File: aln_sink.h

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 (3063 lines) | stat: -rw-r--r-- 101,975 bytes parent folder | download
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
/*
 * Copyright 2011, Ben Langmead <langmea@cs.jhu.edu>
 *
 * This file is part of Bowtie 2.
 *
 * Bowtie 2 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.
 *
 * Bowtie 2 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 Bowtie 2.  If not, see <http://www.gnu.org/licenses/>.
 */

#ifndef ALN_SINK_H_
#define ALN_SINK_H_

#include <limits>
#include "read.h"
#include "unique.h"
#include "sam.h"
#include "ds.h"
#include "simple_func.h"
#include "outq.h"
#include <utility>
#include "alt.h"
#include "splice_site.h"

// Forward decl
template <typename index_t>
class SeedResults;

enum {
	OUTPUT_SAM = 1
};

/**
 * Metrics summarizing the work done by the reporter and summarizing
 * the number of reads that align, that fail to align, and that align
 * non-uniquely.
 */
struct ReportingMetrics {

	ReportingMetrics():mutex_m() {
	    reset();
	}

	void reset() {
		init(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0);
	}

	void init(
		uint64_t nread_,
		uint64_t npaired_,
		uint64_t nunpaired_,
		uint64_t nconcord_uni_,
		uint64_t nconcord_uni1_,
		uint64_t nconcord_uni2_,
		uint64_t nconcord_rep_,
		uint64_t nconcord_0_,
		uint64_t ndiscord_,
		uint64_t nunp_0_uni_,
		uint64_t nunp_0_uni1_,
		uint64_t nunp_0_uni2_,
		uint64_t nunp_0_rep_,
		uint64_t nunp_0_0_,
		uint64_t nunp_rep_uni_,
		uint64_t nunp_rep_uni1_,
		uint64_t nunp_rep_uni2_,
		uint64_t nunp_rep_rep_,
		uint64_t nunp_rep_0_,
		uint64_t nunp_uni_,
		uint64_t nunp_uni1_,
		uint64_t nunp_uni2_,
		uint64_t nunp_rep_,
		uint64_t nunp_0_,
		uint64_t sum_best1_,
		uint64_t sum_best2_,
		uint64_t sum_best_)
	{
		nread         = nread_;
		
		npaired       = npaired_;
		nunpaired     = nunpaired_;
		
		nconcord_uni  = nconcord_uni_;
		nconcord_uni1 = nconcord_uni1_;
		nconcord_uni2 = nconcord_uni2_;
		nconcord_rep  = nconcord_rep_;
		nconcord_0    = nconcord_0_;
		
		ndiscord      = ndiscord_;
		
		nunp_0_uni    = nunp_0_uni_;
		nunp_0_uni1   = nunp_0_uni1_;
		nunp_0_uni2   = nunp_0_uni2_;
		nunp_0_rep    = nunp_0_rep_;
		nunp_0_0      = nunp_0_0_;

		nunp_rep_uni  = nunp_rep_uni_;
		nunp_rep_uni1 = nunp_rep_uni1_;
		nunp_rep_uni2 = nunp_rep_uni2_;
		nunp_rep_rep  = nunp_rep_rep_;
		nunp_rep_0    = nunp_rep_0_;

		nunp_uni      = nunp_uni_;
		nunp_uni1     = nunp_uni1_;
		nunp_uni2     = nunp_uni2_;
		nunp_rep      = nunp_rep_;
		nunp_0        = nunp_0_;

		sum_best1     = sum_best1_;
		sum_best2     = sum_best2_;
		sum_best      = sum_best_;
	}
	
	/**
	 * Merge (add) the counters in the given ReportingMetrics object
	 * into this object.  This is the only safe way to update a
	 * ReportingMetrics shared by multiple threads.
	 */
	void merge(const ReportingMetrics& met, bool getLock = false) {
        ThreadSafe ts(&mutex_m, getLock);
		nread         += met.nread;

		npaired       += met.npaired;
		nunpaired     += met.nunpaired;

		nconcord_uni  += met.nconcord_uni;
		nconcord_uni1 += met.nconcord_uni1;
		nconcord_uni2 += met.nconcord_uni2;
		nconcord_rep  += met.nconcord_rep;
		nconcord_0    += met.nconcord_0;

		ndiscord      += met.ndiscord;

		nunp_0_uni    += met.nunp_0_uni;
		nunp_0_uni1   += met.nunp_0_uni1;
		nunp_0_uni2   += met.nunp_0_uni2;
		nunp_0_rep    += met.nunp_0_rep;
		nunp_0_0      += met.nunp_0_0;

		nunp_rep_uni  += met.nunp_rep_uni;
		nunp_rep_uni1 += met.nunp_rep_uni1;
		nunp_rep_uni2 += met.nunp_rep_uni2;
		nunp_rep_rep  += met.nunp_rep_rep;
		nunp_rep_0    += met.nunp_rep_0;

		nunp_uni      += met.nunp_uni;
		nunp_uni1     += met.nunp_uni1;
		nunp_uni2     += met.nunp_uni2;
		nunp_rep      += met.nunp_rep;
		nunp_0        += met.nunp_0;

		sum_best1     += met.sum_best1;
		sum_best2     += met.sum_best2;
		sum_best      += met.sum_best;
	}

	uint64_t  nread;         // # reads
	uint64_t  npaired;       // # pairs
	uint64_t  nunpaired;     // # unpaired reads
	
	// Paired
	
	//  Concordant
	uint64_t  nconcord_uni;  // # pairs with unique concordant alns
	uint64_t  nconcord_uni1; // # pairs with exactly 1 concordant alns
	uint64_t  nconcord_uni2; // # pairs with >1 concordant aln, still unique
	uint64_t  nconcord_rep;  // # pairs with repetitive concordant alns
	uint64_t  nconcord_0;    // # pairs with 0 concordant alns
	//  Discordant
	uint64_t  ndiscord;      // # pairs with 1 discordant aln
	
	//  Unpaired from failed pairs
	uint64_t  nunp_0_uni;    // # unique from nconcord_0_ - ndiscord_
	uint64_t  nunp_0_uni1;   // # pairs with exactly 1 concordant alns
	uint64_t  nunp_0_uni2;   // # pairs with >1 concordant aln, still unique
	uint64_t  nunp_0_rep;    // # repetitive from 
	uint64_t  nunp_0_0;      // # with 0 alignments

