY},
	{(char*)"pause",        no_argument,       &ipause,      1},
	{(char*)"orig",         required_argument, 0,            ARG_ORIG},
	{(char*)"all",          no_argument,       0,            'a'},
	{(char*)"solexa-quals", no_argument,       0,            ARG_SOLEXA_QUALS},
	{(char*)"integer-quals",no_argument,       0,            ARG_INTEGER_QUALS},
	{(char*)"int-quals",    no_argument,       0,            ARG_INTEGER_QUALS},
	{(char*)"metrics",      required_argument, 0,            ARG_METRIC_IVAL},
	{(char*)"metrics-file", required_argument, 0,            ARG_METRIC_FILE},
	{(char*)"metrics-stderr",no_argument,      0,            ARG_METRIC_STDERR},
	{(char*)"metrics-per-read", no_argument,   0,            ARG_METRIC_PER_READ},
	{(char*)"met-read",     no_argument,       0,            ARG_METRIC_PER_READ},
	{(char*)"met",          required_argument, 0,            ARG_METRIC_IVAL},
	{(char*)"met-file",     required_argument, 0,            ARG_METRIC_FILE},
	{(char*)"met-stderr",   no_argument,       0,            ARG_METRIC_STDERR},
	{(char*)"time",         no_argument,       0,            't'},
	{(char*)"trim3",        required_argument, 0,            '3'},
	{(char*)"trim5",        required_argument, 0,            '5'},
	{(char*)"seed",         required_argument, 0,            ARG_SEED},
	{(char*)"qupto",        required_argument, 0,            'u'},
	{(char*)"upto",         required_argument, 0,            'u'},
	{(char*)"version",      no_argument,       0,            ARG_VERSION},
	{(char*)"filepar",      no_argument,       0,            ARG_FILEPAR},
	{(char*)"help",         no_argument,       0,            'h'},
	{(char*)"threads",      required_argument, 0,            'p'},
	{(char*)"khits",        required_argument, 0,            'k'},
	{(char*)"minins",       required_argument, 0,            'I'},
	{(char*)"maxins",       required_argument, 0,            'X'},
	{(char*)"quals",        required_argument, 0,            'Q'},
	{(char*)"Q1",           required_argument, 0,            ARG_QUALS1},
	{(char*)"Q2",           required_argument, 0,            ARG_QUALS2},
	{(char*)"refidx",       no_argument,       0,            ARG_REFIDX},
	{(char*)"partition",    required_argument, 0,            ARG_PARTITION},
	{(char*)"ff",           no_argument,       0,            ARG_FF},
	{(char*)"fr",           no_argument,       0,            ARG_FR},
	{(char*)"rf",           no_argument,       0,            ARG_RF},
	{(char*)"cachelim",     required_argument, 0,            ARG_CACHE_LIM},
	{(char*)"cachesz",      required_argument, 0,            ARG_CACHE_SZ},
	{(char*)"nofw",         no_argument,       0,            ARG_NO_FW},
	{(char*)"norc",         no_argument,       0,            ARG_NO_RC},
	{(char*)"skip",         required_argument, 0,            's'},
	{(char*)"12",           required_argument, 0,            ARG_ONETWO},
	{(char*)"tab5",         required_argument, 0,            ARG_TAB5},
	{(char*)"tab6",         required_argument, 0,            ARG_TAB6},
	{(char*)"phred33-quals", no_argument,      0,            ARG_PHRED33},
	{(char*)"phred64-quals", no_argument,      0,            ARG_PHRED64},
	{(char*)"phred33",       no_argument,      0,            ARG_PHRED33},
	{(char*)"phred64",      no_argument,       0,            ARG_PHRED64},
	{(char*)"solexa1.3-quals", no_argument,    0,            ARG_PHRED64},
	{(char*)"mm",           no_argument,       0,            ARG_MM},
	{(char*)"shmem",        no_argument,       0,            ARG_SHMEM},
	{(char*)"mmsweep",      no_argument,       0,            ARG_MMSWEEP},
	{(char*)"hadoopout",    no_argument,       0,            ARG_HADOOPOUT},
	{(char*)"fuzzy",        no_argument,       0,            ARG_FUZZY},
	{(char*)"fullref",      no_argument,       0,            ARG_FULLREF},
	{(char*)"usage",        no_argument,       0,            ARG_USAGE},
	{(char*)"sam-no-qname-trunc", no_argument, 0,            ARG_SAM_NO_QNAME_TRUNC},
	{(char*)"sam-omit-sec-seq", no_argument,   0,            ARG_SAM_OMIT_SEC_SEQ},
	{(char*)"omit-sec-seq", no_argument,       0,            ARG_SAM_OMIT_SEC_SEQ},
	{(char*)"sam-no-head",  no_argument,       0,            ARG_SAM_NOHEAD},
	{(char*)"sam-nohead",   no_argument,       0,            ARG_SAM_NOHEAD},
	{(char*)"sam-noHD",     no_argument,       0,            ARG_SAM_NOHEAD},
	{(char*)"sam-no-hd",    no_argument,       0,            ARG_SAM_NOHEAD},
	{(char*)"sam-nosq",     no_argument,       0,            ARG_SAM_NOSQ},
	{(char*)"sam-no-sq",    no_argument,       0,            ARG_SAM_NOSQ},
	{(char*)"sam-noSQ",     no_argument,       0,            ARG_SAM_NOSQ},
	{(char*)"no-head",      no_argument,       0,            ARG_SAM_NOHEAD},
	{(char*)"no-hd",        no_argument,       0,            ARG_SAM_NOHEAD},
	{(char*)"no-sq",        no_argument,       0,            ARG_SAM_NOSQ},
	{(char*)"no-HD",        no_argument,       0,            ARG_SAM_NOHEAD},
	{(char*)"no-SQ",        no_argument,       0,            ARG_SAM_NOSQ},
	{(char*)"no-unal",      no_argument,       0,            ARG_SAM_NO_UNAL},
	{(char*)"color",        no_argument,       0,            'C'},
	{(char*)"sam-RG",       required_argument, 0,            ARG_SAM_RG},
	{(char*)"sam-rg",       required_argument, 0,            ARG_SAM_RG},
	{(char*)"sam-rg-id",    required_argument, 0,            ARG_SAM_RGID},
	{(char*)"RG",           required_argument, 0,            ARG_SAM_RG},
	{(char*)"rg",           required_argument, 0,            ARG_SAM_RG},
	{(char*)"rg-id",        required_argument, 0,            ARG_SAM_RGID},
	{(char*)"snpphred",     required_argument, 0,            ARG_SNPPHRED},
	{(char*)"snpfrac",      required_argument, 0,            ARG_SNPFRAC},
	{(char*)"gbar",         required_argument, 0,            ARG_GAP_BAR},
	{(char*)"qseq",         no_argument,       0,            ARG_QSEQ},
	{(char*)"policy",       required_argument, 0,            ARG_ALIGN_POLICY},
	{(char*)"preset",       required_argument, 0,            'P'},
	{(char*)"seed-summ",    no_argument,       0,            ARG_SEED_SUMM},
	{(char*)"seed-summary", no_argument,       0,            ARG_SEED_SUMM},
	{(char*)"overhang",     no_argument,       0,            ARG_OVERHANG},
	{(char*)"no-cache",     no_argument,       0,            ARG_NO_CACHE},
	{(char*)"cache",        no_argument,       0,            ARG_USE_CACHE},
	{(char*)"454",          no_argument,       0,            ARG_NOISY_HPOLY},
	{(char*)"ion-torrent",  no_argument,       0,            ARG_NOISY_HPOLY},
	{(char*)"no-mixed",     no_argument,       0,            ARG_NO_MIXED},
	{(char*)"no-discordant",no_argument,       0,            ARG_NO_DISCORDANT},
	{(char*)"local",        no_argument,       0,            ARG_LOCAL},
	{(char*)"end-to-end",   no_argument,       0,            ARG_END_TO_END},
	{(char*)"ungapped",     no_argument,       0,            ARG_UNGAPPED},
	{(char*)"no-ungapped",  no_argument,       0,            ARG_UNGAPPED_NO},
	{(char*)"sse8",         no_argument,       0,            ARG_SSE8},
	{(char*)"no-sse8",      no_argument,       0,            ARG_SSE8_NO},
	{(char*)"scan-narrowed",no_argument,       0,            ARG_SCAN_NARROWED},
	{(char*)"qc-filter",    no_argument,       0,            ARG_QC_FILTER},
	{(char*)"bwa-sw-like",  no_argument,       0,            ARG_BWA_SW_LIKE},
	{(char*)"multiseed",        required_argument, 0,        ARG_MULTISEED_IVAL},
	{(char*)"ma",               required_argument, 0,        ARG_SCORE_MA},
	{(char*)"mp",               required_argument, 0,        ARG_SCORE_MMP},
	{(char*)"np",               required_argument, 0,        ARG_SCORE_NP},
	{(char*)"rdg",              required_argument, 0,        ARG_SCORE_RDG},
	{(char*)"rfg",              required_argument, 0,        ARG_SCORE_RFG},
	{(char*)"score-min",        required_argument, 0,        ARG_SCORE_MIN},
	{(char*)"min-score",        required_argument, 0,        ARG_SCORE_MIN},
	{(char*)"n-ceil",           required_argument, 0,        ARG_N_CEIL},
	{(char*)"dpad",             required_argument, 0,        ARG_DPAD},
	{(char*)"mapq-print-inputs",no_argument,       0,        ARG_SAM_PRINT_YI},
	{(char*)"very-fast",        no_argument,       0,        ARG_PRESET_VERY_FAST},
	{(char*)"fast",             no_argument,       0,        ARG_PRESET_FAST},
	{(char*)"sensitive",        no_argument,       0,        ARG_PRESET_SENSITIVE},
	{(char*)"very-sensitive",   no_argument,       0,        ARG_PRESET_VERY_SENSITIVE},
	{(char*)"very-fast-local",      no_argument,   0,        ARG_PRESET_VERY_FAST_LOCAL},
	{(char*)"fast-local",           no_argument,   0,        ARG_PRESET_FAST_LOCAL},
	{(char*)"sensitive-local",      no_argument,   0,        ARG_PRESET_SENSITIVE_LOCAL},
	{(char*)"very-sensitive-local", no_argument,   0,        ARG_PRESET_VERY_SENSITIVE_LOCAL},
	{(char*)"no-score-priority",no_argument,       0,        ARG_NO_SCORE_PRIORITY},
	{(char*)"seedlen",          required_argument, 0,        'L'},
	{(char*)"seedmms",          required_argument, 0,        'N'},
	{(char*)"seedival",         required_argument, 0,        'i'},
	{(char*)"ignore-quals",     no_argument,       0,        ARG_IGNORE_QUALS},
	{(char*)"index",            required_argument, 0,        'x'},
	{(char*)"arg-desc",         no_argument,       0,        ARG_DESC},
	{(char*)"wrapper",          required_argument, 0,        ARG_WRAPPER},
	{(char*)"unpaired",         required_argument, 0,        'U'},
	{(char*)"output",           required_argument, 0,        'S'},
	{(char*)"mapq-v",           required_argument, 0,        ARG_MAPQ_V},
	{(char*)"dovetail",         no_argument,       0,        ARG_DOVETAIL},
	{(char*)"no-dovetail",      no_argument,       0,        ARG_NO_DOVETAIL},
	{(char*)"contain",          no_argument,       0,        ARG_CONTAIN},
	{(char*)"no-contain",       no_argument,       0,        ARG_NO_CONTAIN},
	{(char*)"overlap",          no_argument,       0,        ARG_OVERLAP},
	{(char*)"no-overlap",       no_argument,       0,        ARG_NO_OVERLAP},
	{(char*)"tighten",          required_argument, 0,        ARG_TIGHTEN},
	{(char*)"exact-upfront",    no_argument,       0,        ARG_EXACT_UPFRONT},
	{(char*)"1mm-upfront",      no_argument,       0,        ARG_1MM_UPFRONT},
	{(char*)"no-exact-upfront", no_argument,       0,        ARG_EXACT_UPFRONT_NO},
	{(char*)"no-1mm-upfront",   no_argument,       0,        ARG_1MM_UPFRONT_NO},
	{(char*)"1mm-minlen",       required_argument, 0,        ARG_1MM_MINLEN},
	{(char*)"seed-off",         required_argument, 0,        'O'},
	{(char*)"seed-boost",       required_argument, 0,        ARG_SEED_BOOST_THRESH},
	{(char*)"read-times",       no_argument,       0,        ARG_READ_TIMES},
	{(char*)"show-rand-seed",   no_argument,       0,        ARG_SHOW_RAND_SEED},
	{(char*)"dp-fail-streak",   required_argument, 0,        ARG_DP_FAIL_STREAK_THRESH},
	{(char*)"ee-fail-streak",   required_argument, 0,        ARG_EE_FAIL_STREAK_THRESH},
	{(char*)"ug-fail-streak",   required_argument, 0,        ARG_UG_FAIL_STREAK_THRESH},
	{(char*)"fail-streak",      required_argument, 0,        'D'},
	{(char*)"dp-fails",         required_argument, 0,        ARG_DP_FAIL_THRESH},
	{(char*)"ug-fails",         required_argument, 0,        ARG_UG_FAIL_THRESH},
	{(char*)"extends",          required_argument, 0,        ARG_EXTEND_ITERS},
	{(char*)"no-extend",        no_argument,       0,        ARG_NO_EXTEND},
	{(char*)"mapq-extra",       no_argument,       0,        ARG_MAPQ_EX},
	{(char*)"seed-rounds",      required_argument, 0,        'R'},
	{(char*)"reorder",          no_argument,       0,        ARG_REORDER},
	{(char*)"passthrough",      no_argument,       0,        ARG_READ_PASSTHRU},
	{(char*)"sample",           required_argument, 0,        ARG_SAMPLE},
	{(char*)"cp-min",           required_argument, 0,        ARG_CP_MIN},
	{(char*)"cp-ival",          required_argument, 0,        ARG_CP_IVAL},
	{(char*)"tri",              no_argument,       0,        ARG_TRI},
	{(char*)"nondeterministic", no_argument,       0,        ARG_NON_DETERMINISTIC},
	{(char*)"non-deterministic", no_argument,      0,        ARG_NON_DETERMINISTIC},
	{(char*)"local-seed-cache-sz", required_argument, 0,     ARG_LOCAL_SEED_CACHE_SZ},
	{(char*)"seed-cache-sz",       required_argument, 0,     ARG_CURRENT_SEED_CACHE_SZ},
	{(char*)"no-unal",          no_argument,       0,        ARG_SAM_NO_UNAL},
	{(char*)"test-25",          no_argument,       0,        ARG_TEST_25},
	// TODO: following should be a function of read length?
	{(char*)"desc-kb",          required_argument, 0,        ARG_DESC_KB},
	{(char*)"desc-landing",     required_argument, 0,        ARG_DESC_LANDING},
	{(char*)"desc-exp",         required_argument, 0,        ARG_DESC_EXP},
	{(char*)"desc-fmops",       required_argument, 0,        ARG_DESC_FMOPS},
    {(char*)"no-temp-splicesite",  no_argument, 0,     ARG_NO_TEMPSPLICESITE},
    {(char*)"pen-cansplice",  required_argument, 0,        ARG_PEN_CANSPLICE},
    {(char*)"pen-noncansplice",  required_argument, 0,     ARG_PEN_NONCANSPLICE},
    {(char*)"pen-intronlen",  required_argument, 0,     ARG_PEN_INTRONLEN},
    {(char*)"known-splicesite-infile",       required_argument, 0,        ARG_KNOWN_SPLICESITE_INFILE},
    {(char*)"novel-splicesite-infile",       required_argument, 0,        ARG_NOVEL_SPLICESITE_INFILE},
    {(char*)"novel-splicesite-outfile",      required_argument, 0,        ARG_NOVEL_SPLICESITE_OUTFILE},
    {(char*)"no-spliced-alignment",   no_argument, 0,        ARG_NO_SPLICED_ALIGNMENT},
    {(char*)"rna-strandness",   required_argument, 0,        ARG_RNA_STRANDNESS},
	{(char*)0, 0, 0, 0} // terminator
};

/**
 * Print out a concise description of what options are taken and whether they
 * take an argument.
 */
static void printArgDesc(ostream& out) {
	// struct option {
	//   const char *name;
	//   int has_arg;
	//   int *flag;
	//   int val;
	// };
	size_t i = 0;
	while(long_options[i].name != 0) {
		out << long_options[i].name << "\t"
		    << (long_options[i].has_arg == no_argument ? 0 : 1)
		    << endl;
		i++;
	}
	size_t solen = strlen(short_options);
	for(i = 0; i < solen; i++) {
		// Has an option?  Does if next char is :
		if(i == solen-1) {
			assert_neq(':', short_options[i]);
			cout << (char)short_options[i] << "\t" << 0 << endl;
		} else {
			if(short_options[i+1] == ':') {
				// Option with argument
				cout << (char)short_options[i] << "\t" << 1 << endl;
				i++; // skip the ':'
			} else {
				// Option with no argument
				cout << (char)short_options[i] << "\t" << 0 << endl;
			}
		}
	}
}

/**
 * Print a summary usage message to the provided output stream.
 */
static void printUsage(ostream& out) {
	out << "HISAT version " << string(HISAT_VERSION).c_str() << " by Daehwan Kim (infphilo@gmail.com, www.ccb.jhu.edu/people/infphilo)" << endl;
	string tool_name = "hisat2-align";
	if(wrapper == "basic-0") {
		tool_name = "hisat";
	}
	out << "Usage: " << endl
	    << "  " << tool_name.c_str() << " [options]* -x <ht2-idx> {-1 <m1> -2 <m2> | -U <r>} [-S <sam>]" << endl
	    << endl
		<<     "  <ht2-idx>  Index filename prefix (minus trailing .X." << gfm_ext << ")." << endl
	    <<     "  <m1>       Files with #1 mates, paired with files in <m2>." << endl;
	if(wrapper == "basic-0") {
		out << "             Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2)." << endl;
	}
	out <<     "  <m2>       Files with #2 mates, paired with files in <m1>." << endl;
	if(wrapper == "basic-0") {
		out << "             Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2)." << endl;
	}
	out <<     "  <r>        Files with unpaired reads." << endl;
	if(wrapper == "basic-0") {
		out << "             Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2)." << endl;
	}
	out <<     "  <sam>      File for SAM output (default: stdout)" << endl
	    << endl
	    << "  <m1>, <m2>, <r> can be comma-separated lists (no whitespace) and can be" << endl
		<< "  specified many times.  E.g. '-U file1.fq,file2.fq -U file3.fq'." << endl
		// Wrapper script should write <bam> line next
		<< endl
	    << "Options (defaults in parentheses):" << endl
		<< endl
	    << " Input:" << endl
	    << "  -q                 query input files are FASTQ .fq/.fastq (default)" << endl
	    << "  --qseq             query input files are in Illumina's qseq format" << endl
	    << "  -f                 query input files are (multi-)FASTA .fa/.mfa" << endl
	    << "  -r                 query input files are raw one-sequence-per-line" << endl
	    << "  -c                 <m1>, <m2>, <r> are sequences themselves, not files" << endl
	    << "  -s/--skip <int>    skip the first <int> reads/pairs in the input (none)" << endl
	    << "  -u/--upto <int>    stop after first <int> reads/pairs (no limit)" << endl
	    << "  -5/--trim5 <int>   trim <int> bases from 5'/left end of reads (0)" << endl
	    << "  -3/--trim3 <int>   trim <int> bases from 3'/right end of reads (0)" << endl
	    << "  --phred33          qualities are Phred+33 (default)" << endl
	    << "  --phred64          qualities are Phred+64" << endl
	    << "  --int-quals        qualities encoded as space-delimited integers" << endl
		<< endl
	    << " Presets:                 Same as:" << endl
		<< "  For --end-to-end:" << endl
		<< "   --very-fast            -D 5 -R 1 -N 0 -L 22 -i S,0,2.50" << endl
		<< "   --fast                 -D 10 -R 2 -N 0 -L 22 -i S,0,2.50" << endl
		<< "   --sensitive            -D 15 -R 2 -N 0 -L 22 -i S,1,1.15 (default)" << endl
		<< "   --very-sensitive       -D 20 -R 3 -N 0 -L 20 -i S,1,0.50" << endl
		<< endl
		<< "  For --local:" << endl
		<< "   --very-fast-local      -D 5 -R 1 -N 0 -L 25 -i S,1,2.00" << endl
		<< "   --fast-local           -D 10 -R 2 -N 0 -L 22 -i S,1,1.75" << endl
		<< "   --sensitive-local      -D 15 -R 2 -N 0 -L 20 -i S,1,0.75 (default)" << endl
		<< "   --very-sensitive-local -D 20 -R 3 -N 0 -L 20 -i S,1,0.50" << endl
		<< endl
	    << " Alignment:" << endl
		<< "  -N <int>           max # mismatches in seed alignment; can be 0 or 1 (0)" << endl
		<< "  -L <int>           length of seed substrings; must be >3, <32 (22)" << endl
		<< "  -i <func>          interval between seed substrings w/r/t read len (S,1,1.15)" << endl
		<< "  --n-ceil <func>    func for max # non-A/C/G/Ts permitted in aln (L,0,0.15)" << endl
		<< "  --dpad <int>       include <int> extra ref chars on sides of DP table (15)" << endl
		<< "  --gbar <int>       disallow gaps within <int> nucs of read extremes (4)" << endl
		<< "  --ignore-quals     treat all quality values as 30 on Phred scale (off)" << endl
	    << "  --nofw             do not align forward (original) version of read (off)" << endl
	    << "  --norc             do not align reverse-complement version of read (off)" << endl
		<< endl
        << " Spliced Alignment:" << endl
        << "  --pen-cansplice <int>              penalty for a canonical splice site (0)" << endl
        << "  --pen-noncansplice <int>           penalty for a non-canonical splice site (3)" << endl
        << "  --pen-intronlen <func>             penalty for long introns (G,-8,1)" << endl
        << "  --known-splicesite-infile <path>   provide a list of known splice sites" << endl
        << "  --novel-splicesite-outfile <path>  report a list of splice sites" << endl
        << "  --novel-splicesite-infile <path>   provide a list of novel splice sites" << endl
        << "  --no-temp-splicesite               disable the use of splice sites found" << endl
        << "  --no-spliced-alignment             disable spliced alignment" << endl
        << "  --rna-strandness <string>          Specify strand-specific information (unstranded)" << endl
        << endl
		<< " Scoring:" << endl
		<< "  --ma <int>         match bonus (0 for --end-to-end, 2 for --local) " << endl
		<< "  --mp <int>         max penalty for mismatch; lower qual = lower penalty (6)" << endl
		<< "  --np <int>         penalty for non-A/C/G/Ts in read/ref (1)" << endl
		<< "  --rdg <int>,<int>  read gap open, extend penalties (5,3)" << endl
		<< "  --rfg <int>,<int>  reference gap open, extend penalties (5,3)" << endl
		<< "  --score-min <func> min acceptable alignment score w/r/t read length" << endl
		<< "                     (G,20,8 for local, L,-0.6,-0.6 for end-to-end)" << endl
		<< endl
	    << " Reporting:" << endl
	    << "  (default)          look for multiple alignments, report best, with MAPQ" << endl
		<< "   OR" << endl
	    << "  -k <int>           report up to <int> alns per read; MAPQ not meaningful" << endl
		<< "   OR" << endl
	    << "  -a/--all           report all alignments; very slow, MAPQ not meaningful" << endl
		<< endl
	    << " Effort:" << endl
	    << "  -D <int>           give up extending after <int> failed extends in a row (15)" << endl
	    << "  -R <int>           for reads w/ repetitive seeds, try <int> sets of seeds (2)" << endl
		<< endl
		<< " Paired-end:" << endl
	    << "  -I/--minins <int>  minimum fragment length (0)" << endl
	    << "  -X/--maxins <int>  maximum fragment length (500)" << endl
	    << "  --fr/--rf/--ff     -1, -2 mates align fw/rev, rev/fw, fw/fw (--fr)" << endl
		<< "  --no-mixed         suppress unpaired alignments for paired reads" << endl
		<< "  --no-discordant    suppress discordant alignments for paired reads" << endl
		<< "  --no-dovetail      not concordant when mates extend past each other" << endl
		<< "  --no-contain       not concordant when one mate alignment contains other" << endl
		<< "  --no-overlap       not concordant when mates overlap at all" << endl
		<< endl
	    << " Output:" << endl;
	//if(wrapper == "basic-0") {
	//	out << "  --bam              output directly to BAM (by piping through 'samtools view')" << endl;
	//}
	out << "  -t/--time          print wall-clock time taken by search phases" << endl;
	if(wrapper == "basic-0") {
	out << "  --un <path>           write unpaired reads that didn't align to <path>" << endl
	    << "  --al <path>           write unpaired reads that aligned at least once to <path>" << endl
	    << "  --un-conc <path>      write pairs that didn't align concordantly to <path>" << endl
	    << "  --al-conc <path>      write pairs that aligned concordantly at least once to <path>" << endl
	    << "  (Note: for --un, --al, --un-conc, or --al-conc, add '-gz' to the option name, e.g." << endl
		<< "  --un-gz <path>, to gzip compress output, or add '-bz2' to bzip2 compress output.)" << endl;
	}
	out << "  --quiet            print nothing to stderr except serious errors" << endl
	//  << "  --refidx           refer to ref. seqs by 0-based index rather than name" << endl
		<< "  --met-file <path>  send metrics to file at <path> (off)" << endl
		<< "  --met-stderr       send metrics to stderr (off)" << endl
		<< "  --met <int>        report internal counters & metrics every <int> secs (1)" << endl
	// Following is supported in the wrapper instead
	//  << "  --no-unal          supppress SAM records for unaligned reads" << endl
	    << "  --no-head          supppress header lines, i.e. lines starting with @" << endl
	    << "  --no-sq            supppress @SQ header lines" << endl
	    << "  --rg-id <text>     set read group id, reflected in @RG line and RG:Z: opt field" << endl
	    << "  --rg <text>        add <text> (\"lab:value\") to @RG line of SAM header." << endl
	    << "                     Note: @RG line only printed when --rg-id is set." << endl
	    << "  --omit-sec-seq     put '*' in SEQ and QUAL fields for secondary alignments." << endl
		<< endl
	    << " Performance:" << endl
	    << "  -o/--offrate <int> override offrate of index; must be >= index's offrate" << endl
	    << "  -p/--threads <int> number of alignment threads to launch (1)" << endl
	    << "  --reorder          force SAM output order to match order of input reads" << endl
#ifdef BOWTIE_MM
	    << "  --mm               use memory-mapped I/O for index; many 'hisat2's can share" << endl
#endif
#ifdef BOWTIE_SHARED_MEM
		//<< "  --shmem            use shared mem for index; many 'hisat2's can share" << endl
#endif
		<< endl
	    << " Other:" << endl
		<< "  --qc-filter        filter out reads that are bad according to QSEQ filter" << endl
	    << "  --seed <int>       seed for random number generator (0)" << endl
	    << "  --non-deterministic seed rand. gen. arbitrarily instead of using read attributes" << endl
	//  << "  --verbose          verbose output for debugging" << endl
	    << "  --version          print version information and quit" << endl
	    << "  -h/--help          print this usage message" << endl
	    ;
	if(wrapper.empty()) {
		cerr << endl
		     << "*** Warning ***" << endl
			 << "'hisat2-align' was run directly.  It is recommended that you run the wrapper script 'hisat2' instead." << endl
			 << endl;
	}
}

/**
 * Parse an int out of optarg and enforce that it be at least 'lower';
 * if it is less than 'lower', than output the given error message and
 * exit with an error and a usage message.
 */
static int parseInt(int lower, int upper, const char *errmsg, const char *arg) {
	long l;
	char *endPtr= NULL;
	l = strtol(arg, &endPtr, 10);
	if (endPtr != NULL) {
		if (l < lower || l > upper) {
			cerr << errmsg << endl;
			printUsage(cerr);
			throw 1;
		}
		return (int32_t)l;
	}
	cerr << errmsg << endl;
	printUsage(cerr);
	throw 1;
	return -1;
}

/**
 * Upper is maximum int by default.
 */
static int parseInt(int lower, const char *errmsg, const char *arg) {
	return parseInt(lower, std::numeric_limits<int>::max(), errmsg, arg);
}

/**
 * Parse a T string 'str'.
 */
template<typename T>
T parse(const char *s) {
	T tmp;
	stringstream ss(s);
	ss >> tmp;
	return tmp;
}

/**
 * Parse a pair of Ts from a string, 'str', delimited with 'delim'.
 */
template<typename T>
pair<T, T> parsePair(const char *str, char delim) {
	string s(str);
	EList<string> ss;
	tokenize(s, delim, ss);
	pair<T, T> ret;
	ret.first = parse<T>(ss[0].c_str());
	ret.second = parse<T>(ss[1].c_str());
	return ret;
}

/**
 * Parse a pair of Ts from a string, 'str', delimited with 'delim'.
 */
template<typename T>
void parseTuple(const char *str, char delim, EList<T>& ret) {
	string s(str);
	EList<string> ss;
	tokenize(s, delim, ss);
	for(size_t i = 0; i < ss.size(); i++) {
		ret.push_back(parse<T>(ss[i].c_str()));
	}
}

static string applyPreset(const string& sorig, Presets& presets) {
	string s = sorig;
	size_t found = s.find("%LOCAL%");
	if(found != string::npos) {
		s.replace(found, strlen("%LOCAL%"), localAlign ? "-local" : "");
	}
	if(gVerbose) {
		cerr << "Applying preset: '" << s.c_str() << "' using preset menu '"
			 << presets.name() << "'" << endl;
	}
	string pol;
	presets.apply(s, pol, extra_opts);
	return pol;
}

static bool saw_M;
static bool saw_a;
static bool saw_k;
static EList<string> presetList;