	//  Unpaired from repetitive pairs
	uint64_t  nunp_rep_uni;  // # pairs with unique concordant alns
	uint64_t  nunp_rep_uni1; // # pairs with exactly 1 concordant alns
	uint64_t  nunp_rep_uni2; // # pairs with >1 concordant aln, still unique
	uint64_t  nunp_rep_rep;  // # pairs with repetitive concordant alns
	uint64_t  nunp_rep_0;    // # pairs with 0 concordant alns
	
	// Unpaired
	
	uint64_t  nunp_uni;      // # unique from nconcord_0_ - ndiscord_
	uint64_t  nunp_uni1;     // # pairs with exactly 1 concordant alns
	uint64_t  nunp_uni2;     // # pairs with >1 concordant aln, still unique
	uint64_t  nunp_rep;      // # repetitive from 
	uint64_t  nunp_0;        // # with 0 alignments

	
	uint64_t  sum_best1;     // Sum of all the best alignment scores
	uint64_t  sum_best2;     // Sum of all the second-best alignment scores
	uint64_t  sum_best;      // Sum of all the best and second-best

	MUTEX_T mutex_m;
};

// Type for expression numbers of hits
typedef int64_t THitInt;

/**
 * Parameters affecting reporting of alignments, specifically -k & -a,
 * -m & -M.
 */
struct ReportingParams {

	explicit ReportingParams(
                             THitInt khits_,
                             THitInt kseeds_,
                             THitInt mhits_,
                             THitInt pengap_,
                             bool msample_,
                             bool discord_,
                             bool mixed_)
	{
		init(khits_, kseeds_, mhits_, pengap_, msample_, discord_, mixed_);
	}

	void init(
              THitInt khits_,
              THitInt kseeds_,
              THitInt mhits_,
              THitInt pengap_,
              bool msample_,
              bool discord_,
              bool mixed_)
	{
		khits   = khits_;     // -k (or high if -a)
        kseeds  = kseeds_;
		mhits   = ((mhits_ == 0) ? std::numeric_limits<THitInt>::max() : mhits_);
		pengap  = pengap_;
		msample = msample_;
		discord = discord_;
		mixed   = mixed_;
	}
	
#ifndef NDEBUG
	/**
	 * Check that reporting parameters are internally consistent.
	 */
	bool repOk() const {
		assert_geq(khits, 1);
		assert_geq(mhits, 1);
		return true;
	}
#endif
	
	/**
	 * Return true iff a -m or -M limit was set by the user.
	 */
	inline bool mhitsSet() const {
		return mhits < std::numeric_limits<THitInt>::max();
	}
	
	/**
	 * Return a multiplier that indicates how many alignments we might look for
	 * (max).  We can use this to boost parameters like ROWM and POSF
	 * appropriately.
	 */
	inline THitInt mult() const {
		if(mhitsSet()) {
			return mhits+1;
		}
		return khits;
	}

	/**
	 * Given ROWM, POSF thresholds, boost them according to mult().
	 */
	void boostThreshold(SimpleFunc& func) {
		THitInt mul = mult();
		assert_gt(mul, 0);
		if(mul == std::numeric_limits<THitInt>::max()) {
			func.setMin(std::numeric_limits<double>::max());
		} else if(mul > 1) {
			func.mult(mul);
		}
	}
	
	/**
	 * Return true iff we are reporting all hits.
	 */
	bool allHits() const {
		return khits == std::numeric_limits<THitInt>::max();
	}

	// Number of alignments to report
	THitInt khits;
    
    // Number of seeds allowed to extend
    THitInt kseeds;
	
	// Read is non-unique if mhits-1 next-best alignments are within
	// pengap of the best alignment
	THitInt mhits, pengap;
	
	// true if -M is specified, meaning that if the -M ceiling is
	// exceeded, we should report 'khits' alignments chosen at random
	// from those found
	bool msample;
	
	// true iff we should seek and report discordant paired-end alignments for
	// paired-end reads.
	bool discord;

	// true iff we should seek and report unpaired mate alignments when there
	// are paired-end alignments for a paired-end read, or if the number of
	// paired-end alignments exceeds the -m ceiling.
	bool mixed;
};

/**
 * A state machine keeping track of the number and type of alignments found so
 * far.  Its purpose is to inform the caller as to what stage the alignment is
 * in and what categories of alignment are still of interest.  This information
 * should allow the caller to short-circuit some alignment work.  Another
 * purpose is to tell the AlnSinkWrap how many and what type of alignment to
 * report.
 *
 * TODO: This class does not keep accurate information about what
 * short-circuiting took place.  If a read is identical to a previous read,
 * there should be a way to query this object to determine what work, if any,
 * has to be re-done for the new read.
 */
class ReportingState {

public:

	enum {
		NO_READ = 1,        // haven't got a read yet
		CONCORDANT_PAIRS,   // looking for concordant pairs
		DISCORDANT_PAIRS,   // looking for discordant pairs
		UNPAIRED,           // looking for unpaired
		DONE                // finished looking
	};

	// Flags for different ways we can finish out a category of potential
	// alignments.
	
	enum {
		EXIT_DID_NOT_EXIT = 1,        // haven't finished
		EXIT_DID_NOT_ENTER,           // never tried search	
		EXIT_SHORT_CIRCUIT_k,         // -k exceeded
		EXIT_SHORT_CIRCUIT_M,         // -M exceeded
		EXIT_SHORT_CIRCUIT_TRUMPED,   // made irrelevant
		EXIT_CONVERTED_TO_DISCORDANT, // unpair became discord
		EXIT_NO_ALIGNMENTS,           // none found
		EXIT_WITH_ALIGNMENTS          // some found
	};
	
	ReportingState(const ReportingParams& p) : p_(p) { reset(); }
	
	/**
	 * Set all state to uninitialized defaults.
	 */
	void reset() {
		state_ = ReportingState::NO_READ;
		paired_ = false;
		nconcord_ = 0;
		ndiscord_ = 0;
		nunpair1_ = 0;
		nunpair2_ = 0;
		doneConcord_ = false;
		doneDiscord_ = false;
		doneUnpair_  = false;
		doneUnpair1_ = false;
		doneUnpair2_ = false;
		exitConcord_ = ReportingState::EXIT_DID_NOT_ENTER;
		exitDiscord_ = ReportingState::EXIT_DID_NOT_ENTER;
		exitUnpair1_ = ReportingState::EXIT_DID_NOT_ENTER;
		exitUnpair2_ = ReportingState::EXIT_DID_NOT_ENTER;
		done_ = false;
	}
	
	/**
	 * Return true iff this ReportingState has been initialized with a call to
	 * nextRead() since the last time reset() was called.
	 */
	bool inited() const { return state_ != ReportingState::NO_READ; }