/**
 * TODO: Argument parsing is very, very flawed.  The biggest problem is that
 * there are two separate worlds of arguments, the ones set via polstr, and
 * the ones set directly in variables.  This makes for nasty interactions,
 * e.g., with the -M option being resolved at an awkward time relative to
 * the -k and -a options.
 */
static void parseOption(int next_option, const char *arg) {
	switch (next_option) {
		case ARG_TEST_25: bowtie2p5 = true; break;
		case ARG_DESC_KB: descentTotSz = SimpleFunc::parse(arg, 0.0, 1024.0, 1024.0, DMAX); break;
		case ARG_DESC_FMOPS: descentTotFmops = SimpleFunc::parse(arg, 0.0, 10.0, 100.0, DMAX); break;
		case ARG_DESC_LANDING: descentLanding = parse<int>(arg); break;
		case ARG_DESC_EXP: {
			descConsExp = parse<double>(arg);
			if(descConsExp < 0.0) {
				cerr << "Error: --desc-exp must be greater than or equal to 0" << endl;
				throw 1;
			}
			break;
		}
		case '1': tokenize(arg, ",", mates1); break;
		case '2': tokenize(arg, ",", mates2); break;
		case ARG_ONETWO: tokenize(arg, ",", mates12); format = TAB_MATE5; break;
		case ARG_TAB5:   tokenize(arg, ",", mates12); format = TAB_MATE5; break;
		case ARG_TAB6:   tokenize(arg, ",", mates12); format = TAB_MATE6; break;
		case 'f': format = FASTA; break;
		case 'F': {
			format = FASTA_CONT;
			pair<uint32_t, uint32_t> p = parsePair<uint32_t>(arg, ',');
			fastaContLen = p.first;
			fastaContFreq = p.second;
			break;
		}
		case ARG_BWA_SW_LIKE: {
			bwaSwLikeC = 5.5f;
			bwaSwLikeT = 30;
			bwaSwLike = true;
			localAlign = true;
			// -a INT   Score of a match [1]
			// -b INT   Mismatch penalty [3]
			// -q INT   Gap open penalty [5]
			// -r INT   Gap extension penalty. The penalty for a contiguous
			//          gap of size k is q+k*r. [2] 
			polstr += ";MA=1;MMP=C3;RDG=5,2;RFG=5,2";
			break;
		}
		case 'q': format = FASTQ; break;
		case 'r': format = RAW; break;
		case 'c': format = CMDLINE; break;
		case ARG_QSEQ: format = QSEQ; break;
		case 'C': {
			cerr << "Error: -C specified but Bowtie 2 does not support colorspace input." << endl;
			throw 1;
			break;
		}
		case 'I':
			gMinInsert = parseInt(0, "-I arg must be positive", arg);
			break;
		case 'X':
			gMaxInsert = parseInt(1, "-X arg must be at least 1", arg);
			break;
		case ARG_NO_DISCORDANT: gReportDiscordant = false; break;
		case ARG_NO_MIXED: gReportMixed = false; break;
		case 's':
			skipReads = (uint32_t)parseInt(0, "-s arg must be positive", arg);
			break;
		case ARG_FF: gMate1fw = true;  gMate2fw = true;  break;
		case ARG_RF: gMate1fw = false; gMate2fw = true;  break;
		case ARG_FR: gMate1fw = true;  gMate2fw = false; break;
		case ARG_SHMEM: useShmem = true; break;
		case ARG_SEED_SUMM: seedSumm = true; break;
		case ARG_MM: {
#ifdef BOWTIE_MM
			useMm = true;
			break;
#else
			cerr << "Memory-mapped I/O mode is disabled because bowtie was not compiled with" << endl
				 << "BOWTIE_MM defined.  Memory-mapped I/O is not supported under Windows.  If you" << endl
				 << "would like to use memory-mapped I/O on a platform that supports it, please" << endl
				 << "refrain from specifying BOWTIE_MM=0 when compiling Bowtie." << endl;
			throw 1;
#endif
		}
		case ARG_MMSWEEP: mmSweep = true; break;
		case ARG_HADOOPOUT: hadoopOut = true; break;
		case ARG_SOLEXA_QUALS: solexaQuals = true; break;
		case ARG_INTEGER_QUALS: integerQuals = true; break;
		case ARG_PHRED64: phred64Quals = true; break;
		case ARG_PHRED33: solexaQuals = false; phred64Quals = false; break;
		case ARG_OVERHANG: gReportOverhangs = true; break;
		case ARG_NO_CACHE: msNoCache = true; break;
		case ARG_USE_CACHE: msNoCache = false; break;
		case ARG_LOCAL_SEED_CACHE_SZ:
			seedCacheLocalMB = (uint32_t)parseInt(1, "--local-seed-cache-sz arg must be at least 1", arg);
			break;
		case ARG_CURRENT_SEED_CACHE_SZ:
			seedCacheCurrentMB = (uint32_t)parseInt(1, "--seed-cache-sz arg must be at least 1", arg);
			break;
		case ARG_REFIDX: noRefNames = true; break;
		case ARG_FUZZY: fuzzy = true; break;
		case ARG_FULLREF: fullRef = true; break;
		case ARG_GAP_BAR:
			gGapBarrier = parseInt(1, "--gbar must be no less than 1", arg);
			break;
		case ARG_SEED:
			seed = parseInt(0, "--seed arg must be at least 0", arg);
			break;
		case ARG_NON_DETERMINISTIC:
			arbitraryRandom = true;
			break;
		case 'u':
			qUpto = (uint32_t)parseInt(1, "-u/--qupto arg must be at least 1", arg);
			break;
		case 'Q':
			tokenize(arg, ",", qualities);
			integerQuals = true;
			break;
		case ARG_QUALS1:
			tokenize(arg, ",", qualities1);
			integerQuals = true;
			break;
		case ARG_QUALS2:
			tokenize(arg, ",", qualities2);
			integerQuals = true;
			break;
		case ARG_CACHE_LIM:
			cacheLimit = (uint32_t)parseInt(1, "--cachelim arg must be at least 1", arg);
			break;
		case ARG_CACHE_SZ:
			cacheSize = (uint32_t)parseInt(1, "--cachesz arg must be at least 1", arg);
			cacheSize *= (1024 * 1024); // convert from MB to B
			break;
		case ARG_WRAPPER: wrapper = arg; break;
		case 'p':
			nthreads = parseInt(1, "-p/--threads arg must be at least 1", arg);
			break;
		case ARG_FILEPAR:
			fileParallel = true;
			break;
		case '3': gTrim3 = parseInt(0, "-3/--trim3 arg must be at least 0", arg); break;
		case '5': gTrim5 = parseInt(0, "-5/--trim5 arg must be at least 0", arg); break;
		case 'h': printUsage(cout); throw 0; break;
		case ARG_USAGE: printUsage(cout); throw 0; break;
		//
		// NOTE that unlike in Bowtie 1, -M, -a and -k are mutually
		// exclusive here.
		//
		case 'M': {
			msample = true;
			mhits = parse<uint32_t>(arg);
			if(saw_a || saw_k) {
				cerr << "Warning: -M, -k and -a are mutually exclusive. "
					 << "-M will override" << endl;
				khits = 1;
			}
			assert_eq(1, khits);
			saw_M = true;
			cerr << "Warning: -M is deprecated.  Use -D and -R to adjust " <<
			        "effort instead." << endl;
			break;
		}
		case ARG_EXTEND_ITERS: {
			maxIters = parse<size_t>(arg);
			break;
		}
		case ARG_NO_EXTEND: {
			doExtend = false;
			break;
		}
		case 'R': { polstr += ";ROUNDS="; polstr += arg; break; }
		case 'D': { polstr += ";DPS=";    polstr += arg; break; }
		case ARG_DP_MATE_STREAK_THRESH: {
			maxMateStreak = parse<size_t>(arg);
			break;
		}
		case ARG_DP_FAIL_STREAK_THRESH: {
			maxDpStreak = parse<size_t>(arg);
			break;
		}
		case ARG_EE_FAIL_STREAK_THRESH: {
			maxEeStreak = parse<size_t>(arg);
			break;
		}
		case ARG_UG_FAIL_STREAK_THRESH: {
			maxUgStreak = parse<size_t>(arg);
			break;
		}
		case ARG_DP_FAIL_THRESH: {
			maxDp = parse<size_t>(arg);
			break;
		}
		case ARG_UG_FAIL_THRESH: {
			maxUg = parse<size_t>(arg);
			break;
		}
		case ARG_SEED_BOOST_THRESH: {
			seedBoostThresh = parse<int>(arg);
			break;
		}
		case 'a': {
			msample = false;
			allHits = true;
			mhits = 0; // disable -M
			if(saw_M || saw_k) {
				cerr << "Warning: -M, -k and -a are mutually exclusive. "
					 << "-a will override" << endl;
			}
			saw_a = true;
			break;
		}
		case 'k': {
			msample = false;
			khits = (uint32_t)parseInt(1, "-k arg must be at least 1", arg);
			mhits = 0; // disable -M
			if(saw_M || saw_a) {
				cerr << "Warning: -M, -k and -a are mutually exclusive. "
					 << "-k will override" << endl;
			}
			saw_k = true;
			break;
		}
		case ARG_VERBOSE: gVerbose = 1; break;
		case ARG_STARTVERBOSE: startVerbose = true; break;
		case ARG_QUIET: gQuiet = true; break;
		case ARG_SANITY: sanityCheck = true; break;
		case 't': timing = true; break;
		case ARG_METRIC_IVAL: {
			metricsIval = parseInt(1, "--metrics arg must be at least 1", arg);
			break;
		}
		case ARG_METRIC_FILE: metricsFile = arg; break;
		case ARG_METRIC_STDERR: metricsStderr = true; break;
		case ARG_METRIC_PER_READ: metricsPerRead = true; break;
		case ARG_NO_FW: gNofw = true; break;
		case ARG_NO_RC: gNorc = true; break;
		case ARG_SAM_NO_QNAME_TRUNC: samTruncQname = false; break;
		case ARG_SAM_OMIT_SEC_SEQ: samOmitSecSeqQual = true; break;
		case ARG_SAM_NO_UNAL: samNoUnal = true; break;
		case ARG_SAM_NOHEAD: samNoHead = true; break;
		case ARG_SAM_NOSQ: samNoSQ = true; break;
		case ARG_SAM_PRINT_YI: sam_print_yi = true; break;
		case ARG_REORDER: reorder = true; break;
		case ARG_MAPQ_EX: {
			sam_print_zp = true;
			sam_print_zu = true;
			sam_print_xp = true;
			sam_print_xss = true;
			sam_print_yn = true;
			break;
		}
		case ARG_SHOW_RAND_SEED: {
			sam_print_zs = true;
			break;
		}
		case ARG_SAMPLE:
			sampleFrac = parse<float>(arg);
			break;
		case ARG_CP_MIN:
			cminlen = parse<size_t>(arg);
			break;
		case ARG_CP_IVAL:
			cpow2 = parse<size_t>(arg);
			break;
		case ARG_TRI:
			doTri = true;
			break;
		case ARG_READ_PASSTHRU: {
			sam_print_xr = true;
			break;
		}
		case ARG_READ_TIMES: {
			sam_print_xt = true;
			sam_print_xd = true;
			sam_print_xu = true;
			sam_print_yl = true;
			sam_print_ye = true;
			sam_print_yu = true;
			sam_print_yr = true;
			sam_print_zb = true;
			sam_print_zr = true;
			sam_print_zf = true;
			sam_print_zm = true;
			sam_print_zi = true;
			break;
		}
		case ARG_SAM_RG: {
			string argstr = arg;
			if(argstr.substr(0, 3) == "ID:") {
				rgid = "\t";
				rgid += argstr;
				rgs_optflag = "RG:Z:" + argstr.substr(3);
			} else {
				rgs += '\t';
				rgs += argstr;
			}
			break;
		}
		case ARG_SAM_RGID: {
			string argstr = arg;
			rgid = "\t";
			rgid = "\tID:" + argstr;
			rgs_optflag = "RG:Z:" + argstr;
			break;
		}
		case ARG_PARTITION: partitionSz = parse<int>(arg); break;
		case ARG_DPAD:
			maxhalf = parseInt(0, "--dpad must be no less than 0", arg);
			break;
		case ARG_ORIG:
			if(arg == NULL || strlen(arg) == 0) {
				cerr << "--orig arg must be followed by a string" << endl;
				printUsage(cerr);
				throw 1;
			}
			origString = arg;
			break;
		case ARG_LOCAL: localAlign = true; break;
		case ARG_END_TO_END: localAlign = false; break;
		case ARG_SSE8: enable8 = true; break;
		case ARG_SSE8_NO: enable8 = false; break;
		case ARG_UNGAPPED: doUngapped = true; break;
		case ARG_UNGAPPED_NO: doUngapped = false; break;
		case ARG_NO_DOVETAIL: gDovetailMatesOK = false; break;
		case ARG_NO_CONTAIN:  gContainMatesOK  = false; break;
		case ARG_NO_OVERLAP:  gOlapMatesOK     = false; break;
		case ARG_DOVETAIL:    gDovetailMatesOK = true;  break;
		case ARG_CONTAIN:     gContainMatesOK  = true;  break;
		case ARG_OVERLAP:     gOlapMatesOK     = true;  break;
		case ARG_QC_FILTER: qcFilter = true; break;
		case ARG_NO_SCORE_PRIORITY: sortByScore = false; break;
		case ARG_IGNORE_QUALS: ignoreQuals = true; break;
		case ARG_MAPQ_V: mapqv = parse<int>(arg); break;
		case ARG_TIGHTEN: tighten = parse<int>(arg); break;
		case ARG_EXACT_UPFRONT:    doExactUpFront = true; break;
		case ARG_1MM_UPFRONT:      do1mmUpFront   = true; break;
		case ARG_EXACT_UPFRONT_NO: doExactUpFront = false; break;
		case ARG_1MM_UPFRONT_NO:   do1mmUpFront   = false; break;
		case ARG_1MM_MINLEN:       do1mmMinLen = parse<size_t>(arg); break;
		case ARG_NOISY_HPOLY: noisyHpolymer = true; break;
		case 'x': bt2index = arg; break;
		case ARG_PRESET_VERY_FAST_LOCAL: localAlign = true;
		case ARG_PRESET_VERY_FAST: {
			presetList.push_back("very-fast%LOCAL%"); break;
		}
		case ARG_PRESET_FAST_LOCAL: localAlign = true;
		case ARG_PRESET_FAST: {
			presetList.push_back("fast%LOCAL%"); break;
		}
		case ARG_PRESET_SENSITIVE_LOCAL: localAlign = true;
		case ARG_PRESET_SENSITIVE: {
			presetList.push_back("sensitive%LOCAL%"); break;
		}
		case ARG_PRESET_VERY_SENSITIVE_LOCAL: localAlign = true;
		case ARG_PRESET_VERY_SENSITIVE: {
			presetList.push_back("very-sensitive%LOCAL%"); break;
		}
		case 'P': { presetList.push_back(arg); break; }
		case ARG_ALIGN_POLICY: {
			if(strlen(arg) > 0) {
				polstr += ";"; polstr += arg;
			}
			break;
		}
		case 'N': { polstr += ";SEED="; polstr += arg; break; }
		case 'L': {
			int64_t len = parse<size_t>(arg);
			if(len < 0) {
				cerr << "Error: -L argument must be >= 0; was " << arg << endl;
				throw 1;
			}
			if(len > 32) {
				cerr << "Error: -L argument must be <= 32; was" << arg << endl;
				throw 1;
			}
			polstr += ";SEEDLEN="; polstr += arg; break;
		}
		case 'O':
			multiseedOff = parse<size_t>(arg);
			break;
		case 'i': {
			EList<string> args;
			tokenize(arg, ",", args);
			if(args.size() > 3 || args.size() == 0) {
				cerr << "Error: expected 3 or fewer comma-separated "
					 << "arguments to -i option, got "
					 << args.size() << endl;
				throw 1;
			}
			// Interval-settings arguments
			polstr += (";IVAL=" + args[0]); // Function type
			if(args.size() > 1) {
				polstr += ("," + args[1]);  // Constant term
			}
			if(args.size() > 2) {
				polstr += ("," + args[2]);  // Coefficient
			}
			break;
		}
		case ARG_MULTISEED_IVAL: {
			polstr += ";";
			// Split argument by comma
			EList<string> args;
			tokenize(arg, ",", args);
			if(args.size() > 5 || args.size() == 0) {
				cerr << "Error: expected 5 or fewer comma-separated "
					 << "arguments to --multiseed option, got "
					 << args.size() << endl;
				throw 1;
			}
			// Seed mm and length arguments
			polstr += "SEED=";
			polstr += (args[0]); // # mismatches
			if(args.size() >  1) polstr += ("," + args[ 1]); // length
			if(args.size() >  2) polstr += (";IVAL=" + args[2]); // Func type
			if(args.size() >  3) polstr += ("," + args[ 3]); // Constant term
			if(args.size() >  4) polstr += ("," + args[ 4]); // Coefficient
			break;
		}
		case ARG_N_CEIL: {
			// Split argument by comma
			EList<string> args;
			tokenize(arg, ",", args);
			if(args.size() > 3) {
				cerr << "Error: expected 3 or fewer comma-separated "
					 << "arguments to --n-ceil option, got "
					 << args.size() << endl;
				throw 1;
			}
			if(args.size() == 0) {
				cerr << "Error: expected at least one argument to --n-ceil option" << endl;
				throw 1;
			}
			polstr += ";NCEIL=";
			if(args.size() == 3) {
				polstr += (args[0] + "," + args[1] + "," + args[2]);
			} else {
                if(args.size() == 1) {
                    polstr += ("C," + args[0]);
                } else {
					polstr += (args[0] + "," + args[1]);
				}
			}
			break;
		}
		case ARG_SCORE_MA:  polstr += ";MA=";    polstr += arg; break;
		case ARG_SCORE_MMP: {
			EList<string> args;
			tokenize(arg, ",", args);
			if(args.size() > 2 || args.size() == 0) {
				cerr << "Error: expected 1 or 2 comma-separated "
					 << "arguments to --mmp option, got " << args.size() << endl;
				throw 1;
			}
			if(args.size() >= 1) {
				polstr += ";MMP=Q,";
				polstr += args[0];
				if(args.size() >= 2) {
					polstr += ",";
					polstr += args[1];
				}
			}
			break;
		}
		case ARG_SCORE_NP:  polstr += ";NP=C";   polstr += arg; break;
		case ARG_SCORE_RDG: polstr += ";RDG=";   polstr += arg; break;
		case ARG_SCORE_RFG: polstr += ";RFG=";   polstr += arg; break;
		case ARG_SCORE_MIN: {
			polstr += ";";
			EList<string> args;
			tokenize(arg, ",", args);
			if(args.size() > 3 && args.size() == 0) {
				cerr << "Error: expected 3 or fewer comma-separated "
					 << "arguments to --n-ceil option, got "
					 << args.size() << endl;
				throw 1;
			}
			polstr += ("MIN=" + args[0]);
			if(args.size() > 1) {
				polstr += ("," + args[1]);
			}
			if(args.size() > 2) {
				polstr += ("," + args[2]);
			}
			break;
		}
		case ARG_DESC: printArgDesc(cout); throw 0;
		case 'S': outfile = arg; break;
		case 'U': {
			EList<string> args;
			tokenize(arg, ",", args);
			for(size_t i = 0; i < args.size(); i++) {
				queries.push_back(args[i]);
			}
			break;
		}
		case ARG_VERSION: showVersion = 1; break;
        case ARG_NO_TEMPSPLICESITE: useTempSpliceSite = false; break;
        case ARG_PEN_CANSPLICE: {
            penCanSplice = parseInt(0, "-k arg must be at least 0", arg);
            break;
        }
        case ARG_PEN_NONCANSPLICE: {
            penNoncanSplice = parseInt(0, "-k arg must be at least 0", arg);
            break;
        }
        case ARG_PEN_INTRONLEN: {
			polstr += ";";
			EList<string> args;
			tokenize(arg, ",", args);
			if(args.size() > 3 && args.size() == 0) {
				cerr << "Error: expected 3 or fewer comma-separated "
                << "arguments to --n-ceil option, got "
                << args.size() << endl;
				throw 1;
			}
			polstr += ("INTRONLEN=" + args[0]);
			if(args.size() > 1) {
				polstr += ("," + args[1]);
			}
			if(args.size() > 2) {
				polstr += ("," + args[2]);
			}
			break;
		}
        case ARG_KNOWN_SPLICESITE_INFILE: knownSpliceSiteInfile = arg; break;
        case ARG_NOVEL_SPLICESITE_INFILE: novelSpliceSiteInfile = arg; break;
        case ARG_NOVEL_SPLICESITE_OUTFILE: novelSpliceSiteOutfile = arg; break;
        case ARG_NO_SPLICED_ALIGNMENT: no_spliced_alignment = true; break;
        case ARG_RNA_STRANDNESS: {
            string strandness = arg;
            if(strandness == "F")       rna_strandness = RNA_STRANDNESS_F;
            else if(strandness == "R")  rna_strandness = RNA_STRANDNESS_R;
            else if(strandness == "FR") rna_strandness = RNA_STRANDNESS_FR;
            else if(strandness == "RF") rna_strandness = RNA_STRANDNESS_RF;
            else {
                // daehwan - throw exception with details
                cerr << "Error: should be one of F, R, FR, or RF " << endl;
				throw 1;
            }
            break;
        }
		default:
			printUsage(cerr);
			throw 1;
	}
}

/**
 * Read command-line arguments
 */
static void parseOptions(int argc, const char **argv) {
	int option_index = 0;
	int next_option;
	saw_M = false;
	saw_a = false;
	saw_k = true;
	presetList.clear();
	if(startVerbose) { cerr << "Parsing options: "; logTime(cerr, true); }
	while(true) {
		next_option = getopt_long(
			argc, const_cast<char**>(argv),
			short_options, long_options, &option_index);
		const char * arg = optarg;
		if(next_option == EOF) {
			if(extra_opts_cur < extra_opts.size()) {
				next_option = extra_opts[extra_opts_cur].first;
				arg = extra_opts[extra_opts_cur].second.c_str();
				extra_opts_cur++;
			} else {
				break;
			}
		}
		parseOption(next_option, arg);
	}
	// Now parse all the presets.  Might want to pick which presets version to
	// use according to other parameters.
	auto_ptr<Presets> presets(new PresetsV0());
	// Apply default preset
	if(!defaultPreset.empty()) {
		polstr = applyPreset(defaultPreset, *presets.get()) + polstr;
	}
	// Apply specified presets
	for(size_t i = 0; i < presetList.size(); i++) {
		polstr += applyPreset(presetList[i], *presets.get());
	}
	for(size_t i = 0; i < extra_opts.size(); i++) {
		next_option = extra_opts[extra_opts_cur].first;
		const char *arg = extra_opts[extra_opts_cur].second.c_str();
		parseOption(next_option, arg);
	}
	// Remove initial semicolons
	while(!polstr.empty() && polstr[0] == ';') {
		polstr = polstr.substr(1);
	}
	if(gVerbose) {
		cerr << "Final policy string: '" << polstr.c_str() << "'" << endl;
	}
	size_t failStreakTmp = 0;
	SeedAlignmentPolicy::parseString(
		polstr,
		localAlign,
		noisyHpolymer,
		ignoreQuals,
		bonusMatchType,
		bonusMatch,
		penMmcType,
		penMmcMax,
		penMmcMin,
		penNType,
		penN,
		penRdGapConst,
		penRfGapConst,
		penRdGapLinear,
		penRfGapLinear,
		scoreMin,
		nCeil,
		penNCatPair,
		multiseedMms,
		multiseedLen,
		msIval,
		failStreakTmp,
		nSeedRounds,
        &penIntronLen);
	if(failStreakTmp > 0) {
		maxEeStreak = failStreakTmp;
		maxUgStreak = failStreakTmp;
		maxDpStreak = failStreakTmp;
	}
	if(saw_a || saw_k) {
		msample = false;
		mhits = 0;
	} else {
		assert_gt(mhits, 0);
		msample = true;
	}
	if(mates1.size() != mates2.size()) {
		cerr << "Error: " << mates1.size() << " mate files/sequences were specified with -1, but " << mates2.size() << endl
		     << "mate files/sequences were specified with -2.  The same number of mate files/" << endl
		     << "sequences must be specified with -1 and -2." << endl;
		throw 1;
	}
	if(qualities.size() && format != FASTA) {
		cerr << "Error: one or more quality files were specified with -Q but -f was not" << endl
		     << "enabled.  -Q works only in combination with -f and -C." << endl;
		throw 1;
	}
	if(qualities1.size() && format != FASTA) {
		cerr << "Error: one or more quality files were specified with --Q1 but -f was not" << endl
		     << "enabled.  --Q1 works only in combination with -f and -C." << endl;
		throw 1;
	}
	if(qualities2.size() && format != FASTA) {
		cerr << "Error: one or more quality files were specified with --Q2 but -f was not" << endl
		     << "enabled.  --Q2 works only in combination with -f and -C." << endl;
		throw 1;
	}
	if(qualities1.size() > 0 && mates1.size() != qualities1.size()) {
		cerr << "Error: " << mates1.size() << " mate files/sequences were specified with -1, but " << qualities1.size() << endl
		     << "quality files were specified with --Q1.  The same number of mate and quality" << endl
		     << "files must sequences must be specified with -1 and --Q1." << endl;
		throw 1;
	}
	if(qualities2.size() > 0 && mates2.size() != qualities2.size()) {
		cerr << "Error: " << mates2.size() << " mate files/sequences were specified with -2, but " << qualities2.size() << endl
		     << "quality files were specified with --Q2.  The same number of mate and quality" << endl
		     << "files must sequences must be specified with -2 and --Q2." << endl;
		throw 1;
	}
	if(!rgs.empty() && rgid.empty()) {
		cerr << "Warning: --rg was specified without --rg-id also "
		     << "being specified.  @RG line is not printed unless --rg-id "
			 << "is specified." << endl;
	}
	// Check for duplicate mate input files
	if(format != CMDLINE) {
		for(size_t i = 0; i < mates1.size(); i++) {
			for(size_t j = 0; j < mates2.size(); j++) {
				if(mates1[i] == mates2[j] && !gQuiet) {
					cerr << "Warning: Same mate file \"" << mates1[i].c_str() << "\" appears as argument to both -1 and -2" << endl;
				}
			}
		}
	}
	// If both -s and -u are used, we need to adjust qUpto accordingly
	// since it uses rdid to know if we've reached the -u limit (and
	// rdids are all shifted up by skipReads characters)
	if(qUpto + skipReads > qUpto) {
		qUpto += skipReads;
	}
	if(useShmem && useMm && !gQuiet) {
		cerr << "Warning: --shmem overrides --mm..." << endl;
		useMm = false;
	}
	if(gGapBarrier < 1) {
		cerr << "Warning: --gbar was set less than 1 (=" << gGapBarrier
		     << "); setting to 1 instead" << endl;
		gGapBarrier = 1;
	}
	if(multiseedMms >= multiseedLen) {
		assert_gt(multiseedLen, 0);
		cerr << "Warning: seed mismatches (" << multiseedMms
		     << ") is less than seed length (" << multiseedLen
			 << "); setting mismatches to " << (multiseedMms-1)
			 << " instead" << endl;
		multiseedMms = multiseedLen-1;
	}
	sam_print_zm = sam_print_zm && bowtie2p5;
#ifndef NDEBUG
	if(!gQuiet) {
		cerr << "Warning: Running in debug mode.  Please use debug mode only "
			 << "for diagnosing errors, and not for typical use of HISAT."
			 << endl;
	}
#endif
}

static const char *argv0 = NULL;

/// Create a PatternSourcePerThread for the current thread according
/// to the global params and return a pointer to it
static PatternSourcePerThreadFactory*
createPatsrcFactory(PairedPatternSource& _patsrc, int tid) {
	PatternSourcePerThreadFactory *patsrcFact;
	patsrcFact = new WrappedPatternSourcePerThreadFactory(_patsrc);
	assert(patsrcFact != NULL);
	return patsrcFact;
}

#define PTHREAD_ATTRS (PTHREAD_CREATE_JOINABLE | PTHREAD_CREATE_DETACHED)

typedef TIndexOffU index_t;
typedef uint16_t local_index_t;
static PairedPatternSource*              multiseed_patsrc;
static HierEbwt<index_t>*                multiseed_ebwtFw;
static HierEbwt<index_t>*                multiseed_ebwtBw;
static Scoring*                          multiseed_sc;
static BitPairReference*                 multiseed_refs;
static AlignmentCache<index_t>*          multiseed_ca; // seed cache
static AlnSink<index_t>*                 multiseed_msink;
static EList<string>                     multiseed_refnames;
static OutFileBuf*                       multiseed_metricsOfb;
static SpliceSiteDB*                     ssdb;
static MUTEX_T                           multiseed_mutex;

/**
 * Metrics for measuring the work done by the outer read alignment
 * loop.
 */
struct OuterLoopMetrics {

	OuterLoopMetrics() {
	    reset();
	}

	/**
	 * Set all counters to 0.
	 */
	void reset() {
		reads = bases = srreads = srbases =
		freads = fbases = ureads = ubases = 0;
	}

	/**
	 * Sum the counters in m in with the conters in this object.  This
	 * is the only safe way to update an OuterLoopMetrics that's shared
	 * by multiple threads.
	 */
	void merge(
		const OuterLoopMetrics& m,
		bool getLock = false)
	{
		ThreadSafe ts(&mutex_m, getLock);
		reads += m.reads;
		bases += m.bases;
		srreads += m.srreads;
		srbases += m.srbases;
		freads += m.freads;
		fbases += m.fbases;
		ureads += m.ureads;
		ubases += m.ubases;
	}

	uint64_t reads;   // total reads
	uint64_t bases;   // total bases
	uint64_t srreads; // same-read reads
	uint64_t srbases; // same-read bases
	uint64_t freads;  // filtered reads
	uint64_t fbases;  // filtered bases
	uint64_t ureads;  // unfiltered reads
	uint64_t ubases;  // unfiltered bases
	MUTEX_T mutex_m;
};

/**
 * Collection of all relevant performance metrics when aligning in
 * multiseed mode.
 */
struct PerfMetrics {

	PerfMetrics() : first(true) { reset(); }

	/**
	 * Set all counters to 0.
	 */
	void reset() {
		olm.reset();
		sdm.reset();
		wlm.reset();
		swmSeed.reset();
		swmMate.reset();
		rpm.reset();
		dpSse8Seed.reset();   // 8-bit SSE seed extensions
		dpSse8Mate.reset();   // 8-bit SSE mate finds
		dpSse16Seed.reset();  // 16-bit SSE seed extensions
		dpSse16Mate.reset();  // 16-bit SSE mate finds
		nbtfiltst = 0;
		nbtfiltsc = 0;
		nbtfiltdo = 0;
		
		olmu.reset();
		sdmu.reset();
		wlmu.reset();
		swmuSeed.reset();
		swmuMate.reset();
		rpmu.reset();
		dpSse8uSeed.reset();  // 8-bit SSE seed extensions
		dpSse8uMate.reset();  // 8-bit SSE mate finds
		dpSse16uSeed.reset(); // 16-bit SSE seed extensions
		dpSse16uMate.reset(); // 16-bit SSE mate finds
		nbtfiltst_u = 0;
		nbtfiltsc_u = 0;
		nbtfiltdo_u = 0;
        
        him.reset();
	}

	/**
	 * Merge a set of specific metrics into this object.
	 */
	void merge(
		const OuterLoopMetrics *ol,
		const SeedSearchMetrics *sd,
		const WalkMetrics *wl,
		const SwMetrics *swSeed,
		const SwMetrics *swMate,
		const ReportingMetrics *rm,
		const SSEMetrics *dpSse8Ex,
		const SSEMetrics *dpSse8Ma,
		const SSEMetrics *dpSse16Ex,
		const SSEMetrics *dpSse16Ma,
		uint64_t nbtfiltst_,
		uint64_t nbtfiltsc_,
		uint64_t nbtfiltdo_,
        const HIMetrics *hi,
		bool getLock)
	{
		ThreadSafe ts(&mutex_m, getLock);
		if(ol != NULL) {
			olmu.merge(*ol, false);
		}
		if(sd != NULL) {
			sdmu.merge(*sd, false);
		}
		if(wl != NULL) {
			wlmu.merge(*wl, false);
		}
		if(swSeed != NULL) {
			swmuSeed.merge(*swSeed, false);
		}
		if(swMate != NULL) {
			swmuMate.merge(*swMate, false);
		}
		if(rm != NULL) {
			rpmu.merge(*rm, false);
		}
		if(dpSse8Ex != NULL) {
			dpSse8uSeed.merge(*dpSse8Ex, false);
		}
		if(dpSse8Ma != NULL) {
			dpSse8uMate.merge(*dpSse8Ma, false);
		}
		if(dpSse16Ex != NULL) {
			dpSse16uSeed.merge(*dpSse16Ex, false);
		}
		if(dpSse16Ma != NULL) {
			dpSse16uMate.merge(*dpSse16Ma, false);
		}
		nbtfiltst_u += nbtfiltst_;
		nbtfiltsc_u += nbtfiltsc_;
		nbtfiltdo_u += nbtfiltdo_;
        if(hi != NULL) {
            him.merge(*hi, false);
        }
	}

	/**
	 * Reports a matrix of results, incl. column labels, to an OutFileBuf.
	 * Optionally also sends results to stderr (unbuffered).  Can optionally
	 * print a per-read record with the read name at the beginning.
	 */
	void reportInterval(
		OutFileBuf* o,        // file to send output to
		bool metricsStderr,   // additionally output to stderr?
		bool total,           // true -> report total, otherwise incremental
		bool sync,            //  synchronize output
		const BTString *name) // non-NULL name pointer if is per-read record
	{
		ThreadSafe ts(&mutex_m, sync);
		ostringstream stderrSs;
		time_t curtime = time(0);
		char buf[1024];
		if(first) {
			const char *str =
				/*  1 */ "Time"           "\t"
				/*  2 */ "Read"           "\t"
				/*  3 */ "Base"           "\t"
				/*  4 */ "SameRead"       "\t"
				/*  5 */ "SameReadBase"   "\t"
				/*  6 */ "UnfilteredRead" "\t"
				/*  7 */ "UnfilteredBase" "\t"
				
				/*  8 */ "Paired"         "\t"
				/*  9 */ "Unpaired"       "\t"
				/* 10 */ "AlConUni"       "\t"
				/* 11 */ "AlConRep"       "\t"
				/* 12 */ "AlConFail"      "\t"
				/* 13 */ "AlDis"          "\t"
				/* 14 */ "AlConFailUni"   "\t"
				/* 15 */ "AlConFailRep"   "\t"
				/* 16 */ "AlConFailFail"  "\t"
				/* 17 */ "AlConRepUni"    "\t"
				/* 18 */ "AlConRepRep"    "\t"
				/* 19 */ "AlConRepFail"   "\t"
				/* 20 */ "AlUnpUni"       "\t"
				/* 21 */ "AlUnpRep"       "\t"
				/* 22 */ "AlUnpFail"      "\t"
				
				/* 23 */ "SeedSearch"     "\t"
				/* 24 */ "IntraSCacheHit" "\t"
				/* 25 */ "InterSCacheHit" "\t"
				/* 26 */ "OutOfMemory"    "\t"
				/* 27 */ "AlBWOp"         "\t"
				/* 28 */ "AlBWBranch"     "\t"
				/* 29 */ "ResBWOp"        "\t"
				/* 30 */ "ResBWBranch"    "\t"
				/* 31 */ "ResResolve"     "\t"
				/* 34 */ "ResReport"      "\t"
				/* 35 */ "RedundantSHit"  "\t"

				/* 36 */ "BestMinEdit0"   "\t"
				/* 37 */ "BestMinEdit1"   "\t"
				/* 38 */ "BestMinEdit2"   "\t"

				/* 39 */ "ExactAttempts"  "\t"
				/* 40 */ "ExactSucc"      "\t"
				/* 41 */ "ExactRanges"    "\t"
				/* 42 */ "ExactRows"      "\t"
				/* 43 */ "ExactOOMs"      "\t"

				/* 44 */ "1mmAttempts"    "\t"
				/* 45 */ "1mmSucc"        "\t"
				/* 46 */ "1mmRanges"      "\t"
				/* 47 */ "1mmRows"        "\t"
				/* 48 */ "1mmOOMs"        "\t"

				/* 49 */ "UngappedSucc"   "\t"
				/* 50 */ "UngappedFail"   "\t"
				/* 51 */ "UngappedNoDec"  "\t"

				/* 52 */ "DPExLt10Gaps"   "\t"
				/* 53 */ "DPExLt5Gaps"    "\t"
				/* 54 */ "DPExLt3Gaps"    "\t"

				/* 55 */ "DPMateLt10Gaps" "\t"
				/* 56 */ "DPMateLt5Gaps"  "\t"
				/* 57 */ "DPMateLt3Gaps"  "\t"

				/* 58 */ "DP16ExDps"      "\t"
				/* 59 */ "DP16ExDpSat"    "\t"
				/* 60 */ "DP16ExDpFail"   "\t"
				/* 61 */ "DP16ExDpSucc"   "\t"
				/* 62 */ "DP16ExCol"      "\t"
				/* 63 */ "DP16ExCell"     "\t"
				/* 64 */ "DP16ExInner"    "\t"
				/* 65 */ "DP16ExFixup"    "\t"
				/* 66 */ "DP16ExGathSol"  "\t"
				/* 67 */ "DP16ExBt"       "\t"
				/* 68 */ "DP16ExBtFail"   "\t"
				/* 69 */ "DP16ExBtSucc"   "\t"
				/* 70 */ "DP16ExBtCell"   "\t"
				/* 71 */ "DP16ExCoreRej"  "\t"
				/* 72 */ "DP16ExNRej"     "\t"

				/* 73 */ "DP8ExDps"       "\t"
				/* 74 */ "DP8ExDpSat"     "\t"
				/* 75 */ "DP8ExDpFail"    "\t"
				/* 76 */ "DP8ExDpSucc"    "\t"
				/* 77 */ "DP8ExCol"       "\t"
				/* 78 */ "DP8ExCell"      "\t"
				/* 79 */ "DP8ExInner"     "\t"
				/* 80 */ "DP8ExFixup"     "\t"
				/* 81 */ "DP8ExGathSol"   "\t"
				/* 82 */ "DP8ExBt"        "\t"
				/* 83 */ "DP8ExBtFail"    "\t"
				/* 84 */ "DP8ExBtSucc"    "\t"
				/* 85 */ "DP8ExBtCell"    "\t"
				/* 86 */ "DP8ExCoreRej"   "\t"
				/* 87 */ "DP8ExNRej"      "\t"

				/* 88 */ "DP16MateDps"     "\t"
				/* 89 */ "DP16MateDpSat"   "\t"
				/* 90 */ "DP16MateDpFail"  "\t"
				/* 91 */ "DP16MateDpSucc"  "\t"
				/* 92 */ "DP16MateCol"     "\t"
				/* 93 */ "DP16MateCell"    "\t"
				/* 94 */ "DP16MateInner"   "\t"
				/* 95 */ "DP16MateFixup"   "\t"
				/* 96 */ "DP16MateGathSol" "\t"
				/* 97 */ "DP16MateBt"      "\t"
				/* 98 */ "DP16MateBtFail"  "\t"
				/* 99 */ "DP16MateBtSucc"  "\t"
				/* 100 */ "DP16MateBtCell"  "\t"
				/* 101 */ "DP16MateCoreRej" "\t"
				/* 102 */ "DP16MateNRej"    "\t"

				/* 103 */ "DP8MateDps"     "\t"
				/* 104 */ "DP8MateDpSat"   "\t"
				/* 105 */ "DP8MateDpFail"  "\t"
				/* 106 */ "DP8MateDpSucc"  "\t"
				/* 107 */ "DP8MateCol"     "\t"
				/* 108 */ "DP8MateCell"    "\t"
				/* 109 */ "DP8MateInner"   "\t"
				/* 110 */ "DP8MateFixup"   "\t"
				/* 111 */ "DP8MateGathSol" "\t"
				/* 112 */ "DP8MateBt"      "\t"
				/* 113 */ "DP8MateBtFail"  "\t"
				/* 114 */ "DP8MateBtSucc"  "\t"
				/* 115 */ "DP8MateBtCell"  "\t"
				/* 116 */ "DP8MateCoreRej" "\t"
				/* 117 */ "DP8MateNRej"    "\t"

				/* 118 */ "DPBtFiltStart"  "\t"
				/* 119 */ "DPBtFiltScore"  "\t"
				/* 120 */ "DpBtFiltDom"    "\t"

				/* 121 */ "MemPeak"        "\t"
				/* 122 */ "UncatMemPeak"   "\t" // 0
				/* 123 */ "EbwtMemPeak"    "\t" // EBWT_CAT
				/* 124 */ "CacheMemPeak"   "\t" // CA_CAT
				/* 125 */ "ResolveMemPeak" "\t" // GW_CAT
				/* 126 */ "AlignMemPeak"   "\t" // AL_CAT
				/* 127 */ "DPMemPeak"      "\t" // DP_CAT
				/* 128 */ "MiscMemPeak"    "\t" // MISC_CAT
				/* 129 */ "DebugMemPeak"   "\t" // DEBUG_CAT
            
                /* 130 */ "LocalSearch"         "\t"
                /* 131 */ "AnchorSearch"        "\t"
                /* 132 */ "LocalIndexSearch"    "\t"
                /* 133 */ "LocalExtSearch"      "\t"
                /* 134 */ "LocalSearchRecur"    "\t"
                /* 135 */ "GlobalGenomeCoords"  "\t"
                /* 136 */ "LocalGenomeCoords"   "\t"
            
            
				"\n";
			
			if(name != NULL) {
				if(o != NULL) o->writeChars("Name\t");
				if(metricsStderr) stderrSs << "Name\t";
			}
			
			if(o != NULL) o->writeChars(str);
			if(metricsStderr) stderrSs << str;
			first = false;
		}
		
		if(total) mergeIncrementals();
		
		// 0. Read name, if needed
		if(name != NULL) {
			if(o != NULL) {
				o->writeChars(name->toZBuf());
				o->write('\t');
			}
			if(metricsStderr) {
				stderrSs << (*name) << '\t';
			}
		}
			
		// 1. Current time in secs
		itoa10<time_t>(curtime, buf);
		if(metricsStderr) stderrSs << buf << '\t';
		if(o != NULL) { o->writeChars(buf); o->write('\t'); }
		
		const OuterLoopMetrics& ol = total ? olm : olmu;
		
		// 2. Reads
		itoa10<uint64_t>(ol.reads, buf);
		if(metricsStderr) stderrSs << buf << '\t';
		if(o != NULL) { o->writeChars(buf); o->write('\t'); }
		// 3. Bases
		itoa10<uint64_t>(ol.bases, buf);
		if(metricsStderr) stderrSs << buf << '\t';
		if(o != NULL) { o->writeChars(buf); o->write('\t'); }
		// 4. Same-read reads
		itoa10<uint64_t>(ol.srreads, buf);
		if(metricsStderr) stderrSs << buf << '\t';
		if(o != NULL) { o->writeChars(buf); o->write('\t'); }
		// 5. Same-read bases
		itoa10<uint64_t>(ol.srbases, buf);
		if(metricsStderr) stderrSs << buf << '\t';
		if(o != NULL) { o->writeChars(buf); o->write('\t'); }
		// 6. Unfiltered reads
		itoa10<uint64_t>(ol.ureads, buf);
		if(metricsStderr) stderrSs << buf << '\t';
		if(o != NULL) { o->writeChars(buf); o->write('\t'); }
		// 7. Unfiltered bases
		itoa10<uint64_t>(ol.ubases, buf);
		if(metricsStderr) stderrSs << buf << '\t';
		if(o != NULL) { o->writeChars(buf); o->write('\t'); }

		const ReportingMetrics& rp = total ? rpm : rpmu;

		// 8. Paired reads
		itoa10<uint64_t>(rp.npaired, buf);
		if(metricsStderr) stderrSs << buf << '\t';
		if(o != NULL) { o->writeChars(buf); o->write('\t'); }
		// 9. Unpaired reads
		itoa10<uint64_t>(rp.nunpaired, buf);
		if(metricsStderr) stderrSs << buf << '\t';
		if(o != NULL) { o->writeChars(buf); o->write('\t'); }
		// 10. Pairs with unique concordant alignments
		itoa10<uint64_t>(rp.nconcord_uni, buf);
		if(metricsStderr) stderrSs << buf << '\t';
		if(o != NULL) { o->writeChars(buf); o->write('\t'); }
		// 11. Pairs with repetitive concordant alignments
		itoa10<uint64_t>(rp.nconcord_rep, buf);
		if(metricsStderr) stderrSs << buf << '\t';
		if(o != NULL) { o->writeChars(buf); o->write('\t'); }
		// 12. Pairs with 0 concordant alignments
		itoa10<uint64_t>(rp.nconcord_0, buf);
		if(metricsStderr) stderrSs << buf << '\t';
		if(o != NULL) { o->writeChars(buf); o->write('\t'); }
		// 13. Pairs with 1 discordant alignment
		itoa10<uint64_t>(rp.ndiscord, buf);
		if(metricsStderr) stderrSs << buf << '\t';
		if(o != NULL) { o->writeChars(buf); o->write('\t'); }
		// 14. Mates from unaligned pairs that align uniquely
		itoa10<uint64_t>(rp.nunp_0_uni, buf);
		if(metricsStderr) stderrSs << buf << '\t';
		if(o != NULL) { o->writeChars(buf); o->write('\t'); }
		// 15. Mates from unaligned pairs that align repetitively
		itoa10<uint64_t>(rp.nunp_0_rep, buf);
		if(metricsStderr) stderrSs << buf << '\t';
		if(o != NULL) { o->writeChars(buf); o->write('\t'); }
		// 16. Mates from unaligned pairs that fail to align
		itoa10<uint64_t>(rp.nunp_0_0, buf);
		if(metricsStderr) stderrSs << buf << '\t';
		if(o != NULL) { o->writeChars(buf); o->write('\t'); }
		// 17. Mates from repetitive pairs that align uniquely
		itoa10<uint64_t>(rp.nunp_rep_uni, buf);
		if(metricsStderr) stderrSs << buf << '\t';
		if(o != NULL) { o->writeChars(buf); o->write('\t'); }
		// 18. Mates from repetitive pairs that align repetitively
		itoa10<uint64_t>(rp.nunp_rep_rep, buf);
		if(metricsStderr) stderrSs << buf << '\t';
		if(o != NULL) { o->writeChars(buf); o->write('\t'); }
		// 19. Mates from repetitive pairs that fail to align
		itoa10<uint64_t>(rp.nunp_rep_0, buf);
		if(metricsStderr) stderrSs << buf << '\t';
		if(o != NULL) { o->writeChars(buf); o->write('\t'); }
		// 20. Unpaired reads that align uniquely
		itoa10<uint64_t>(rp.nunp_uni, buf);
		if(metricsStderr) stderrSs << buf << '\t';
		if(o != NULL) { o->writeChars(buf); o->write('\t'); }
		// 21. Unpaired reads that align repetitively
		itoa10<uint64_t>(rp.nunp_rep, buf);
		if(metricsStderr) stderrSs << buf << '\t';
		if(o != NULL) { o->writeChars(buf); o->write('\t'); }
		// 22. Unpaired reads that fail to align
		itoa10<uint64_t>(rp.nunp_0, buf);
		if(metricsStderr) stderrSs << buf << '\t';
		if(o != NULL) { o->writeChars(buf); o->write('\t'); }

		const SeedSearchMetrics& sd = total ? sdm : sdmu;
		