	/**
	 * Initialize state machine with a new read.  The state we start in depends
	 * on whether it's paired-end or unpaired.
	 */
	void nextRead(bool paired);

	/**
	 * Caller uses this member function to indicate that one additional
	 * concordant alignment has been found.
	 */
	bool foundConcordant();

	/**
	 * Caller uses this member function to indicate that one additional
	 * discordant alignment has been found.
	 */
	bool foundUnpaired(bool mate1);
	
	/**
	 * Called to indicate that the aligner has finished searching for
	 * alignments.  This gives us a chance to finalize our state.
	 *
	 * TODO: Keep track of short-circuiting information.
	 */
	void finish();
	
	/**
	 * Populate given counters with the number of various kinds of alignments
	 * to report for this read.  Concordant alignments are preferable to (and
	 * mutually exclusive with) discordant alignments, and paired-end
	 * alignments are preferable to unpaired alignments.
	 *
	 * The caller also needs some additional information for the case where a
	 * pair or unpaired read aligns repetitively.  If the read is paired-end
	 * and the paired-end has repetitive concordant alignments, that should be
	 * reported, and 'pairMax' is set to true to indicate this.  If the read is
	 * paired-end, does not have any conordant alignments, but does have
	 * repetitive alignments for one or both mates, then that should be
	 * reported, and 'unpair1Max' and 'unpair2Max' are set accordingly.
	 *
	 * Note that it's possible in the case of a paired-end read for the read to
	 * have repetitive concordant alignments, but for one mate to have a unique
	 * unpaired alignment.
	 */
	void getReport(
		uint64_t& nconcordAln, // # concordant alignments to report
		uint64_t& ndiscordAln, // # discordant alignments to report
		uint64_t& nunpair1Aln, // # unpaired alignments for mate #1 to report
		uint64_t& nunpair2Aln, // # unpaired alignments for mate #2 to report
		bool& pairMax,         // repetitive concordant alignments
		bool& unpair1Max,      // repetitive alignments for mate #1
		bool& unpair2Max)      // repetitive alignments for mate #2
		const;

	/**
	 * Return an integer representing the alignment state we're in.
	 */
	inline int state() const { return state_; }
	
	/**
	 * If false, there's no need to solve any more dynamic programming problems
	 * for finding opposite mates.
	 */
	inline bool doneConcordant() const { return doneConcord_; }
	
	/**
	 * If false, there's no need to seek any more discordant alignment.
	 */
	inline bool doneDiscordant() const { return doneDiscord_; }
	
	/**
	 * If false, there's no need to seek any more unpaired alignments for the
	 * specified mate.  Note: this doesn't necessarily mean we can stop looking
	 * for alignments for the mate, since this might be necessary for finding
	 * concordant and discordant alignments.
	 */
	inline bool doneUnpaired(bool mate1) const {
		return mate1 ? doneUnpair1_ : doneUnpair2_;
	}
	
	/**
	 * If false, no further consideration of the given mate is necessary.  It's
	 * not needed for *any* class of alignment: concordant, discordant or
	 * unpaired.
	 */
	inline bool doneWithMate(bool mate1) const {
		bool doneUnpair = mate1 ? doneUnpair1_ : doneUnpair2_;
		uint64_t nun = mate1 ? nunpair1_ : nunpair2_;
		if(!doneUnpair || !doneConcord_) {
			return false; // still needed for future concordant/unpaired alns
		}
		if(!doneDiscord_ && nun == 0) {
			return false; // still needed for future discordant alignments
		}
		return true; // done
	}

	/**
	 * Return true iff there's no need to seek any more unpaired alignments.
	 */
	inline bool doneUnpaired() const { return doneUnpair_; }
	
	/**
	 * Return true iff all alignment stages have been exited.
	 */
	inline bool done() const { return done_; }

	inline uint64_t numConcordant() const { return nconcord_; }
	inline uint64_t numDiscordant() const { return ndiscord_; }
	inline uint64_t numUnpaired1()  const { return nunpair1_; }
	inline uint64_t numUnpaired2()  const { return nunpair2_; }

	inline int exitConcordant() const { return exitConcord_; }
	inline int exitDiscordant() const { return exitDiscord_; }
	inline int exitUnpaired1()  const { return exitUnpair1_; }
	inline int exitUnpaired2()  const { return exitUnpair2_; }

#ifndef NDEBUG
	/**
	 * Check that ReportingState is internally consistent.
	 */
	bool repOk() const {
		assert(p_.discord || doneDiscord_);
		assert(p_.mixed   || !paired_ || doneUnpair_);
		assert(doneUnpair_ || !doneUnpair1_ || !doneUnpair2_);
		if(p_.mhitsSet()) {
			assert_leq(numConcordant(), (uint64_t)p_.mhits+1);
			assert_leq(numDiscordant(), (uint64_t)p_.mhits+1);
			assert(paired_ || numUnpaired1() <= (uint64_t)p_.mhits+1);
			assert(paired_ || numUnpaired2() <= (uint64_t)p_.mhits+1);
		}
		assert(done() || !doneWithMate(true) || !doneWithMate(false));
		return true;
	}
#endif

	/**
	 * Return ReportingParams object governing this ReportingState.
	 */
	const ReportingParams& params() const {
		return p_;
	}

protected:

	/**
	 * Update state to reflect situation after converting two unique unpaired
	 * alignments, one for mate 1 and one for mate 2, into a single discordant
	 * alignment.
	 */
	void convertUnpairedToDiscordant() {
		assert_eq(1, numUnpaired1());
		assert_eq(1, numUnpaired2());
		assert_eq(0, numDiscordant());
		exitUnpair1_ = exitUnpair2_ = ReportingState::EXIT_CONVERTED_TO_DISCORDANT;
		nunpair1_ = nunpair2_ = 0;
		ndiscord_ = 1;
		assert_eq(1, numDiscordant());
	}

	/**
	 * Given the number of alignments in a category, check whether we
	 * short-circuited out of the category.  Set the done and exit arguments to
	 * indicate whether and how we short-circuited.
	 */
	inline void areDone(
		uint64_t cnt,     // # alignments in category
		bool& done,       // out: whether we short-circuited out of category
		int& exit) const; // out: if done, how we short-circuited (-k? -m? etc)
	
	/**
	 * Update done_ field to reflect whether we're totally done now.
	 */
	inline void updateDone() {
		doneUnpair_ = doneUnpair1_ && doneUnpair2_;
		done_ = doneUnpair_ && doneDiscord_ && doneConcord_;
	}

	const ReportingParams& p_;  // reporting parameters
	int state_;          // state we're currently in
	bool paired_;        // true iff read we're currently handling is paired
	uint64_t nconcord_;  // # concordants found so far
	uint64_t ndiscord_;  // # discordants found so far
	uint64_t nunpair1_;  // # unpaired alignments found so far for mate 1
	uint64_t nunpair2_;  // # unpaired alignments found so far for mate 2
	bool doneConcord_;   // true iff we're no longner interested in concordants
	bool doneDiscord_;   // true iff we're no longner interested in discordants
	bool doneUnpair_;    // no longner interested in unpaired alns
	bool doneUnpair1_;   // no longner interested in unpaired alns for mate 1
	bool doneUnpair2_;   // no longner interested in unpaired alns for mate 2
	int exitConcord_;    // flag indicating how we exited concordant state
	int exitDiscord_;    // flag indicating how we exited discordant state
	int exitUnpair1_;    // flag indicating how we exited unpaired 1 state
	int exitUnpair2_;    // flag indicating how we exited unpaired 2 state
	bool done_;          // done with all alignments
};

/**
 * Global hit sink for hits from the MultiSeed aligner.  Encapsulates
 * all aspects of the MultiSeed aligner hitsink that are global to all
 * threads.  This includes aspects relating to:
 *
 * (a) synchronized access to the output stream
 * (b) the policy to be enforced by the per-thread wrapper
 *
 * TODO: Implement splitting up of alignments into separate files
 * according to genomic coordinate.
 */
template <typename index_t>
class AlnSink {

	typedef EList<std::string> StrList;

public:

	explicit AlnSink(
                     OutputQueue& oq,
                     const StrList& refnames,
                     bool quiet,
                     ALTDB<index_t>* altdb = NULL,
                     SpliceSiteDB* ssdb = NULL) :
    oq_(oq),
    refnames_(refnames),
    quiet_(quiet),
    altdb_(altdb),
    spliceSiteDB_(ssdb)
	{ }

	/**
	 * Destroy HitSinkobject;
	 */
	virtual ~AlnSink() { }

	/**
	 * Called when the AlnSink is wrapped by a new AlnSinkWrap.  This helps us
	 * keep track of whether the main lock or any of the per-stream locks will
	 * be contended by multiple threads.
	 */
	void addWrapper() { numWrappers_++; }

	/**
	 * Append a single hit to the given output stream.  If
	 * synchronization is required, append() assumes the caller has
	 * already grabbed the appropriate lock.
	 */
	virtual void append(
		BTString&             o,
		StackedAln&           staln,
		size_t                threadId,
		const Read           *rd1,
		const Read           *rd2,
		const TReadId         rdid,
		AlnRes               *rs1,
		AlnRes               *rs2,
		const AlnSetSumm&     summ,
		const SeedAlSumm&     ssm1,
		const SeedAlSumm&     ssm2,
		const AlnFlags*       flags1,
		const AlnFlags*       flags2,
		const PerReadMetrics& prm,
		const Mapq&           mapq,
		const Scoring&        sc,
		bool                  report2) = 0;

	/**
	 * Report a given batch of hits for the given read or read pair.
	 * Should be called just once per read pair.  Assumes all the
	 * alignments are paired, split between rs1 and rs2.
	 *
	 * The caller hasn't decided which alignments get reported as primary
	 * or secondary; that's up to the routine.  Because the caller might
	 * want to know this, we use the pri1 and pri2 out arguments to
	 * convey this.
	 */
	virtual void reportHits(
		BTString&             o,              // write to this buffer
		StackedAln&           staln,       // StackedAln to write stacked alignment
		size_t                threadId,       // which thread am I?
		const Read           *rd1,            // mate #1
		const Read           *rd2,            // mate #2
		const TReadId         rdid,           // read ID
		const EList<size_t>&  select1,        // random subset of rd1s
		const EList<size_t>*  select2,        // random subset of rd2s
		EList<AlnRes>        *rs1,            // alignments for mate #1
		EList<AlnRes>        *rs2,            // alignments for mate #2
		bool                  maxed,          // true iff -m/-M exceeded
		const AlnSetSumm&     summ,           // summary
		const SeedAlSumm&     ssm1,           // seed alignment summ
		const SeedAlSumm&     ssm2,           // seed alignment summ
		const AlnFlags*       flags1,         // flags for mate #1
		const AlnFlags*       flags2,         // flags for mate #2
		const PerReadMetrics& prm,            // per-read metrics
		const Mapq&           mapq,           // MAPQ generator
		const Scoring&        sc,             // scoring scheme
		bool                  getLock = true) // true iff lock held by caller
	{
		// There are a few scenarios:
		// 1. Read is unpaired, in which case rd2 is NULL
		// 2. Read is paired-end and we're reporting concordant alignments
		// 3. Read is paired-end and we're reporting discordant alignments
		// 4. Read is paired-end and we're reporting unpaired alignments for
		//    both mates
		// 5. Read is paired-end and we're reporting an unpaired alignments for
		//    just one mate or the other
		assert(rd1 != NULL || rd2 != NULL);
		assert(rs1 != NULL || rs2 != NULL);
		AlnFlags flagscp1, flagscp2;
		if(flags1 != NULL) {
			flagscp1 = *flags1;
			flags1 = &flagscp1;
			flagscp1.setPrimary(true);
		}
		if(flags2 != NULL) {
			flagscp2 = *flags2;
			flags2 = &flagscp2;
			flagscp2.setPrimary(true);
		}
		if(select2 != NULL) {
			// Handle case 5
			assert(rd1 != NULL); assert(flags1 != NULL);
			assert(rd2 != NULL); assert(flags2 != NULL);
			assert_gt(select1.size(), 0);
			assert_gt(select2->size(), 0);
			AlnRes* r1pri = ((rs1 != NULL) ? &rs1->get(select1[0]) : NULL);
			AlnRes* r2pri = ((rs2 != NULL) ? &rs2->get((*select2)[0]) : NULL);
			append(o, staln, threadId, rd1, rd2, rdid, r1pri, r2pri, summ,
			       ssm1, ssm2, flags1, flags2, prm, mapq, sc, true);
			flagscp1.setPrimary(false);
			flagscp2.setPrimary(false);
			for(size_t i = 1; i < select1.size(); i++) {
				AlnRes* r1 = ((rs1 != NULL) ? &rs1->get(select1[i]) : NULL);
				append(o, staln, threadId, rd1, rd2, rdid, r1, r2pri, summ,
				       ssm1, ssm2, flags1, flags2, prm, mapq, sc, false);
			}
			for(size_t i = 1; i < select2->size(); i++) {
				AlnRes* r2 = ((rs2 != NULL) ? &rs2->get((*select2)[i]) : NULL);
				append(o, staln, threadId, rd2, rd1, rdid, r2, r1pri, summ,
				       ssm2, ssm1, flags2, flags1, prm, mapq, sc, false);
			}
		} else {
			// Handle cases 1-4
			for(size_t i = 0; i < select1.size(); i++) {
				AlnRes* r1 = ((rs1 != NULL) ? &rs1->get(select1[i]) : NULL);
				AlnRes* r2 = ((rs2 != NULL) ? &rs2->get(select1[i]) : NULL);
				append(o, staln, threadId, rd1, rd2, rdid, r1, r2, summ,
				       ssm1, ssm2, flags1, flags2, prm, mapq, sc, true);
				if(flags1 != NULL) {
					flagscp1.setPrimary(false);
				}
				if(flags2 != NULL) {
					flagscp2.setPrimary(false);
				}
			}
		}
	}