		// 23. Seed searches
		itoa10<uint64_t>(sd.seedsearch, buf);
		if(metricsStderr) stderrSs << buf << '\t';
		if(o != NULL) { o->writeChars(buf); o->write('\t'); }
		// 24. Hits in 'current' cache
		itoa10<uint64_t>(sd.intrahit, buf);
		if(metricsStderr) stderrSs << buf << '\t';
		if(o != NULL) { o->writeChars(buf); o->write('\t'); }
		// 25. Hits in 'local' cache
		itoa10<uint64_t>(sd.interhit, buf);
		if(metricsStderr) stderrSs << buf << '\t';
		if(o != NULL) { o->writeChars(buf); o->write('\t'); }
		// 26. Out of memory
		itoa10<uint64_t>(sd.ooms, buf);
		if(metricsStderr) stderrSs << buf << '\t';
		if(o != NULL) { o->writeChars(buf); o->write('\t'); }
		// 27. Burrows-Wheeler ops in aligner
		itoa10<uint64_t>(sd.bwops, buf);
		if(metricsStderr) stderrSs << buf << '\t';
		if(o != NULL) { o->writeChars(buf); o->write('\t'); }
		// 28. Burrows-Wheeler branches (edits) in aligner
		itoa10<uint64_t>(sd.bweds, buf);
		if(metricsStderr) stderrSs << buf << '\t';
		if(o != NULL) { o->writeChars(buf); o->write('\t'); }
		
		const WalkMetrics& wl = total ? wlm : wlmu;
		
		// 29. Burrows-Wheeler ops in resolver
		itoa10<uint64_t>(wl.bwops, buf);
		if(metricsStderr) stderrSs << buf << '\t';
		if(o != NULL) { o->writeChars(buf); o->write('\t'); }
		// 30. Burrows-Wheeler branches in resolver
		itoa10<uint64_t>(wl.branches, buf);
		if(metricsStderr) stderrSs << buf << '\t';
		if(o != NULL) { o->writeChars(buf); o->write('\t'); }
		// 31. Burrows-Wheeler offset resolutions
		itoa10<uint64_t>(wl.resolves, buf);
		if(metricsStderr) stderrSs << buf << '\t';
		if(o != NULL) { o->writeChars(buf); o->write('\t'); }
		// 34. Offset reports
		itoa10<uint64_t>(wl.reports, buf);
		if(metricsStderr) stderrSs << buf << '\t';
		if(o != NULL) { o->writeChars(buf); o->write('\t'); }
		
		// 35. Redundant seed hit
		itoa10<uint64_t>(total ? swmSeed.rshit : swmuSeed.rshit, buf);
		if(metricsStderr) stderrSs << buf << '\t';
		if(o != NULL) { o->writeChars(buf); o->write('\t'); }

		// 36. # times the best (out of fw/rc) minimum # edits was 0
		itoa10<uint64_t>(total ? sdm.bestmin0 : sdmu.bestmin0, buf);
		if(metricsStderr) stderrSs << buf << '\t';
		if(o != NULL) { o->writeChars(buf); o->write('\t'); }
		// 37. # times the best (out of fw/rc) minimum # edits was 1
		itoa10<uint64_t>(total ? sdm.bestmin1 : sdmu.bestmin1, buf);
		if(metricsStderr) stderrSs << buf << '\t';
		if(o != NULL) { o->writeChars(buf); o->write('\t'); }
		// 38. # times the best (out of fw/rc) minimum # edits was 2
		itoa10<uint64_t>(total ? sdm.bestmin2 : sdmu.bestmin2, buf);
		if(metricsStderr) stderrSs << buf << '\t';
		if(o != NULL) { o->writeChars(buf); o->write('\t'); }
		
		// 39. Exact aligner attempts
		itoa10<uint64_t>(total ? swmSeed.exatts : swmuSeed.exatts, buf);
		if(metricsStderr) stderrSs << buf << '\t';
		if(o != NULL) { o->writeChars(buf); o->write('\t'); }
		// 40. Exact aligner successes
		itoa10<uint64_t>(total ? swmSeed.exsucc : swmuSeed.exsucc, buf);
		if(metricsStderr) stderrSs << buf << '\t';
		if(o != NULL) { o->writeChars(buf); o->write('\t'); }
		// 41. Exact aligner ranges
		itoa10<uint64_t>(total ? swmSeed.exranges : swmuSeed.exranges, buf);
		if(metricsStderr) stderrSs << buf << '\t';
		if(o != NULL) { o->writeChars(buf); o->write('\t'); }
		// 42. Exact aligner rows
		itoa10<uint64_t>(total ? swmSeed.exrows : swmuSeed.exrows, buf);
		if(metricsStderr) stderrSs << buf << '\t';
		if(o != NULL) { o->writeChars(buf); o->write('\t'); }
		// 43. Exact aligner OOMs
		itoa10<uint64_t>(total ? swmSeed.exooms : swmuSeed.exooms, buf);
		if(metricsStderr) stderrSs << buf << '\t';
		if(o != NULL) { o->writeChars(buf); o->write('\t'); }

		// 44. 1mm aligner attempts
		itoa10<uint64_t>(total ? swmSeed.mm1atts : swmuSeed.mm1atts, buf);
		if(metricsStderr) stderrSs << buf << '\t';
		if(o != NULL) { o->writeChars(buf); o->write('\t'); }
		// 45. 1mm aligner successes
		itoa10<uint64_t>(total ? swmSeed.mm1succ : swmuSeed.mm1succ, buf);
		if(metricsStderr) stderrSs << buf << '\t';
		if(o != NULL) { o->writeChars(buf); o->write('\t'); }
		// 46. 1mm aligner ranges
		itoa10<uint64_t>(total ? swmSeed.mm1ranges : swmuSeed.mm1ranges, buf);
		if(metricsStderr) stderrSs << buf << '\t';
		if(o != NULL) { o->writeChars(buf); o->write('\t'); }
		// 47. 1mm aligner rows
		itoa10<uint64_t>(total ? swmSeed.mm1rows : swmuSeed.mm1rows, buf);
		if(metricsStderr) stderrSs << buf << '\t';
		if(o != NULL) { o->writeChars(buf); o->write('\t'); }
		// 48. 1mm aligner OOMs
		itoa10<uint64_t>(total ? swmSeed.mm1ooms : swmuSeed.mm1ooms, buf);
		if(metricsStderr) stderrSs << buf << '\t';
		if(o != NULL) { o->writeChars(buf); o->write('\t'); }

		// 49 Ungapped aligner success
		itoa10<uint64_t>(total ? swmSeed.ungapsucc : swmuSeed.ungapsucc, buf);
		if(metricsStderr) stderrSs << buf << '\t';
		if(o != NULL) { o->writeChars(buf); o->write('\t'); }
		// 50. Ungapped aligner fail
		itoa10<uint64_t>(total ? swmSeed.ungapfail : swmuSeed.ungapfail, buf);
		if(metricsStderr) stderrSs << buf << '\t';
		if(o != NULL) { o->writeChars(buf); o->write('\t'); }
		// 51. Ungapped aligner no decision
		itoa10<uint64_t>(total ? swmSeed.ungapnodec : swmuSeed.ungapnodec, buf);
		if(metricsStderr) stderrSs << buf << '\t';
		if(o != NULL) { o->writeChars(buf); o->write('\t'); }

		// 52. # seed-extend DPs with < 10 gaps
		itoa10<uint64_t>(total ? swmSeed.sws10 : swmuSeed.sws10, buf);
		if(metricsStderr) stderrSs << buf << '\t';
		if(o != NULL) { o->writeChars(buf); o->write('\t'); }
		// 53. # seed-extend DPs with < 5 gaps
		itoa10<uint64_t>(total ? swmSeed.sws5 : swmuSeed.sws5, buf);
		if(metricsStderr) stderrSs << buf << '\t';
		if(o != NULL) { o->writeChars(buf); o->write('\t'); }
		// 54. # seed-extend DPs with < 3 gaps
		itoa10<uint64_t>(total ? swmSeed.sws3 : swmuSeed.sws3, buf);
		if(metricsStderr) stderrSs << buf << '\t';
		if(o != NULL) { o->writeChars(buf); o->write('\t'); }

		// 55. # seed-extend DPs with < 10 gaps
		itoa10<uint64_t>(total ? swmMate.sws10 : swmuMate.sws10, buf);
		if(metricsStderr) stderrSs << buf << '\t';
		if(o != NULL) { o->writeChars(buf); o->write('\t'); }
		// 56. # seed-extend DPs with < 5 gaps
		itoa10<uint64_t>(total ? swmMate.sws5 : swmuMate.sws5, buf);
		if(metricsStderr) stderrSs << buf << '\t';
		if(o != NULL) { o->writeChars(buf); o->write('\t'); }
		// 57. # seed-extend DPs with < 3 gaps
		itoa10<uint64_t>(total ? swmMate.sws3 : swmuMate.sws3, buf);
		if(metricsStderr) stderrSs << buf << '\t';
		if(o != NULL) { o->writeChars(buf); o->write('\t'); }
		
		const SSEMetrics& dpSse16s = total ? dpSse16Seed : dpSse16uSeed;
		
		// 58. 16-bit SSE seed-extend DPs tried
		itoa10<uint64_t>(dpSse16s.dp, buf);
		if(metricsStderr) stderrSs << buf << '\t';
		if(o != NULL) { o->writeChars(buf); o->write('\t'); }
		// 59. 16-bit SSE seed-extend DPs saturated
		itoa10<uint64_t>(dpSse16s.dpsat, buf);
		if(metricsStderr) stderrSs << buf << '\t';
		if(o != NULL) { o->writeChars(buf); o->write('\t'); }
		// 60. 16-bit SSE seed-extend DPs failed
		itoa10<uint64_t>(dpSse16s.dpfail, buf);
		if(metricsStderr) stderrSs << buf << '\t';
		if(o != NULL) { o->writeChars(buf); o->write('\t'); }
		// 61. 16-bit SSE seed-extend DPs succeeded
		itoa10<uint64_t>(dpSse16s.dpsucc, buf);
		if(metricsStderr) stderrSs << buf << '\t';
		if(o != NULL) { o->writeChars(buf); o->write('\t'); }
		// 62. 16-bit SSE seed-extend DP columns completed
		itoa10<uint64_t>(dpSse16s.col, buf);
		if(metricsStderr) stderrSs << buf << '\t';
		if(o != NULL) { o->writeChars(buf); o->write('\t'); }
		// 63. 16-bit SSE seed-extend DP cells completed
		itoa10<uint64_t>(dpSse16s.cell, buf);
		if(metricsStderr) stderrSs << buf << '\t';
		if(o != NULL) { o->writeChars(buf); o->write('\t'); }
		// 64. 16-bit SSE seed-extend DP inner loop iters completed
		itoa10<uint64_t>(dpSse16s.inner, buf);
		if(metricsStderr) stderrSs << buf << '\t';
		if(o != NULL) { o->writeChars(buf); o->write('\t'); }
		// 65. 16-bit SSE seed-extend DP fixup loop iters completed
		itoa10<uint64_t>(dpSse16s.fixup, buf);
		if(metricsStderr) stderrSs << buf << '\t';
		if(o != NULL) { o->writeChars(buf); o->write('\t'); }
		// 66. 16-bit SSE seed-extend DP gather, cells with potential solutions
		itoa10<uint64_t>(dpSse16s.gathsol, buf);
		if(metricsStderr) stderrSs << buf << '\t';
		if(o != NULL) { o->writeChars(buf); o->write('\t'); }
		// 67. 16-bit SSE seed-extend DP backtrace attempts
		itoa10<uint64_t>(dpSse16s.bt, buf);
		if(metricsStderr) stderrSs << buf << '\t';
		if(o != NULL) { o->writeChars(buf); o->write('\t'); }
		// 68. 16-bit SSE seed-extend DP failed backtrace attempts
		itoa10<uint64_t>(dpSse16s.btfail, buf);
		if(metricsStderr) stderrSs << buf << '\t';
		if(o != NULL) { o->writeChars(buf); o->write('\t'); }
		// 69. 16-bit SSE seed-extend DP succesful backtrace attempts
		itoa10<uint64_t>(dpSse16s.btsucc, buf);
		if(metricsStderr) stderrSs << buf << '\t';
		if(o != NULL) { o->writeChars(buf); o->write('\t'); }
		// 70. 16-bit SSE seed-extend DP backtrace cells
		itoa10<uint64_t>(dpSse16s.btcell, buf);
		if(metricsStderr) stderrSs << buf << '\t';
		if(o != NULL) { o->writeChars(buf); o->write('\t'); }
		// 71. 16-bit SSE seed-extend DP core-diag rejections
		itoa10<uint64_t>(dpSse16s.corerej, buf);
		if(metricsStderr) stderrSs << buf << '\t';
		if(o != NULL) { o->writeChars(buf); o->write('\t'); }
		// 72. 16-bit SSE seed-extend DP N rejections
		itoa10<uint64_t>(dpSse16s.nrej, buf);
		if(metricsStderr) stderrSs << buf << '\t';
		if(o != NULL) { o->writeChars(buf); o->write('\t'); }
		
		const SSEMetrics& dpSse8s = total ? dpSse8Seed : dpSse8uSeed;
		
		// 73. 8-bit SSE seed-extend DPs tried
		itoa10<uint64_t>(dpSse8s.dp, buf);
		if(metricsStderr) stderrSs << buf << '\t';
		if(o != NULL) { o->writeChars(buf); o->write('\t'); }
		// 74. 8-bit SSE seed-extend DPs saturated
		itoa10<uint64_t>(dpSse8s.dpsat, buf);
		if(metricsStderr) stderrSs << buf << '\t';
		if(o != NULL) { o->writeChars(buf); o->write('\t'); }
		// 75. 8-bit SSE seed-extend DPs failed
		itoa10<uint64_t>(dpSse8s.dpfail, buf);
		if(metricsStderr) stderrSs << buf << '\t';
		if(o != NULL) { o->writeChars(buf); o->write('\t'); }
		// 76. 8-bit SSE seed-extend DPs succeeded
		itoa10<uint64_t>(dpSse8s.dpsucc, buf);
		if(metricsStderr) stderrSs << buf << '\t';
		if(o != NULL) { o->writeChars(buf); o->write('\t'); }
		// 77. 8-bit SSE seed-extend DP columns completed
		itoa10<uint64_t>(dpSse8s.col, buf);
		if(metricsStderr) stderrSs << buf << '\t';
		if(o != NULL) { o->writeChars(buf); o->write('\t'); }
		// 78. 8-bit SSE seed-extend DP cells completed
		itoa10<uint64_t>(dpSse8s.cell, buf);
		if(metricsStderr) stderrSs << buf << '\t';
		if(o != NULL) { o->writeChars(buf); o->write('\t'); }
		// 79. 8-bit SSE seed-extend DP inner loop iters completed
		itoa10<uint64_t>(dpSse8s.inner, buf);
		if(metricsStderr) stderrSs << buf << '\t';
		if(o != NULL) { o->writeChars(buf); o->write('\t'); }
		// 80. 8-bit SSE seed-extend DP fixup loop iters completed
		itoa10<uint64_t>(dpSse8s.fixup, buf);
		if(metricsStderr) stderrSs << buf << '\t';
		if(o != NULL) { o->writeChars(buf); o->write('\t'); }
		// 81. 16-bit SSE seed-extend DP gather, cells with potential solutions
		itoa10<uint64_t>(dpSse8s.gathsol, buf);
		if(metricsStderr) stderrSs << buf << '\t';
		if(o != NULL) { o->writeChars(buf); o->write('\t'); }
		// 82. 16-bit SSE seed-extend DP backtrace attempts
		itoa10<uint64_t>(dpSse8s.bt, buf);
		if(metricsStderr) stderrSs << buf << '\t';
		if(o != NULL) { o->writeChars(buf); o->write('\t'); }
		// 83. 16-bit SSE seed-extend DP failed backtrace attempts
		itoa10<uint64_t>(dpSse8s.btfail, buf);
		if(metricsStderr) stderrSs << buf << '\t';
		if(o != NULL) { o->writeChars(buf); o->write('\t'); }
		// 84. 16-bit SSE seed-extend DP succesful backtrace attempts
		itoa10<uint64_t>(dpSse8s.btsucc, buf);
		if(metricsStderr) stderrSs << buf << '\t';
		if(o != NULL) { o->writeChars(buf); o->write('\t'); }
		// 85. 16-bit SSE seed-extend DP backtrace cells
		itoa10<uint64_t>(dpSse8s.btcell, buf);
		if(metricsStderr) stderrSs << buf << '\t';
		if(o != NULL) { o->writeChars(buf); o->write('\t'); }
		// 86. 16-bit SSE seed-extend DP core-diag rejections
		itoa10<uint64_t>(dpSse8s.corerej, buf);
		if(metricsStderr) stderrSs << buf << '\t';
		if(o != NULL) { o->writeChars(buf); o->write('\t'); }
		// 87. 16-bit SSE seed-extend DP N rejections
		itoa10<uint64_t>(dpSse8s.nrej, buf);
		if(metricsStderr) stderrSs << buf << '\t';
		if(o != NULL) { o->writeChars(buf); o->write('\t'); }
		
		const SSEMetrics& dpSse16m = total ? dpSse16Mate : dpSse16uMate;
		
		// 88. 16-bit SSE mate-finding DPs tried
		itoa10<uint64_t>(dpSse16m.dp, buf);
		if(metricsStderr) stderrSs << buf << '\t';
		if(o != NULL) { o->writeChars(buf); o->write('\t'); }
		// 89. 16-bit SSE mate-finding DPs saturated
		itoa10<uint64_t>(dpSse16m.dpsat, buf);
		if(metricsStderr) stderrSs << buf << '\t';
		if(o != NULL) { o->writeChars(buf); o->write('\t'); }
		// 90. 16-bit SSE mate-finding DPs failed
		itoa10<uint64_t>(dpSse16m.dpfail, buf);
		if(metricsStderr) stderrSs << buf << '\t';
		if(o != NULL) { o->writeChars(buf); o->write('\t'); }
		// 91. 16-bit SSE mate-finding DPs succeeded
		itoa10<uint64_t>(dpSse16m.dpsucc, buf);
		if(metricsStderr) stderrSs << buf << '\t';
		if(o != NULL) { o->writeChars(buf); o->write('\t'); }
		// 92. 16-bit SSE mate-finding DP columns completed
		itoa10<uint64_t>(dpSse16m.col, buf);
		if(metricsStderr) stderrSs << buf << '\t';
		if(o != NULL) { o->writeChars(buf); o->write('\t'); }
		// 93. 16-bit SSE mate-finding DP cells completed
		itoa10<uint64_t>(dpSse16m.cell, buf);
		if(metricsStderr) stderrSs << buf << '\t';
		if(o != NULL) { o->writeChars(buf); o->write('\t'); }
		// 94. 16-bit SSE mate-finding DP inner loop iters completed
		itoa10<uint64_t>(dpSse16m.inner, buf);
		if(metricsStderr) stderrSs << buf << '\t';
		if(o != NULL) { o->writeChars(buf); o->write('\t'); }
		// 95. 16-bit SSE mate-finding DP fixup loop iters completed
		itoa10<uint64_t>(dpSse16m.fixup, buf);
		if(metricsStderr) stderrSs << buf << '\t';
		if(o != NULL) { o->writeChars(buf); o->write('\t'); }
		// 96. 16-bit SSE mate-finding DP gather, cells with potential solutions
		itoa10<uint64_t>(dpSse16m.gathsol, buf);
		if(metricsStderr) stderrSs << buf << '\t';
		if(o != NULL) { o->writeChars(buf); o->write('\t'); }
		// 97. 16-bit SSE mate-finding DP backtrace attempts
		itoa10<uint64_t>(dpSse16m.bt, buf);
		if(metricsStderr) stderrSs << buf << '\t';
		if(o != NULL) { o->writeChars(buf); o->write('\t'); }
		// 98. 16-bit SSE mate-finding DP failed backtrace attempts
		itoa10<uint64_t>(dpSse16m.btfail, buf);
		if(metricsStderr) stderrSs << buf << '\t';
		if(o != NULL) { o->writeChars(buf); o->write('\t'); }
		// 99. 16-bit SSE mate-finding DP succesful backtrace attempts
		itoa10<uint64_t>(dpSse16m.btsucc, buf);
		if(metricsStderr) stderrSs << buf << '\t';
		if(o != NULL) { o->writeChars(buf); o->write('\t'); }
		// 100. 16-bit SSE mate-finding DP backtrace cells
		itoa10<uint64_t>(dpSse16m.btcell, buf);
		if(metricsStderr) stderrSs << buf << '\t';
		if(o != NULL) { o->writeChars(buf); o->write('\t'); }
		// 101. 16-bit SSE mate-finding DP core-diag rejections
		itoa10<uint64_t>(dpSse16m.corerej, buf);
		if(metricsStderr) stderrSs << buf << '\t';
		if(o != NULL) { o->writeChars(buf); o->write('\t'); }
		// 102. 16-bit SSE mate-finding DP N rejections
		itoa10<uint64_t>(dpSse16m.nrej, buf);
		if(metricsStderr) stderrSs << buf << '\t';
		if(o != NULL) { o->writeChars(buf); o->write('\t'); }
		
		const SSEMetrics& dpSse8m = total ? dpSse8Mate : dpSse8uMate;
		