	/**
	 * Report an unaligned read.  Typically we do nothing, but we might
	 * want to print a placeholder when output is chained.
	 */
	virtual void reportUnaligned(
		BTString&             o,              // write to this string
		StackedAln&           staln,          // StackedAln to write stacked alignment
		size_t                threadId,       // which thread am I?
		const Read           *rd1,            // mate #1
		const Read           *rd2,            // mate #2
		const TReadId         rdid,           // read ID
		const AlnSetSumm&     summ,           // summary
		const SeedAlSumm&     ssm1,           // seed alignment summary
		const SeedAlSumm&     ssm2,           // seed alignment summary
		const AlnFlags*       flags1,         // flags for mate #1
		const AlnFlags*       flags2,         // flags for mate #2
		const PerReadMetrics& prm,            // per-read metrics
		const Mapq&           mapq,           // MAPQ calculator
		const Scoring&        sc,             // scoring scheme
		bool                  report2,        // report alns for both mates?
		bool                  getLock = true) // true iff lock held by caller
	{
		append(o, staln, threadId, rd1, rd2, rdid, NULL, NULL, summ,
		       ssm1, ssm2, flags1, flags2, prm, mapq, sc, report2);
	}

	/**
	 * Print summary of how many reads aligned, failed to align and aligned
	 * repetitively.  Write it to stderr.  Optionally write Hadoop counter
	 * updates.
	 */
	void printAlSumm(
        ostream& out,
		const ReportingMetrics& met,
		size_t repThresh, // threshold for uniqueness, or max if no thresh
		bool discord,     // looked for discordant alignments
		bool mixed,       // looked for unpaired alignments where paired failed?
        bool newSummary,  // alignment summary in a new style
		bool hadoopOut);  // output Hadoop counters?

	/**
	 * Called when all alignments are complete.  It is assumed that no
	 * synchronization is necessary.
	 */
	void finish(
                ostream& out,
                size_t repThresh,
                bool discord,
                bool mixed,
                bool newSummary,
                bool hadoopOut)
	{
		// Close output streams
		if(!quiet_) {
			printAlSumm(
                        out,
                        met_,
                        repThresh,
                        discord,
                        mixed,
                        newSummary,
                        hadoopOut);
		}
	}

#ifndef NDEBUG
	/**
	 * Check that hit sink is internally consistent.
	 */
	bool repOk() const { return true; }
#endif
	
	//
	// Related to reporting seed hits
	//

	/**
	 * Given a Read and associated, filled-in SeedResults objects,
	 * print a record summarizing the seed hits.
	 */
	void reportSeedSummary(
		BTString&          o,
		const Read&        rd,
		TReadId            rdid,
		size_t             threadId,
		const SeedResults<index_t>& rs,
		bool               getLock = true);

	/**
	 * Given a Read, print an empty record (all 0s).
	 */
	void reportEmptySeedSummary(
		BTString&          o,
		const Read&        rd,
		TReadId            rdid,
		size_t             threadId,
		bool               getLock = true);

	/**
	 * Append a batch of unresolved seed alignment results (i.e. seed
	 * alignments where all we know is the reference sequence aligned
	 * to and its SA range, not where it falls in the reference
	 * sequence) to the given output stream in Bowtie's seed-alignment
	 * verbose-mode format.
	 */
	virtual void appendSeedSummary(
		BTString&     o,
		const Read&   rd,
		const TReadId rdid,
		size_t        seedsTried,
		size_t        nonzero,
		size_t        ranges,
		size_t        elts,
		size_t        seedsTriedFw,
		size_t        nonzeroFw,
		size_t        rangesFw,
		size_t        eltsFw,
		size_t        seedsTriedRc,
		size_t        nonzeroRc,
		size_t        rangesRc,
		size_t        eltsRc);

	/**
	 * Merge given metrics in with ours by summing all individual metrics.
	 */
	void mergeMetrics(const ReportingMetrics& met, bool getLock = true) {
		met_.merge(met, getLock);
	}

	/**
	 * Return mutable reference to the shared OutputQueue.
	 */
	OutputQueue& outq() {
		return oq_;
	}

protected:

	OutputQueue&       oq_;           // output queue
	int                numWrappers_;  // # threads owning a wrapper for this HitSink
	const StrList&     refnames_;     // reference names
	bool               quiet_;        // true -> don't print alignment stats at the end
	ReportingMetrics   met_;          // global repository of reporting metrics
    ALTDB<index_t>*    altdb_;
    SpliceSiteDB*      spliceSiteDB_; //
};

/**
 * Per-thread hit sink "wrapper" for the MultiSeed aligner.  Encapsulates
 * aspects of the MultiSeed aligner hit sink that are per-thread.  This
 * includes aspects relating to:
 *
 * (a) Enforcement of the reporting policy
 * (b) Tallying of results
 * (c) Storing of results for the previous read in case this allows us to
 *     short-circuit some work for the next read (i.e. if it's identical)
 *
 * PHASED ALIGNMENT ASSUMPTION
 *
 * We make some assumptions about how alignment proceeds when we try to
 * short-circuit work for identical reads.  Specifically, we assume that for
 * each read the aligner proceeds in a series of stages (or perhaps just one
 * stage).  In each stage, the aligner either:
 *
 * (a)  Finds no alignments, or
 * (b)  Finds some alignments and short circuits out of the stage with some
 *      random reporting involved (e.g. in -k and/or -M modes), or
 * (c)  Finds all of the alignments in the stage
 *
 * In the event of (a), the aligner proceeds to the next stage and keeps
 * trying; we can skip the stage entirely for the next read if it's identical.
 * In the event of (b), or (c), the aligner stops and does not proceed to
 * further stages.  In the event of (b1), if the next read is identical we
 * would like to tell the aligner to start again at the beginning of the stage
 * that was short-circuited.
 *
 * In any event, the rs1_/rs2_/rs1u_/rs2u_ fields contain the alignments found
 * in the last alignment stage attempted.
 *
 * HANDLING REPORTING LIMITS
 *
 * The user can specify reporting limits, like -k (specifies number of
 * alignments to report out of those found) and -M (specifies a ceiling s.t. if
 * there are more alignments than the ceiling, read is called repetitive and
 * best found is reported).  Enforcing these limits is straightforward for
 * unpaired alignments: if a new alignment causes us to exceed the -M ceiling,
 * we can stop looking.
 *
 * The case where both paired-end and unpaired alignments are possible is
 * trickier.  Once we have a number of unpaired alignments that exceeds the
 * ceiling, we can stop looking *for unpaired alignments* - but we can't
 * necessarily stop looking for paired-end alignments, since there may yet be
 * more to find.  However, if the input read is not a pair, then we can stop at
 * this point.  If the input read is a pair and we have a number of paired
 * aligments that exceeds the -M ceiling, we can stop looking.
 *
 * CONCORDANT & DISCORDANT, PAIRED & UNPAIRED
 *
 * A note on paired-end alignment: Clearly, if an input read is
 * paired-end and we find either concordant or discordant paired-end
 * alignments for the read, then we would like to tally and report
 * those alignments as such (and not as groups of 2 unpaired
 * alignments).  And if we fail to find any paired-end alignments, but
 * we do find some unpaired alignments for one mate or the other, then
 * we should clearly tally and report those alignments as unpaired
 * alignments (if the user so desires).
 *
 * The situation is murkier when there are no paired-end alignments,
 * but there are unpaired alignments for *both* mates.  In this case,
 * we might want to pick out zero or more pairs of mates and classify
 * those pairs as discordant paired-end alignments.  And we might want
 * to classify the remaining alignments as unpaired.  But how do we
 * pick which pairs if any to call discordant?
 *
 * Because the most obvious use for discordant pairs is for identifying
 * large-scale variation, like rearrangements or large indels, we would
 * usually like to be conservative about what we call a discordant
 * alignment.  If there's a good chance that one or the other of the
 * two mates has a good alignment to another place on the genome, this
 * compromises the evidence for the large-scale variant.  For this
 * reason, Bowtie 2's policy is: if there are no paired-end alignments
 * and there is *exactly one alignment each* for both mates, then the
 * two alignments are paired and treated as a discordant paired-end
 * alignment.  Otherwise, all alignments are treated as unpaired
 * alignments.
 *
 * When both paired and unpaired alignments are discovered by the
 * aligner, only the paired alignments are reported by default.  This
 * is sensible considering relative likelihoods: if a good paired-end
 * alignment is found, it is much more likely that the placement of
 * the two mates implied by that paired alignment is correct than any
 * placement implied by an unpaired alignment.
 *
 * 
 */
template <typename index_t>
class AlnSinkWrap {
public:

	AlnSinkWrap(
                AlnSink<index_t>& g,       // AlnSink being wrapped
                const ReportingParams& rp, // Parameters governing reporting
                Mapq& mapq,                // Mapq calculator
                size_t threadId,           // Thread ID
                bool secondary = false,    // Secondary alignments
                const SpliceSiteDB* ssdb = NULL, // splice sites
                uint64_t threads_rids_mindist = 0) : // synchronization
		g_(g),
		rp_(rp),
        threadid_(threadId),
        mapq_(mapq),
    	secondary_(secondary),
        ssdb_(ssdb),
        threads_rids_mindist_(threads_rids_mindist),
		init_(false),   
		maxed1_(false),       // read is pair and we maxed out mate 1 unp alns
		maxed2_(false),       // read is pair and we maxed out mate 2 unp alns
		maxedOverall_(false), // alignments found so far exceed -m/-M ceiling
		bestPair_(std::numeric_limits<TAlScore>::min()),
		best2Pair_(std::numeric_limits<TAlScore>::min()),
		bestUnp1_(std::numeric_limits<TAlScore>::min()),
		best2Unp1_(std::numeric_limits<TAlScore>::min()),
		bestUnp2_(std::numeric_limits<TAlScore>::min()),
		best2Unp2_(std::numeric_limits<TAlScore>::min()),
        bestSplicedPair_(0),
        best2SplicedPair_(0),
        bestSplicedUnp1_(0),
        best2SplicedUnp1_(0),
        bestSplicedUnp2_(0),
        best2SplicedUnp2_(0),
		rd1_(NULL),    // mate 1
		rd2_(NULL),    // mate 2
		rdid_(std::numeric_limits<TReadId>::max()), // read id
		rs1_(),        // mate 1 alignments for paired-end alignments
		rs2_(),        // mate 2 alignments for paired-end alignments
		rs1u_(),       // mate 1 unpaired alignments
		rs2u_(),       // mate 2 unpaired alignments
		select1_(),    // for selecting random subsets for mate 1
		select2_(),    // for selecting random subsets for mate 2
		st_(rp)        // reporting state - what's left to do?
	{
		assert(rp_.repOk());
	}

	/**
	 * Initialize the wrapper with a new read pair and return an
	 * integer >= -1 indicating which stage the aligner should start
	 * at.  If -1 is returned, the aligner can skip the read entirely.
	 * at.  If .  Checks if the new read pair is identical to the
	 * previous pair.  If it is, then we return the id of the first
	 * stage to run.
	 */
	int nextRead(
		// One of the other of rd1, rd2 will = NULL if read is unpaired
		const Read* rd1,      // new mate #1
		const Read* rd2,      // new mate #2
		TReadId rdid,         // read ID for new pair
		bool qualitiesMatter);// aln policy distinguishes b/t quals?