		// 103. 8-bit SSE mate-finding DPs tried
		itoa10<uint64_t>(dpSse8m.dp, buf);
		if(metricsStderr) stderrSs << buf << '\t';
		if(o != NULL) { o->writeChars(buf); o->write('\t'); }
		// 104. 8-bit SSE mate-finding DPs saturated
		itoa10<uint64_t>(dpSse8m.dpsat, buf);
		if(metricsStderr) stderrSs << buf << '\t';
		if(o != NULL) { o->writeChars(buf); o->write('\t'); }
		// 105. 8-bit SSE mate-finding DPs failed
		itoa10<uint64_t>(dpSse8m.dpfail, buf);
		if(metricsStderr) stderrSs << buf << '\t';
		if(o != NULL) { o->writeChars(buf); o->write('\t'); }
		// 106. 8-bit SSE mate-finding DPs succeeded
		itoa10<uint64_t>(dpSse8m.dpsucc, buf);
		if(metricsStderr) stderrSs << buf << '\t';
		if(o != NULL) { o->writeChars(buf); o->write('\t'); }
		// 107. 8-bit SSE mate-finding DP columns completed
		itoa10<uint64_t>(dpSse8m.col, buf);
		if(metricsStderr) stderrSs << buf << '\t';
		if(o != NULL) { o->writeChars(buf); o->write('\t'); }
		// 108. 8-bit SSE mate-finding DP cells completed
		itoa10<uint64_t>(dpSse8m.cell, buf);
		if(metricsStderr) stderrSs << buf << '\t';
		if(o != NULL) { o->writeChars(buf); o->write('\t'); }
		// 109. 8-bit SSE mate-finding DP inner loop iters completed
		itoa10<uint64_t>(dpSse8m.inner, buf);
		if(metricsStderr) stderrSs << buf << '\t';
		if(o != NULL) { o->writeChars(buf); o->write('\t'); }
		// 110. 8-bit SSE mate-finding DP fixup loop iters completed
		itoa10<uint64_t>(dpSse8m.fixup, buf);
		if(metricsStderr) stderrSs << buf << '\t';
		if(o != NULL) { o->writeChars(buf); o->write('\t'); }
		// 111. 16-bit SSE mate-finding DP gather, cells with potential solutions
		itoa10<uint64_t>(dpSse8m.gathsol, buf);
		if(metricsStderr) stderrSs << buf << '\t';
		if(o != NULL) { o->writeChars(buf); o->write('\t'); }
		// 112. 16-bit SSE mate-finding DP backtrace attempts
		itoa10<uint64_t>(dpSse8m.bt, buf);
		if(metricsStderr) stderrSs << buf << '\t';
		if(o != NULL) { o->writeChars(buf); o->write('\t'); }
		// 113. 16-bit SSE mate-finding DP failed backtrace attempts
		itoa10<uint64_t>(dpSse8m.btfail, buf);
		if(metricsStderr) stderrSs << buf << '\t';
		if(o != NULL) { o->writeChars(buf); o->write('\t'); }
		// 114. 16-bit SSE mate-finding DP succesful backtrace attempts
		itoa10<uint64_t>(dpSse8m.btsucc, buf);
		if(metricsStderr) stderrSs << buf << '\t';
		if(o != NULL) { o->writeChars(buf); o->write('\t'); }
		// 115. 16-bit SSE mate-finding DP backtrace cells
		itoa10<uint64_t>(dpSse8m.btcell, buf);
		if(metricsStderr) stderrSs << buf << '\t';
		if(o != NULL) { o->writeChars(buf); o->write('\t'); }
		// 116. 16-bit SSE mate-finding DP core rejections
		itoa10<uint64_t>(dpSse8m.corerej, buf);
		if(metricsStderr) stderrSs << buf << '\t';
		if(o != NULL) { o->writeChars(buf); o->write('\t'); }
		// 117. 16-bit SSE mate-finding N rejections
		itoa10<uint64_t>(dpSse8m.nrej, buf);
		if(metricsStderr) stderrSs << buf << '\t';
		if(o != NULL) { o->writeChars(buf); o->write('\t'); }
		
		// 118. Backtrace candidates filtered due to starting cell
		itoa10<uint64_t>(total ? nbtfiltst : nbtfiltst_u, buf);
		if(metricsStderr) stderrSs << buf << '\t';
		if(o != NULL) { o->writeChars(buf); o->write('\t'); }
		// 119. Backtrace candidates filtered due to low score
		itoa10<uint64_t>(total ? nbtfiltsc : nbtfiltsc_u, buf);
		if(metricsStderr) stderrSs << buf << '\t';
		if(o != NULL) { o->writeChars(buf); o->write('\t'); }
		// 120. Backtrace candidates filtered due to domination
		itoa10<uint64_t>(total ? nbtfiltdo : nbtfiltdo_u, buf);
		if(metricsStderr) stderrSs << buf << '\t';
		if(o != NULL) { o->writeChars(buf); o->write('\t'); }
		
		// 121. Overall memory peak
		itoa10<size_t>(gMemTally.peak() >> 20, buf);
		if(metricsStderr) stderrSs << buf << '\t';
		if(o != NULL) { o->writeChars(buf); o->write('\t'); }
		// 122. Uncategorized memory peak
		itoa10<size_t>(gMemTally.peak(0) >> 20, buf);
		if(metricsStderr) stderrSs << buf << '\t';
		if(o != NULL) { o->writeChars(buf); o->write('\t'); }
		// 123. Ebwt memory peak
		itoa10<size_t>(gMemTally.peak(EBWT_CAT) >> 20, buf);
		if(metricsStderr) stderrSs << buf << '\t';
		if(o != NULL) { o->writeChars(buf); o->write('\t'); }
		// 124. Cache memory peak
		itoa10<size_t>(gMemTally.peak(CA_CAT) >> 20, buf);
		if(metricsStderr) stderrSs << buf << '\t';
		if(o != NULL) { o->writeChars(buf); o->write('\t'); }
		// 125. Resolver memory peak
		itoa10<size_t>(gMemTally.peak(GW_CAT) >> 20, buf);
		if(metricsStderr) stderrSs << buf << '\t';
		if(o != NULL) { o->writeChars(buf); o->write('\t'); }
		// 126. Seed aligner memory peak
		itoa10<size_t>(gMemTally.peak(AL_CAT) >> 20, buf);
		if(metricsStderr) stderrSs << buf << '\t';
		if(o != NULL) { o->writeChars(buf); o->write('\t'); }
		// 127. Dynamic programming aligner memory peak
		itoa10<size_t>(gMemTally.peak(DP_CAT) >> 20, buf);
		if(metricsStderr) stderrSs << buf << '\t';
		if(o != NULL) { o->writeChars(buf); o->write('\t'); }
		// 128. Miscellaneous memory peak
		itoa10<size_t>(gMemTally.peak(MISC_CAT) >> 20, buf);
		if(metricsStderr) stderrSs << buf << '\t';
		if(o != NULL) { o->writeChars(buf); o->write('\t'); }
		// 129. Debug memory peak
		itoa10<size_t>(gMemTally.peak(DEBUG_CAT) >> 20, buf);
        if(metricsStderr) stderrSs << buf << '\t';
		if(o != NULL) { o->writeChars(buf); o->write('\t'); }
        
        // 130
        itoa10<size_t>(him.localatts, buf);
		if(metricsStderr) stderrSs << buf << '\t';
		if(o != NULL) { o->writeChars(buf); o->write('\t'); }
        // 131
        itoa10<size_t>(him.anchoratts, buf);
		if(metricsStderr) stderrSs << buf << '\t';
		if(o != NULL) { o->writeChars(buf); o->write('\t'); }
        // 132
        itoa10<size_t>(him.localindexatts, buf);
		if(metricsStderr) stderrSs << buf << '\t';
		if(o != NULL) { o->writeChars(buf); o->write('\t'); }
        // 133
        itoa10<size_t>(him.localextatts, buf);
        if(metricsStderr) stderrSs << buf << '\t';
		if(o != NULL) { o->writeChars(buf); o->write('\t'); }
        // 134
        itoa10<size_t>(him.localsearchrecur, buf);
        if(metricsStderr) stderrSs << buf << '\t';
		if(o != NULL) { o->writeChars(buf); o->write('\t'); }
        // 135
        itoa10<size_t>(him.globalgenomecoords, buf);
        if(metricsStderr) stderrSs << buf << '\t';
		if(o != NULL) { o->writeChars(buf); o->write('\t'); }
        // 136
        itoa10<size_t>(him.localgenomecoords, buf);
        if(metricsStderr) stderrSs << buf;
		if(o != NULL) { o->writeChars(buf); }

		if(o != NULL) { o->write('\n'); }
		if(metricsStderr) cerr << stderrSs.str().c_str() << endl;
		if(!total) mergeIncrementals();
	}
	
	void mergeIncrementals() {
		olm.merge(olmu, false);
		sdm.merge(sdmu, false);
		wlm.merge(wlmu, false);
		swmSeed.merge(swmuSeed, false);
		swmMate.merge(swmuMate, false);
		dpSse8Seed.merge(dpSse8uSeed, false);
		dpSse8Mate.merge(dpSse8uMate, false);
		dpSse16Seed.merge(dpSse16uSeed, false);
		dpSse16Mate.merge(dpSse16uMate, false);
		nbtfiltst_u += nbtfiltst;
		nbtfiltsc_u += nbtfiltsc;
		nbtfiltdo_u += nbtfiltdo;

		olmu.reset();
		sdmu.reset();
		wlmu.reset();
		swmuSeed.reset();
		swmuMate.reset();
		rpmu.reset();
		dpSse8uSeed.reset();
		dpSse8uMate.reset();
		dpSse16uSeed.reset();
		dpSse16uMate.reset();
		nbtfiltst_u = 0;
		nbtfiltsc_u = 0;
		nbtfiltdo_u = 0;
	}

	// Total over the whole job
	OuterLoopMetrics  olm;   // overall metrics
	SeedSearchMetrics sdm;   // metrics related to seed alignment
	WalkMetrics       wlm;   // metrics related to walking left (i.e. resolving reference offsets)
	SwMetrics         swmSeed;  // metrics related to DP seed-extend alignment
	SwMetrics         swmMate;  // metrics related to DP mate-finding alignment
	ReportingMetrics  rpm;   // metrics related to reporting
	SSEMetrics        dpSse8Seed;  // 8-bit SSE seed extensions
	SSEMetrics        dpSse8Mate;    // 8-bit SSE mate finds
	SSEMetrics        dpSse16Seed; // 16-bit SSE seed extensions
	SSEMetrics        dpSse16Mate;   // 16-bit SSE mate finds
	uint64_t          nbtfiltst;
	uint64_t          nbtfiltsc;
	uint64_t          nbtfiltdo;

	// Just since the last update
	OuterLoopMetrics  olmu;  // overall metrics
	SeedSearchMetrics sdmu;  // metrics related to seed alignment
	WalkMetrics       wlmu;  // metrics related to walking left (i.e. resolving reference offsets)
	SwMetrics         swmuSeed; // metrics related to DP seed-extend alignment
	SwMetrics         swmuMate; // metrics related to DP mate-finding alignment
	ReportingMetrics  rpmu;  // metrics related to reporting
	SSEMetrics        dpSse8uSeed;  // 8-bit SSE seed extensions
	SSEMetrics        dpSse8uMate;  // 8-bit SSE mate finds
	SSEMetrics        dpSse16uSeed; // 16-bit SSE seed extensions
	SSEMetrics        dpSse16uMate; // 16-bit SSE mate finds
	uint64_t          nbtfiltst_u;
	uint64_t          nbtfiltsc_u;
	uint64_t          nbtfiltdo_u;
    
    //
    HIMetrics         him;

	MUTEX_T           mutex_m;  // lock for when one ob
	bool              first; // yet to print first line?
	time_t            lastElapsed; // used in reportInterval to measure time since last call
};

static PerfMetrics metrics;

// Cyclic rotations
#define ROTL(n, x) (((x) << (n)) | ((x) >> (32-n)))
#define ROTR(n, x) (((x) >> (n)) | ((x) << (32-n)))

static inline void printMmsSkipMsg(
	const PatternSourcePerThread& ps,
	bool paired,
	bool mate1,
	int seedmms)
{
	ostringstream os;
	if(paired) {
		os << "Warning: skipping mate #" << (mate1 ? '1' : '2')
		   << " of read '" << (mate1 ? ps.bufa().name : ps.bufb().name)
		   << "' because length (" << (mate1 ? ps.bufa().patFw.length() : ps.bufb().patFw.length())
		   << ") <= # seed mismatches (" << seedmms << ")" << endl;
	} else {
		os << "Warning: skipping read '" << (mate1 ? ps.bufa().name : ps.bufb().name)
		   << "' because length (" << (mate1 ? ps.bufa().patFw.length() : ps.bufb().patFw.length())
		   << ") <= # seed mismatches (" << seedmms << ")" << endl;
	}
	cerr << os.str().c_str();
}

static inline void printLenSkipMsg(
	const PatternSourcePerThread& ps,
	bool paired,
	bool mate1)
{
	ostringstream os;
	if(paired) {
		os << "Warning: skipping mate #" << (mate1 ? '1' : '2')
		   << " of read '" << (mate1 ? ps.bufa().name : ps.bufb().name)
		   << "' because it was < 2 characters long" << endl;
	} else {
		os << "Warning: skipping read '" << (mate1 ? ps.bufa().name : ps.bufb().name)
		   << "' because it was < 2 characters long" << endl;
	}
	cerr << os.str().c_str();
}

static inline void printLocalScoreMsg(
	const PatternSourcePerThread& ps,
	bool paired,
	bool mate1)
{
	ostringstream os;
	if(paired) {
		os << "Warning: minimum score function gave negative number in "
		   << "--local mode for mate #" << (mate1 ? '1' : '2')
		   << " of read '" << (mate1 ? ps.bufa().name : ps.bufb().name)
		   << "; setting to 0 instead" << endl;
	} else {
		os << "Warning: minimum score function gave negative number in "
		   << "--local mode for read '" << (mate1 ? ps.bufa().name : ps.bufb().name)
		   << "; setting to 0 instead" << endl;
	}
	cerr << os.str().c_str();
}

static inline void printEEScoreMsg(
	const PatternSourcePerThread& ps,
	bool paired,
	bool mate1)
{
	ostringstream os;
	if(paired) {
		os << "Warning: minimum score function gave positive number in "
		   << "--end-to-end mode for mate #" << (mate1 ? '1' : '2')
		   << " of read '" << (mate1 ? ps.bufa().name : ps.bufb().name)
		   << "; setting to 0 instead" << endl;
	} else {
		os << "Warning: minimum score function gave positive number in "
		   << "--end-to-end mode for read '" << (mate1 ? ps.bufa().name : ps.bufb().name)
		   << "; setting to 0 instead" << endl;
	}
	cerr << os.str().c_str();
}


#define MERGE_METRICS(met, sync) { \
	msink.mergeMetrics(rpm); \
	met.merge( \
		&olm, \
		&sdm, \
		&wlm, \
		&swmSeed, \
		&swmMate, \
		&rpm, \
		&sseU8ExtendMet, \
		&sseU8MateMet, \
		&sseI16ExtendMet, \
		&sseI16MateMet, \
		nbtfiltst, \
		nbtfiltsc, \
		nbtfiltdo, \
        &him, \
		sync); \
	olm.reset(); \
	sdm.reset(); \
	wlm.reset(); \
	swmSeed.reset(); \
	swmMate.reset(); \
	rpm.reset(); \
	sseU8ExtendMet.reset(); \
	sseU8MateMet.reset(); \
	sseI16ExtendMet.reset(); \
	sseI16MateMet.reset(); \
    him.reset(); \
}

#define MERGE_SW(x) { \
	x.merge( \
		sseU8ExtendMet, \
		sseU8MateMet, \
		sseI16ExtendMet, \
		sseI16MateMet, \
		nbtfiltst, \
		nbtfiltsc, \
		nbtfiltdo); \
	x.resetCounters(); \
}

/**
 * Called once per thread.  Sets up per-thread pointers to the shared global
 * data structures, creates per-thread structures, then enters the alignment
 * loop.  The general flow of the alignment loop is:
 *
 * - If it's been a while and we're the master thread, report some alignment
 *   metrics
 * - Get the next read/pair
 * - Check if this read/pair is identical to the previous
 *   + If identical, check whether we can skip any or all alignment stages.  If
 *     we can skip all stages, report the result immediately and move to next
 *     read/pair
 *   + If not identical, continue
 * -
 */
static void multiseedSearchWorker_hisat_bp(void *vp) {
	int tid = *((int*)vp);
	assert(multiseed_ebwtFw != NULL);
	assert(multiseedMms == 0 || multiseed_ebwtBw != NULL);
	PairedPatternSource&             patsrc   = *multiseed_patsrc;
	const HierEbwt<index_t>&         ebwtFw   = *multiseed_ebwtFw;
	const HierEbwt<index_t>&         ebwtBw   = *multiseed_ebwtBw;
	const Scoring&                   sc       = *multiseed_sc;
	const BitPairReference&          ref      = *multiseed_refs;
	AlignmentCache<index_t>&         scShared = *multiseed_ca;
	AlnSink<index_t>&                msink    = *multiseed_msink;
	OutFileBuf*                      metricsOfb = multiseed_metricsOfb;
    
	// Sinks: these are so that we can print tables encoding counts for
	// events of interest on a per-read, per-seed, per-join, or per-SW
	// level.  These in turn can be used to diagnose performance
	// problems, or generally characterize performance.
	
	//const BitPairReference& refs   = *multiseed_refs;
	auto_ptr<PatternSourcePerThreadFactory> patsrcFact(createPatsrcFactory(patsrc, tid));
	auto_ptr<PatternSourcePerThread> ps(patsrcFact->create());
	
	// Thread-local cache for seed alignments
	PtrWrap<AlignmentCache<index_t> > scLocal;
	if(!msNoCache) {
		scLocal.init(new AlignmentCache<index_t>(seedCacheLocalMB * 1024 * 1024, false));
	}
	AlignmentCache<index_t> scCurrent(seedCacheCurrentMB * 1024 * 1024, false);
	// Thread-local cache for current seed alignments
	
	// Interfaces for alignment and seed caches
	AlignmentCacheIface<index_t> ca(
                                    &scCurrent,
                                    scLocal.get(),
                                    msNoCache ? NULL : &scShared);
	
	// Instantiate an object for holding reporting-related parameters.
    ReportingParams rp(
                       (allHits ? std::numeric_limits<THitInt>::max() : khits), // -k
                       mhits,             // -m/-M
                       0,                 // penalty gap (not used now)
                       msample,           // true -> -M was specified, otherwise assume -m
                       gReportDiscordant, // report discordang paired-end alignments?
                       gReportMixed);     // report unpaired alignments for paired reads?
    
	// Instantiate a mapping quality calculator
	auto_ptr<Mapq> bmapq(new_mapq(mapqv, scoreMin, sc));
	
	// Make a per-thread wrapper for the global MHitSink object.
	AlnSinkWrap<index_t> msinkwrap(
                                   msink,         // global sink
                                   rp,            // reporting parameters
                                   *bmapq.get(),  // MAPQ calculator
                                   (size_t)tid);  // thread id
    
    BP_Aligner<index_t, local_index_t> bp_Aligner(
                                                  ebwtFw,
                                                  multiseed_refnames,
                                                  &multiseed_mutex,
                                                  thread_rids_mindist,
                                                  no_spliced_alignment);
	SwAligner sw;
	OuterLoopMetrics olm;
	SeedSearchMetrics sdm;
	WalkMetrics wlm;
	SwMetrics swmSeed, swmMate;
	ReportingMetrics rpm;
	RandomSource rnd, rndArb;
	SSEMetrics sseU8ExtendMet;
	SSEMetrics sseU8MateMet;
	SSEMetrics sseI16ExtendMet;
	SSEMetrics sseI16MateMet;
   	DescentMetrics descm;
	uint64_t nbtfiltst = 0; // TODO: find a new home for these
	uint64_t nbtfiltsc = 0; // TODO: find a new home for these
	uint64_t nbtfiltdo = 0; // TODO: find a new home for these
    HIMetrics him;
    
	ASSERT_ONLY(BTDnaString tmp);
    
	int pepolFlag;
	if(gMate1fw && gMate2fw) {
		pepolFlag = PE_POLICY_FF;
	} else if(gMate1fw && !gMate2fw) {
		pepolFlag = PE_POLICY_FR;
	} else if(!gMate1fw && gMate2fw) {
		pepolFlag = PE_POLICY_RF;
	} else {
		pepolFlag = PE_POLICY_RR;
	}
	assert_geq(gMaxInsert, gMinInsert);
	assert_geq(gMinInsert, 0);
	PairedEndPolicy pepol(
                          pepolFlag,
                          gMaxInsert,
                          gMinInsert,
                          localAlign,
                          gFlippedMatesOK,
                          gDovetailMatesOK,
                          gContainMatesOK,
                          gOlapMatesOK,
                          gExpandToFrag);
    
  	PerfMetrics metricsPt; // per-thread metrics object; for read-level metrics
	BTString nametmp;
	
	PerReadMetrics prm;
    
	// Used by thread with threadid == 1 to measure time elapsed
	time_t iTime = time(0);
    
	// Keep track of whether last search was exhaustive for mates 1 and 2
	bool exhaustive[2] = { false, false };
	// Keep track of whether mates 1/2 were filtered out last time through
	bool filt[2]    = { true, true };
	// Keep track of whether mates 1/2 were filtered out due Ns last time
	bool nfilt[2]   = { true, true };
	// Keep track of whether mates 1/2 were filtered out due to not having
	// enough characters to rise about the score threshold.
	bool scfilt[2]  = { true, true };
	// Keep track of whether mates 1/2 were filtered out due to not having
	// more characters than the number of mismatches permitted in a seed.
	bool lenfilt[2] = { true, true };
	// Keep track of whether mates 1/2 were filtered out by upstream qc
	bool qcfilt[2]  = { true, true };
    
	rndArb.init((uint32_t)time(0));
	int mergei = 0;
	int mergeival = 16;
	while(true) {
		bool success = false, done = false, paired = false;
		ps->nextReadPair(success, done, paired, outType != OUTPUT_SAM);
		if(!success && done) {
			break;
		} else if(!success) {
			continue;
		}
		TReadId rdid = ps->rdid();
        
        if(nthreads > 1 && useTempSpliceSite) {
            while(true) {
                uint64_t min_rdid = 0;
                {
                    // ThreadSafe t(&thread_rids_mutex, nthreads > 1);
                    assert_gt(thread_rids.size(), 0);
                    min_rdid = thread_rids[0];
                    for(size_t i = 1; i < thread_rids.size(); i++) {
                        if(thread_rids[i] < min_rdid) {
                            min_rdid = thread_rids[i];
                        }
                    }
                }
                
                if(min_rdid + thread_rids_mindist < rdid) {
#if defined(_TTHREAD_WIN32_)
                    Sleep(0);
#elif defined(_TTHREAD_POSIX_)
                    sched_yield();
#endif
                } else break;
            }
        }
        
		bool sample = true;
		if(arbitraryRandom) {
			ps->bufa().seed = rndArb.nextU32();
			ps->bufb().seed = rndArb.nextU32();
		}
		if(sampleFrac < 1.0f) {
			rnd.init(ROTL(ps->bufa().seed, 2));
			sample = rnd.nextFloat() < sampleFrac;
		}
		if(rdid >= skipReads && rdid < qUpto && sample) {
			// Align this read/pair
			bool retry = true;
			//
			// Check if there is metrics reporting for us to do.
			//
			if(metricsIval > 0 &&
			   (metricsOfb != NULL || metricsStderr) &&
			   !metricsPerRead &&
			   ++mergei == mergeival)
			{
				// Do a periodic merge.  Update global metrics, in a
				// synchronized manner if needed.
				MERGE_METRICS(metrics, nthreads > 1);
				mergei = 0;
				// Check if a progress message should be printed
				if(tid == 0) {
					// Only thread 1 prints progress messages
					time_t curTime = time(0);
					if(curTime - iTime >= metricsIval) {
						metrics.reportInterval(metricsOfb, metricsStderr, false, true, NULL);
						iTime = curTime;
					}
				}
			}
			prm.reset(); // per-read metrics
			prm.doFmString = false;
			if(sam_print_xt) {
				gettimeofday(&prm.tv_beg, &prm.tz_beg);
			}
			// Try to align this read
			while(retry) {
				retry = false;
				assert_eq(ps->bufa().color, false);
				ca.nextRead(); // clear the cache
				olm.reads++;
				assert(!ca.aligning());
				bool pair = paired;
				const size_t rdlen1 = ps->bufa().length();
				const size_t rdlen2 = pair ? ps->bufb().length() : 0;
				olm.bases += (rdlen1 + rdlen2);
#if 0
				msinkwrap.nextRead(
                                   &ps->bufa(),
                                   pair ? &ps->bufb() : NULL,
                                   rdid,
                                   sc.qualitiesMatter());
				assert(msinkwrap.inited());
#endif
				size_t rdlens[2] = { rdlen1, rdlen2 };
				// Calculate the minimum valid score threshold for the read
				TAlScore minsc[2], maxpen[2];
				maxpen[0] = maxpen[1] = 0;
				minsc[0] = minsc[1] = std::numeric_limits<TAlScore>::max();
				if(bwaSwLike) {
					// From BWA-SW manual: "Given an l-long query, the
					// threshold for a hit to be retained is
					// a*max{T,c*log(l)}."  We try to recreate that here.
					float a = (float)sc.match(30);
					float T = bwaSwLikeT, c = bwaSwLikeC;
					minsc[0] = (TAlScore)max<float>(a*T, a*c*log(rdlens[0]));
					if(paired) {
						minsc[1] = (TAlScore)max<float>(a*T, a*c*log(rdlens[1]));
					}
				} else {
					minsc[0] = scoreMin.f<TAlScore>(rdlens[0]);
					if(paired) minsc[1] = scoreMin.f<TAlScore>(rdlens[1]);
					if(localAlign) {
						if(minsc[0] < 0) {
							if(!gQuiet) printLocalScoreMsg(*ps, paired, true);
							minsc[0] = 0;
						}
						if(paired && minsc[1] < 0) {
							if(!gQuiet) printLocalScoreMsg(*ps, paired, false);
							minsc[1] = 0;
						}
					} else {
						if(minsc[0] > 0) {
							if(!gQuiet) printEEScoreMsg(*ps, paired, true);
							minsc[0] = 0;
						}
						if(paired && minsc[1] > 0) {
							if(!gQuiet) printEEScoreMsg(*ps, paired, false);
							minsc[1] = 0;
						}
					}
				}
                
				// N filter; does the read have too many Ns?
				size_t readns[2] = {0, 0};
				sc.nFilterPair(
                               &ps->bufa().patFw,
                               pair ? &ps->bufb().patFw : NULL,
                               readns[0],
                               readns[1],
                               nfilt[0],
                               nfilt[1]);
				// Score filter; does the read enough character to rise above
				// the score threshold?
				scfilt[0] = sc.scoreFilter(minsc[0], rdlens[0]);
				scfilt[1] = sc.scoreFilter(minsc[1], rdlens[1]);
				lenfilt[0] = lenfilt[1] = true;
				if(rdlens[0] <= (size_t)multiseedMms || rdlens[0] < 2) {
					if(!gQuiet) printMmsSkipMsg(*ps, paired, true, multiseedMms);
					lenfilt[0] = false;
				}
				if((rdlens[1] <= (size_t)multiseedMms || rdlens[1] < 2) && paired) {
					if(!gQuiet) printMmsSkipMsg(*ps, paired, false, multiseedMms);
					lenfilt[1] = false;
				}
				if(rdlens[0] < 2) {
					if(!gQuiet) printLenSkipMsg(*ps, paired, true);
					lenfilt[0] = false;
				}
				if(rdlens[1] < 2 && paired) {
					if(!gQuiet) printLenSkipMsg(*ps, paired, false);
					lenfilt[1] = false;
				}
				qcfilt[0] = qcfilt[1] = true;
				if(qcFilter) {
					qcfilt[0] = (ps->bufa().filter != '0');
					qcfilt[1] = (ps->bufb().filter != '0');
				}
				filt[0] = (nfilt[0] && scfilt[0] && lenfilt[0] && qcfilt[0]);
				filt[1] = (nfilt[1] && scfilt[1] && lenfilt[1] && qcfilt[1]);
				prm.nFilt += (filt[0] ? 0 : 1) + (filt[1] ? 0 : 1);
				Read* rds[2] = { &ps->bufa(), &ps->bufb() };
				// For each mate...
				assert(msinkwrap.empty());
				//size_t minedfw[2] = { 0, 0 };
				//size_t minedrc[2] = { 0, 0 };
				// Calcualte nofw / no rc
				bool nofw[2] = { false, false };
				bool norc[2] = { false, false };
				nofw[0] = paired ? (gMate1fw ? gNofw : gNorc) : gNofw;
				norc[0] = paired ? (gMate1fw ? gNorc : gNofw) : gNorc;
				nofw[1] = paired ? (gMate2fw ? gNofw : gNorc) : gNofw;
				norc[1] = paired ? (gMate2fw ? gNorc : gNofw) : gNorc;
				// Calculate nceil
				int nceil[2] = { 0, 0 };
				nceil[0] = nCeil.f<int>((double)rdlens[0]);
				nceil[0] = min(nceil[0], (int)rdlens[0]);
				if(paired) {
					nceil[1] = nCeil.f<int>((double)rdlens[1]);
					nceil[1] = min(nceil[1], (int)rdlens[1]);
				}
				exhaustive[0] = exhaustive[1] = false;
				//size_t matemap[2] = { 0, 1 };
				bool pairPostFilt = filt[0] && filt[1];
				if(pairPostFilt) {
					rnd.init(ps->bufa().seed ^ ps->bufb().seed);
				} else {
					rnd.init(ps->bufa().seed);
				}
				// Calculate interval length for both mates
				int interval[2] = { 0, 0 };
				for(size_t mate = 0; mate < (pair ? 2:1); mate++) {
					interval[mate] = msIval.f<int>((double)rdlens[mate]);
					if(filt[0] && filt[1]) {
						// Boost interval length by 20% for paired-end reads
						interval[mate] = (int)(interval[mate] * 1.2 + 0.5);
					}
					interval[mate] = max(interval[mate], 1);
				}
				// Calculate streak length
				size_t streak[2]    = { maxDpStreak,   maxDpStreak };
				size_t mtStreak[2]  = { maxMateStreak, maxMateStreak };
				size_t mxDp[2]      = { maxDp,         maxDp       };
				size_t mxUg[2]      = { maxUg,         maxUg       };
				size_t mxIter[2]    = { maxIters,      maxIters    };
				if(allHits) {
					streak[0]   = streak[1]   = std::numeric_limits<size_t>::max();
					mtStreak[0] = mtStreak[1] = std::numeric_limits<size_t>::max();
					mxDp[0]     = mxDp[1]     = std::numeric_limits<size_t>::max();
					mxUg[0]     = mxUg[1]     = std::numeric_limits<size_t>::max();
					mxIter[0]   = mxIter[1]   = std::numeric_limits<size_t>::max();
				} else if(khits > 1) {
					for(size_t mate = 0; mate < 2; mate++) {
						streak[mate]   += (khits-1) * maxStreakIncr;
						mtStreak[mate] += (khits-1) * maxStreakIncr;
						mxDp[mate]     += (khits-1) * maxItersIncr;
						mxUg[mate]     += (khits-1) * maxItersIncr;
						mxIter[mate]   += (khits-1) * maxItersIncr;
					}
				}
				if(filt[0] && filt[1]) {
					streak[0] = (size_t)ceil((double)streak[0] / 2.0);
					streak[1] = (size_t)ceil((double)streak[1] / 2.0);
					assert_gt(streak[1], 0);
				}
				assert_gt(streak[0], 0);
				// Calculate # seed rounds for each mate
				size_t nrounds[2] = { nSeedRounds, nSeedRounds };
				if(filt[0] && filt[1]) {
					nrounds[0] = (size_t)ceil((double)nrounds[0] / 2.0);
					nrounds[1] = (size_t)ceil((double)nrounds[1] / 2.0);
					assert_gt(nrounds[1], 0);
				}
				assert_gt(nrounds[0], 0);
				// Increment counters according to what got filtered
				for(size_t mate = 0; mate < (pair ? 2:1); mate++) {
					if(!filt[mate]) {
						// Mate was rejected by N filter
						olm.freads++;               // reads filtered out
						olm.fbases += rdlens[mate]; // bases filtered out
					} else {
						//shs[mate].clear();
						//shs[mate].nextRead(mate == 0 ? ps->bufa() : ps->bufb());
						//assert(shs[mate].empty());
						olm.ureads++;               // reads passing filter
						olm.ubases += rdlens[mate]; // bases passing filter
					}
				}
				//size_t eePeEeltLimit = std::numeric_limits<size_t>::max();
				// Whether we're done with mate1 / mate2
                bool done[2] = { !filt[0], !filt[1] };
				// size_t nelt[2] = {0, 0};
                if(filt[0] && filt[1]) {
                    bp_Aligner.initReads(rds, nofw, norc, minsc, maxpen);
                } else if(filt[0] || filt[1]) {
                    bp_Aligner.initRead(rds[0], nofw[0], norc[0], minsc[0], maxpen[0], filt[1]);
                }
                if(filt[0] || filt[1]) {
                    int ret = bp_Aligner.go(sc, ebwtFw, ebwtBw, ref, sw, *ssdb, wlm, prm, swmSeed, him, rnd, msinkwrap);
                    MERGE_SW(sw);
                    // daehwan
                    size_t mate = 0;
                    
                    assert_gt(ret, 0);
                    // Clear out the exact hits so that we don't try to
                    // extend them again later!
                    if(ret == EXTEND_EXHAUSTED_CANDIDATES) {
                        // Not done yet
                    } else if(ret == EXTEND_POLICY_FULFILLED) {
                        // Policy is satisfied for this mate at least
                        if(msinkwrap.state().doneWithMate(mate == 0)) {
                            done[mate] = true;
                        }
                        if(msinkwrap.state().doneWithMate(mate == 1)) {
                            done[mate^1] = true;
                        }
                    } else if(ret == EXTEND_PERFECT_SCORE) {
                        // We exhausted this mode at least
                        done[mate] = true;
                    } else if(ret == EXTEND_EXCEEDED_HARD_LIMIT) {
                        // We exceeded a per-read limit
                        done[mate] = true;
                    } else if(ret == EXTEND_EXCEEDED_SOFT_LIMIT) {
                        // Not done yet
                    } else {
                        //
                        cerr << "Bad return value: " << ret << endl;
                        throw 1;
                    }
                    if(!done[mate]) {
                        TAlScore perfectScore = sc.perfectScore(rdlens[mate]);
                        if(!done[mate] && minsc[mate] == perfectScore) {
                            done[mate] = true;
                        }
                    }
                }

                for(size_t i = 0; i < 2; i++) {
                    assert_leq(prm.nExIters, mxIter[i]);
                    assert_leq(prm.nExDps,   mxDp[i]);
                    assert_leq(prm.nMateDps, mxDp[i]);
                    assert_leq(prm.nExUgs,   mxUg[i]);
                    assert_leq(prm.nMateUgs, mxUg[i]);
                    assert_leq(prm.nDpFail,  streak[i]);
                    assert_leq(prm.nUgFail,  streak[i]);
                    assert_leq(prm.nEeFail,  streak[i]);
                }
                
#if 0
				// Commit and report paired-end/unpaired alignments
				msinkwrap.finishRead(
                                     NULL,
                                     NULL,
                                     exhaustive[0],        // exhausted seed hits for mate 1?
                                     exhaustive[1],        // exhausted seed hits for mate 2?
                                     nfilt[0],
                                     nfilt[1],
                                     scfilt[0],
                                     scfilt[1],
                                     lenfilt[0],
                                     lenfilt[1],
                                     qcfilt[0],
                                     qcfilt[1],
                                     sortByScore,          // prioritize by alignment score
                                     rnd,                  // pseudo-random generator
                                     rpm,                  // reporting metrics
                                     prm,                  // per-read metrics
                                     sc,                   // scoring scheme
                                     !seedSumm,            // suppress seed summaries?
                                     seedSumm);            // suppress alignments?
				assert(!retry || msinkwrap.empty());
#endif
                
                if(nthreads > 1 && useTempSpliceSite) {
                    // ThreadSafe t(&thread_rids_mutex, nthreads > 1);
                    assert_gt(tid, 0);
                    assert_leq(tid, thread_rids.size());
                    assert(thread_rids[tid - 1] == 0 || rdid > thread_rids[tid - 1]);
                    thread_rids[tid - 1] = rdid;
                }
			} // while(retry)
		} // if(rdid >= skipReads && rdid < qUpto)
		else if(rdid >= qUpto) {
			break;
		}
		if(metricsPerRead) {
			MERGE_METRICS(metricsPt, nthreads > 1);
			nametmp = ps->bufa().name;
			metricsPt.reportInterval(
                                     metricsOfb, metricsStderr, true, true, &nametmp);
			metricsPt.reset();
		}
	} // while(true)
	