	/**
	 * Inform global, shared AlnSink object that we're finished with
	 * this read.  The global AlnSink is responsible for updating
	 * counters, creating the output record, and delivering the record
	 * to the appropriate output stream.
	 */
	void finishRead(
		const SeedResults<index_t> *sr1, // seed alignment results for mate 1
		const SeedResults<index_t> *sr2, // seed alignment results for mate 2
		bool               exhaust1,     // mate 1 exhausted?
		bool               exhaust2,     // mate 2 exhausted?
		bool               nfilt1,       // mate 1 N-filtered?
		bool               nfilt2,       // mate 2 N-filtered?
		bool               scfilt1,      // mate 1 score-filtered?
		bool               scfilt2,      // mate 2 score-filtered?
		bool               lenfilt1,     // mate 1 length-filtered?
		bool               lenfilt2,     // mate 2 length-filtered?
		bool               qcfilt1,      // mate 1 qc-filtered?
		bool               qcfilt2,      // mate 2 qc-filtered?
		bool               sortByScore,  // prioritize alignments by score
		RandomSource&      rnd,          // pseudo-random generator
		ReportingMetrics&  met,          // reporting metrics
		const PerReadMetrics& prm,       // per-read metrics
		const Scoring& sc,               // scoring scheme
		bool suppressSeedSummary = true,
		bool suppressAlignments = false,
        bool templateLenAdjustment = true);
	
	/**
	 * Called by the aligner when a new unpaired or paired alignment is
	 * discovered in the given stage.  This function checks whether the
	 * addition of this alignment causes the reporting policy to be
	 * violated (by meeting or exceeding the limits set by -k, -m, -M),
	 * in which case true is returned immediately and the aligner is
	 * short circuited.  Otherwise, the alignment is tallied and false
	 * is returned.
	 */
	bool report(
		int stage,
		const AlnRes* rs1,
		const AlnRes* rs2);

#ifndef NDEBUG
	/**
	 * Check that hit sink wrapper is internally consistent.
	 */
	bool repOk() const {
		assert_eq(rs2_.size(), rs1_.size());
		if(rp_.mhitsSet()) {
			assert_gt(rp_.mhits, 0);
			assert_leq((int)rs1_.size(), rp_.mhits+1);
			assert_leq((int)rs2_.size(), rp_.mhits+1);
			assert(readIsPair() || (int)rs1u_.size() <= rp_.mhits+1);
			assert(readIsPair() || (int)rs2u_.size() <= rp_.mhits+1);
		}
		if(init_) {
			assert(rd1_ != NULL);
			assert_neq(std::numeric_limits<TReadId>::max(), rdid_);
		}
		assert_eq(st_.numConcordant() + st_.numDiscordant(), rs1_.size());
		//assert_eq(st_.numUnpaired1(), rs1u_.size());
		//assert_eq(st_.numUnpaired2(), rs2u_.size());
		assert(st_.repOk());
		return true;
	}
#endif
	
	/**
	 * Return true iff no alignments have been reported to this wrapper
	 * since the last call to nextRead().
	 */
	bool empty() const {
		return rs1_.empty() && rs1u_.empty() && rs2u_.empty();
	}
	
	/**
	 * Return true iff we have already encountered a number of alignments that
	 * exceeds the -m/-M ceiling.  TODO: how does this distinguish between
	 * pairs and mates?
	 */
	bool maxed() const {
		return maxedOverall_;
	}
	
	/**
	 * Return true if the current read is paired.
	 */
	bool readIsPair() const {
		return rd1_ != NULL && rd2_ != NULL;
	}
	
	/**
	 * Return true iff nextRead() has been called since the last time
	 * finishRead() was called.
	 */
	bool inited() const { return init_; }

	/**
	 * Return a const ref to the ReportingState object associated with the
	 * AlnSinkWrap.
	 */
	const ReportingState& state() const { return st_; }
    
    const ReportingParams& reportingParams() { return rp_;}
	
	/**
	 * Return true iff we're in -M mode.
	 */
	bool Mmode() const {
		return rp_.mhitsSet();
	}
	
	/**
	 * Return true iff the policy is to report all hits.
	 */
	bool allHits() const {
		return rp_.allHits();
	}
	
	/**
	 * Return true iff at least two alignments have been reported so far for an
	 * unpaired read or mate 1.
	 */
	bool hasSecondBestUnp1() const {
		return best2Unp1_ != std::numeric_limits<TAlScore>::min();
	}

	/**
	 * Return true iff at least two alignments have been reported so far for
	 * mate 2.
	 */
	bool hasSecondBestUnp2() const {
		return best2Unp2_ != std::numeric_limits<TAlScore>::min();
	}

	/**
	 * Return true iff at least two paired-end alignments have been reported so
	 * far.
	 */
	bool hasSecondBestPair() const {
		return best2Pair_ != std::numeric_limits<TAlScore>::min();
	}
	
	/**
	 * Get best score observed so far for an unpaired read or mate 1.
	 */
	TAlScore bestUnp1() const {
		return bestUnp1_;
	}

	/**
	 * Get second-best score observed so far for an unpaired read or mate 1.
	 */
	TAlScore secondBestUnp1() const {
		return best2Unp1_;
	}

	/**
	 * Get best score observed so far for mate 2.
	 */
	TAlScore bestUnp2() const {
		return bestUnp2_;
	}

	/**
	 * Get second-best score observed so far for mate 2.
	 */
	TAlScore secondBestUnp2() const {
		return best2Unp2_;
	}

	/**
	 * Get best score observed so far for paired-end read.
	 */
	TAlScore bestPair() const {
		return bestPair_;
	}

	/**
	 * Get second-best score observed so far for paired-end read.
	 */
	TAlScore secondBestPair() const {
		return best2Pair_;
	}
    
    index_t bestSplicedPair() const {
        return bestSplicedPair_;
    }
    
    index_t best2SplicedPair() const {
        return best2SplicedPair_;
    }
    
    index_t bestSplicedUnp1() const {
        return bestSplicedUnp1_;
    }
    
    index_t best2SplicedUnp1() const {
        return best2SplicedUnp1_;
    }
    
    index_t bestSplicedUnp2() const {
        return bestSplicedUnp2_;
    }
    
    index_t best2SplicedUnp2() const {
        return best2SplicedUnp2_;
    }
    
    bool secondary() const {
        return secondary_;
    }
    
    /**
     *
     */
    void getUnp1(const EList<AlnRes>*& rs) const { rs = &rs1u_; }
    void getUnp2(const EList<AlnRes>*& rs) const { rs = &rs2u_; }
    void getPair(const EList<AlnRes>*& rs1, const EList<AlnRes>*& rs2) const { rs1 = &rs1_; rs2 = &rs2_; }

protected:

	/**
	 * Return true iff the read in rd1/rd2 matches the last read handled, which
	 * should still be in rd1_/rd2_.
	 */
	bool sameRead(
		const Read* rd1,
		const Read* rd2,
		bool qualitiesMatter);