	// One last metrics merge
	MERGE_METRICS(metrics, nthreads > 1);
    
	return;
}

/**
 * Called once per alignment job.  Sets up global pointers to the
 * shared global data structures, creates per-thread structures, then
 * enters the search loop.
 */
static void multiseedSearch(
	Scoring& sc,
	PairedPatternSource& patsrc,  // pattern source
	AlnSink<index_t>& msink,             // hit sink
	HierEbwt<index_t>& ebwtFw,                 // index of original text
	HierEbwt<index_t>& ebwtBw,                 // index of mirror text
    BitPairReference* refs,
    const EList<string>& refnames,
	OutFileBuf *metricsOfb)
{
    multiseed_patsrc = &patsrc;
	multiseed_msink  = &msink;
	multiseed_ebwtFw = &ebwtFw;
	multiseed_ebwtBw = &ebwtBw;
	multiseed_sc     = &sc;
    multiseed_refnames = refnames;
	multiseed_metricsOfb      = metricsOfb;
	multiseed_refs = refs;
	AutoArray<tthread::thread*> threads(nthreads);
	AutoArray<int> tids(nthreads);
	{
		// Load the other half of the index into memory
		assert(!ebwtFw.isInMemory());
		Timer _t(cerr, "Time loading forward index: ", timing);
		ebwtFw.loadIntoMemory(
			0,  // colorspace?
			-1, // not the reverse index
			true,         // load SA samp? (yes, need forward index's SA samp)
			true,         // load ftab (in forward index)
			true,         // load rstarts (in forward index)
			!noRefNames,  // load names?
			startVerbose);
	}
#if 0
	if(multiseedMms > 0 || do1mmUpFront) {
		// Load the other half of the index into memory
		assert(!ebwtBw.isInMemory());
		Timer _t(cerr, "Time loading mirror index: ", timing);
		ebwtBw.loadIntoMemory(
			0, // colorspace?
			// It's bidirectional search, so we need the reverse to be
			// constructed as the reverse of the concatenated strings.
			1,
			true,        // load SA samp in reverse index
			true,         // yes, need ftab in reverse index
			true,        // load rstarts in reverse index
			!noRefNames,  // load names?
			startVerbose);
	}
#endif
	// Start the metrics thread
	{
		Timer _t(cerr, "Multiseed full-index search: ", timing);
        
        thread_rids.resize(nthreads);
        thread_rids.fill(0);
        thread_rids_mindist = (nthreads == 1 || !useTempSpliceSite ? 0 : 1000 * nthreads);

		for(int i = 0; i < nthreads; i++) {
			// Thread IDs start at 1
			tids[i] = i+1;
            threads[i] = new tthread::thread(multiseedSearchWorker_hisat_bp, (void*)&tids[i]);
		}

        for (int i = 0; i < nthreads; i++)
            threads[i]->join();

	}
	if(!metricsPerRead && (metricsOfb != NULL || metricsStderr)) {
		metrics.reportInterval(metricsOfb, metricsStderr, true, false, NULL);
	}
}

static string argstr;

extern void initializeCntLut();
extern void initializeCntBit();

template<typename TStr>
static void driver(
	const char * type,
	const string& bt2indexBase,
	const string& outfile)
{
	if(gVerbose || startVerbose)  {
		cerr << "Entered driver(): "; logTime(cerr, true);
	}
    
    initializeCntLut();
    initializeCntBit();
    
	// Vector of the reference sequences; used for sanity-checking
	EList<SString<char> > names, os;
	EList<size_t> nameLens, seqLens;
	// Read reference sequences from the command-line or from a FASTA file
	if(!origString.empty()) {
		// Read fasta file(s)
		EList<string> origFiles;
		tokenize(origString, ",", origFiles);
		parseFastas(origFiles, names, nameLens, os, seqLens);
	}
	PatternParams pp(
		format,        // file format
		fileParallel,  // true -> wrap files with separate PairedPatternSources
		seed,          // pseudo-random seed
		useSpinlock,   // use spin locks instead of pthreads
		solexaQuals,   // true -> qualities are on solexa64 scale
		phred64Quals,  // true -> qualities are on phred64 scale
		integerQuals,  // true -> qualities are space-separated numbers
		fuzzy,         // true -> try to parse fuzzy fastq
		fastaContLen,  // length of sampled reads for FastaContinuous...
		fastaContFreq, // frequency of sampled reads for FastaContinuous...
		skipReads      // skip the first 'skip' patterns
	);
	if(gVerbose || startVerbose) {
		cerr << "Creating PatternSource: "; logTime(cerr, true);
	}
	PairedPatternSource *patsrc = PairedPatternSource::setupPatternSources(
		queries,     // singles, from argv
		mates1,      // mate1's, from -1 arg
		mates2,      // mate2's, from -2 arg
		mates12,     // both mates on each line, from --12 arg
		qualities,   // qualities associated with singles
		qualities1,  // qualities associated with m1
		qualities2,  // qualities associated with m2
		pp,          // read read-in parameters
		gVerbose || startVerbose); // be talkative
	// Open hit output file
	if(gVerbose || startVerbose) {
		cerr << "Opening hit output file: "; logTime(cerr, true);
	}
	OutFileBuf *fout;
	if(!outfile.empty()) {
		fout = new OutFileBuf(outfile.c_str(), false);
	} else {
		fout = new OutFileBuf();
	}
	// Initialize Ebwt object and read in header
	if(gVerbose || startVerbose) {
		cerr << "About to initialize fw Ebwt: "; logTime(cerr, true);
	}
	adjIdxBase = adjustEbwtBase(argv0, bt2indexBase, gVerbose);
	HierEbwt<index_t, local_index_t> ebwt(
		adjIdxBase,
	    0,        // index is colorspace
		-1,       // fw index
	    true,     // index is for the forward direction
	    /* overriding: */ offRate,
		0, // amount to add to index offrate or <= 0 to do nothing
	    useMm,    // whether to use memory-mapped files
	    useShmem, // whether to use shared memory
	    mmSweep,  // sweep memory-mapped files
	    !noRefNames, // load names?
		true,        // load SA sample?
		true,        // load ftab?
		true,        // load rstarts?
	    gVerbose, // whether to be talkative
	    startVerbose, // talkative during initialization
	    false /*passMemExc*/,
	    sanityCheck);
	HierEbwt<index_t, local_index_t>* ebwtBw = NULL;
#if 0
	// We need the mirror index if mismatches are allowed
	if(multiseedMms > 0 || do1mmUpFront) {
		if(gVerbose || startVerbose) {
			cerr << "About to initialize rev Ebwt: "; logTime(cerr, true);
		}
		ebwtBw = new HierEbwt<index_t, local_index_t>(
			adjIdxBase + ".rev",
			0,       // index is colorspace
			1,       // TODO: maybe not
		    false, // index is for the reverse direction
		    /* overriding: */ offRate,
			0, // amount to add to index offrate or <= 0 to do nothing
		    useMm,    // whether to use memory-mapped files
		    useShmem, // whether to use shared memory
		    mmSweep,  // sweep memory-mapped files
		    !noRefNames, // load names?
			true,        // load SA sample?
			true,        // load ftab?
			true,        // load rstarts?
		    gVerbose,    // whether to be talkative
		    startVerbose, // talkative during initialization
		    false /*passMemExc*/,
		    sanityCheck);
	}
#endif
	if(sanityCheck && !os.empty()) {
		// Sanity check number of patterns and pattern lengths in Ebwt
		// against original strings
		assert_eq(os.size(), ebwt.nPat());
		for(size_t i = 0; i < os.size(); i++) {
			assert_eq(os[i].length(), ebwt.plen()[i]);
		}
	}
	// Sanity-check the restored version of the Ebwt
	if(sanityCheck && !os.empty()) {
		ebwt.loadIntoMemory(
			0,
			-1, // fw index
			true, // load SA sample
			true, // load ftab
			true, // load rstarts
			!noRefNames,
			startVerbose);
		ebwt.checkOrigs(os, false, false);
		ebwt.evictFromMemory();
	}
	OutputQueue oq(
		*fout,                   // out file buffer
		reorder && nthreads > 1, // whether to reorder when there's >1 thread
		nthreads,                // # threads
		nthreads > 1,            // whether to be thread-safe
		skipReads);              // first read will have this rdid
	{
		Timer _t(cerr, "Time searching: ", timing);
		// Set up penalities
		if(bonusMatch > 0 && !localAlign) {
			cerr << "Warning: Match bonus always = 0 in --end-to-end mode; ignoring user setting" << endl;
			bonusMatch = 0;
		}
		Scoring sc(
			bonusMatch,     // constant reward for match
			penMmcType,     // how to penalize mismatches
			penMmcMax,      // max mm pelanty
			penMmcMin,      // min mm pelanty
			scoreMin,       // min score as function of read len
			nCeil,          // max # Ns as function of read len
			penNType,       // how to penalize Ns in the read
			penN,           // constant if N pelanty is a constant
			penNCatPair,    // whether to concat mates before N filtering
			penRdGapConst,  // constant coeff for read gap cost
			penRfGapConst,  // constant coeff for ref gap cost
			penRdGapLinear, // linear coeff for read gap cost
			penRfGapLinear, // linear coeff for ref gap cost
			gGapBarrier,    // # rows at top/bot only entered diagonally
            penCanSplice,   // canonical splicing penalty
            penNoncanSplice,// non-canonical splicing penalty
            &penIntronLen);  // penalty as to intron length
		EList<size_t> reflens;
		for(size_t i = 0; i < ebwt.nPat(); i++) {
			reflens.push_back(ebwt.plen()[i]);
		}
		EList<string> refnames;
		readEbwtRefnames<index_t>(adjIdxBase, refnames);
		SamConfig samc(
			refnames,               // reference sequence names
			reflens,                // reference sequence lengths
			samTruncQname,          // whether to truncate QNAME to 255 chars
			samOmitSecSeqQual,      // omit SEQ/QUAL for 2ndary alignments?
			samNoUnal,              // omit unaligned-read records?
			string("hisat"),      // program id
			string("hisat"),      // program name
			string(HISAT_VERSION), // program version
			argstr,                 // command-line
			rgs_optflag,            // read-group string
            rna_strandness,
			sam_print_as,
			sam_print_xs,
			sam_print_xss,
			sam_print_yn,
			sam_print_xn,
			sam_print_cs,
			sam_print_cq,
			sam_print_x0,
			sam_print_x1,
			sam_print_xm,
			sam_print_xo,
			sam_print_xg,
			sam_print_nm,
			sam_print_md,
			sam_print_yf,
			sam_print_yi,
			sam_print_ym,
			sam_print_yp,
			sam_print_yt,
			sam_print_ys,
			sam_print_zs,
			sam_print_xr,
			sam_print_xt,
			sam_print_xd,
			sam_print_xu,
			sam_print_yl,
			sam_print_ye,
			sam_print_yu,
			sam_print_xp,
			sam_print_yr,
			sam_print_zb,
			sam_print_zr,
			sam_print_zf,
			sam_print_zm,
			sam_print_zi,
			sam_print_zp,
			sam_print_zu,
            sam_print_xs_a);
		// Set up hit sink; if sanityCheck && !os.empty() is true,
		// then instruct the sink to "retain" hits in a vector in
		// memory so that we can easily sanity check them later on
		AlnSink<index_t> *mssink = NULL;
        Timer *_tRef = new Timer(cerr, "Time loading reference: ", timing);
        auto_ptr<BitPairReference> refs(
                                        new BitPairReference(
                                                             adjIdxBase,
                                                             false,
                                                             sanityCheck,
                                                             NULL,
                                                             NULL,
                                                             false,
                                                             useMm,
                                                             useShmem,
                                                             mmSweep,
                                                             gVerbose,
                                                             startVerbose)
                                        );
        delete _tRef;
        if(!refs->loaded()) throw 1;
        
        init_junction_prob();
        bool write = novelSpliceSiteOutfile != "" || useTempSpliceSite;
        bool read = knownSpliceSiteInfile != "" || novelSpliceSiteInfile != "" || useTempSpliceSite;
        ssdb = new SpliceSiteDB(
                                *(refs.get()),
                                refnames,
                                nthreads > 1, // thread-safe
                                write, // write?
                                read);  // read?
        if(ssdb != NULL) {
            if(knownSpliceSiteInfile != "") {
                ifstream ssdb_file(knownSpliceSiteInfile.c_str(), ios::in);
                if(ssdb_file.is_open()) {
                    ssdb->read(ssdb_file, false); // known splice sites
                    ssdb_file.close();
                }
            }
            if(novelSpliceSiteInfile != "") {
                ifstream ssdb_file(novelSpliceSiteInfile.c_str(), ios::in);
                if(ssdb_file.is_open()) {
                    ssdb->read(ssdb_file, true); // novel splice sites
                    ssdb_file.close();
                }
            }
        }
		switch(outType) {
			case OUTPUT_SAM: {
				mssink = new AlnSinkSam<index_t>(
					oq,           // output queue
					samc,         // settings & routines for SAM output
					refnames,     // reference names
					gQuiet,       // don't print alignment summary at end
                    ssdb);
#if 0
				if(!samNoHead) {
					bool printHd = true, printSq = true;
					BTString buf;
					samc.printHeader(buf, rgid, rgs, printHd, !samNoSQ, printSq);
					fout->writeString(buf);
				}
#endif
				break;
			}
			default:
				cerr << "Invalid output type: " << outType << endl;
				throw 1;
		}
		if(gVerbose || startVerbose) {
			cerr << "Dispatching to search driver: "; logTime(cerr, true);
		}
		// Set up global constraint
		OutFileBuf *metricsOfb = NULL;
		if(!metricsFile.empty() && metricsIval > 0) {
			metricsOfb = new OutFileBuf(metricsFile);
		}
		// Do the search for all input reads
		assert(patsrc != NULL);
		assert(mssink != NULL);
		multiseedSearch(
			sc,      // scoring scheme
			*patsrc, // pattern source
			*mssink, // hit sink
			ebwt,    // BWT
			*ebwtBw, // BWT'
            refs.get(),
                        refnames,
			metricsOfb);
		// Evict any loaded indexes from memory
		if(ebwt.isInMemory()) {
			ebwt.evictFromMemory();
		}
		if(ebwtBw != NULL) {
			delete ebwtBw;
		}
		if(!gQuiet && !seedSumm) {
			size_t repThresh = mhits;
			if(repThresh == 0) {
				repThresh = std::numeric_limits<size_t>::max();
			}
#if 0
			mssink->finish(
				repThresh,
				gReportDiscordant,
				gReportMixed,
				hadoopOut);
#endif
		}
        if(ssdb != NULL) {
            if(novelSpliceSiteOutfile != "") {
                ofstream ssdb_file(novelSpliceSiteOutfile.c_str(), ios::out);
                if(ssdb_file.is_open()) {
                    ssdb->print(ssdb_file);
                    ssdb_file.close();
                }
            }
        }
		oq.flush(true);
		assert_eq(oq.numStarted(), oq.numFinished());
		assert_eq(oq.numStarted(), oq.numFlushed());
		delete patsrc;
		delete mssink;
        delete ssdb;
		delete metricsOfb;
		if(fout != NULL) {
			delete fout;
		}
	}
}

// C++ name mangling is disabled for the bowtie() function to make it
// easier to use Bowtie as a library.
extern "C" {

/**
 * Main bowtie entry function.  Parses argc/argv style command-line
 * options, sets global configuration variables, and calls the driver()
 * function.
 */
int hisat(int argc, const char **argv) {
	try {
		// Reset all global state, including getopt state
		opterr = optind = 1;
		resetOptions();
		for(int i = 0; i < argc; i++) {
			argstr += argv[i];
			if(i < argc-1) argstr += " ";
		}
		if(startVerbose) { cerr << "Entered main(): "; logTime(cerr, true); }
		parseOptions(argc, argv);
		argv0 = argv[0];
		if(showVersion) {
			cout << argv0 << " version " << HISAT_VERSION << endl;
			if(sizeof(void*) == 4) {
				cout << "32-bit" << endl;
			} else if(sizeof(void*) == 8) {
				cout << "64-bit" << endl;
			} else {
				cout << "Neither 32- nor 64-bit: sizeof(void*) = " << sizeof(void*) << endl;
			}
			cout << "Built on " << BUILD_HOST << endl;
			cout << BUILD_TIME << endl;
			cout << "Compiler: " << COMPILER_VERSION << endl;
			cout << "Options: " << COMPILER_OPTIONS << endl;
			cout << "Sizeof {int, long, long long, void*, size_t, off_t}: {"
				 << sizeof(int)
				 << ", " << sizeof(long) << ", " << sizeof(long long)
				 << ", " << sizeof(void *) << ", " << sizeof(size_t)
				 << ", " << sizeof(off_t) << "}" << endl;
			return 0;
		}
		{
			Timer _t(cerr, "Overall time: ", timing);
			if(startVerbose) {
				cerr << "Parsing index and read arguments: "; logTime(cerr, true);
			}

			// Get index basename (but only if it wasn't specified via --index)
			if(bt2index.empty()) {
				if(optind >= argc) {
					cerr << "No index, query, or output file specified!" << endl;
					printUsage(cerr);
					return 1;
				}
				bt2index = argv[optind++];
			}

			// Get query filename
			bool got_reads = !queries.empty() || !mates1.empty() || !mates12.empty();
			if(optind >= argc) {
				if(!got_reads) {
					printUsage(cerr);
					cerr << "***" << endl
					     << "Error: Must specify at least one read input with -U/-1/-2" << endl;
					return 1;
				}
			} else if(!got_reads) {
				// Tokenize the list of query files
				tokenize(argv[optind++], ",", queries);
				if(queries.empty()) {
					cerr << "Tokenized query file list was empty!" << endl;
					printUsage(cerr);
					return 1;
				}
			}

			// Get output filename
			if(optind < argc && outfile.empty()) {
				outfile = argv[optind++];
				cerr << "Warning: Output file '" << outfile.c_str()
				     << "' was specified without -S.  This will not work in "
					 << "future HISAT 2 versions.  Please use -S instead."
					 << endl;
			}

			// Extra parametesr?
			if(optind < argc) {
				cerr << "Extra parameter(s) specified: ";
				for(int i = optind; i < argc; i++) {
					cerr << "\"" << argv[i] << "\"";
					if(i < argc-1) cerr << ", ";
				}
				cerr << endl;
				if(mates1.size() > 0) {
					cerr << "Note that if <mates> files are specified using -1/-2, a <singles> file cannot" << endl
						 << "also be specified.  Please run bowtie separately for mates and singles." << endl;
				}
				throw 1;
			}

			// Optionally summarize
			if(gVerbose) {
				cout << "Input bt2 file: \"" << bt2index.c_str() << "\"" << endl;
				cout << "Query inputs (DNA, " << file_format_names[format].c_str() << "):" << endl;
				for(size_t i = 0; i < queries.size(); i++) {
					cout << "  " << queries[i].c_str() << endl;
				}
				cout << "Quality inputs:" << endl;
				for(size_t i = 0; i < qualities.size(); i++) {
					cout << "  " << qualities[i].c_str() << endl;
				}
				cout << "Output file: \"" << outfile.c_str() << "\"" << endl;
				cout << "Local endianness: " << (currentlyBigEndian()? "big":"little") << endl;
				cout << "Sanity checking: " << (sanityCheck? "enabled":"disabled") << endl;
			#ifdef NDEBUG
				cout << "Assertions: disabled" << endl;
			#else
				cout << "Assertions: enabled" << endl;
			#endif
			}
			if(ipause) {
				cout << "Press key to continue..." << endl;
				getchar();
			}
			driver<SString<char> >("DNA", bt2index, outfile);
		}
		return 0;
	} catch(std::exception& e) {
		cerr << "Error: Encountered exception: '" << e.what() << "'" << endl;
		cerr << "Command: ";
		for(int i = 0; i < argc; i++) cerr << argv[i] << " ";
		cerr << endl;
		return 1;
	} catch(int e) {
		if(e != 0) {
			cerr << "Error: Encountered internal HISAT2 exception (#" << e << ")" << endl;
			cerr << "Command: ";
			for(int i = 0; i < argc; i++) cerr << argv[i] << " ";
			cerr << endl;
		}
		return e;
	}
} // bowtie()
} // extern "C"