	/**
	 * If there is a configuration of unpaired alignments that fits our
	 * criteria for there being one or more discordant alignments, then
	 * shift the discordant alignments over to the rs1_/rs2_ lists, clear the
	 * rs1u_/rs2u_ lists and return true.  Otherwise, return false.
	 */
	bool prepareDiscordants();

	/**
	 * Given that rs is already populated with alignments, consider the
	 * alignment policy and make random selections where necessary.  E.g. if we
	 * found 10 alignments and the policy is -k 2 -m 20, select 2 alignments at
	 * random.  We "select" an alignment by setting the parallel entry in the
	 * 'select' list to true.
	 */
	size_t selectAlnsToReport(
		const EList<AlnRes>& rs,     // alignments to select from
		uint64_t             num,    // number of alignments to select
		EList<size_t>&       select, // list to put results in
		RandomSource&        rnd)
		const;

	/**
	 * rs1 (possibly together with rs2 if reads are paired) are populated with
	 * alignments.  Here we prioritize them according to alignment score, and
	 * some randomness to break ties.  Priorities are returned in the 'select'
	 * list.
	 */
	size_t selectByScore(
		const EList<AlnRes>* rs1,    // alignments to select from (mate 1)
		const EList<AlnRes>* rs2,    // alignments to select from (mate 2, or NULL)
		uint64_t             num,    // number of alignments to select
		EList<size_t>&       select, // prioritized list to put results in
		RandomSource&        rnd)
		const;

	AlnSink<index_t>& g_;     // global alignment sink
	ReportingParams   rp_;    // reporting parameters: khits, mhits etc
	size_t            threadid_; // thread ID
	Mapq&             mapq_;  // mapq calculator
    bool              secondary_; // allow for secondary alignments
    const SpliceSiteDB* ssdb_; // splice sites
    uint64_t threads_rids_mindist_; // synchronization
	bool              init_;  // whether we're initialized w/ read pair
	bool              maxed1_; // true iff # unpaired mate-1 alns reported so far exceeded -m/-M
	bool              maxed2_; // true iff # unpaired mate-2 alns reported so far exceeded -m/-M
	bool              maxedOverall_; // true iff # paired-end alns reported so far exceeded -m/-M
	TAlScore          bestPair_;     // greatest score so far for paired-end
	TAlScore          best2Pair_;    // second-greatest score so far for paired-end
	TAlScore          bestUnp1_;     // greatest score so far for unpaired/mate1
	TAlScore          best2Unp1_;    // second-greatest score so far for unpaired/mate1
	TAlScore          bestUnp2_;     // greatest score so far for mate 2
	TAlScore          best2Unp2_;    // second-greatest score so far for mate 2
    index_t           bestSplicedPair_;
    index_t           best2SplicedPair_;
    index_t           bestSplicedUnp1_;
    index_t           best2SplicedUnp1_;
    index_t           bestSplicedUnp2_;
    index_t           best2SplicedUnp2_;
	const Read*       rd1_;   // mate #1
	const Read*       rd2_;   // mate #2
	TReadId           rdid_;  // read ID (potentially used for ordering)
	EList<AlnRes>     rs1_;   // paired alignments for mate #1
	EList<AlnRes>     rs2_;   // paired alignments for mate #2
	EList<AlnRes>     rs1u_;  // unpaired alignments for mate #1
	EList<AlnRes>     rs2u_;  // unpaired alignments for mate #2
	EList<size_t>     select1_; // parallel to rs1_/rs2_ - which to report
	EList<size_t>     select2_; // parallel to rs1_/rs2_ - which to report
	ReportingState    st_;      // reporting state - what's left to do?
	
	EList<std::pair<TAlScore, size_t> > selectBuf_;
	BTString obuf_;
	StackedAln staln_;
    
    EList<SpliceSite> spliceSites_;
};

/**
 * An AlnSink concrete subclass for printing SAM alignments.  The user might
 * want to customize SAM output in various ways.  We encapsulate all these
 * customizations, and some of the key printing routines, in the SamConfig
 * class in sam.h/sam.cpp.
 */
template <typename index_t>
class AlnSinkSam : public AlnSink<index_t> {

	typedef EList<std::string> StrList;

public:

	AlnSinkSam(
               OutputQueue&     oq,            // output queue
               const SamConfig<index_t>& samc, // settings & routines for SAM output
               const StrList&   refnames,      // reference names
               bool             quiet,         // don't print alignment summary at end
               ALTDB<index_t>*  altdb = NULL,
               SpliceSiteDB*    ssdb  = NULL) :
		AlnSink<index_t>(
                         oq,
                         refnames,
                         quiet,
                         altdb,
                         ssdb),
    samc_(samc)
	{ }
	
	virtual ~AlnSinkSam() { }

	/**
	 * Append a single alignment result, which might be paired or
	 * unpaired, to the given output stream in Bowtie's verbose-mode
	 * format.  If the alignment is paired-end, print mate1's alignment
	 * then mate2's alignment.
	 */
	virtual void append(
		BTString&     o,           // write output to this string
		StackedAln&   staln,       // StackedAln to write stacked alignment
		size_t        threadId,    // which thread am I?
		const Read*   rd1,         // mate #1
		const Read*   rd2,         // mate #2
		const TReadId rdid,        // read ID
		AlnRes* rs1,               // alignments for mate #1
		AlnRes* rs2,               // alignments for mate #2
		const AlnSetSumm& summ,    // summary
		const SeedAlSumm& ssm1,    // seed alignment summary
		const SeedAlSumm& ssm2,    // seed alignment summary
		const AlnFlags* flags1,    // flags for mate #1
		const AlnFlags* flags2,    // flags for mate #2
		const PerReadMetrics& prm, // per-read metrics
		const Mapq& mapq,          // MAPQ calculator
		const Scoring& sc,         // scoring scheme
		bool report2)              // report alns for both mates
	{
		assert(rd1 != NULL || rd2 != NULL);
		if(rd1 != NULL) {
			assert(flags1 != NULL);
			appendMate(o, staln, *rd1, rd2, rdid, rs1, rs2, summ, ssm1, ssm2,
			           *flags1, prm, mapq, sc);
            if(rs1 != NULL && rs1->spliced() && this->spliceSiteDB_ != NULL) {
                this->spliceSiteDB_->addSpliceSite(*rd1, *rs1);
            }
		}
		if(rd2 != NULL && report2) {
			assert(flags2 != NULL);
			appendMate(o, staln, *rd2, rd1, rdid, rs2, rs1, summ, ssm2, ssm1,
			           *flags2, prm, mapq, sc);
            if(rs2 != NULL && rs2->spliced() && this->spliceSiteDB_ != NULL) {
                this->spliceSiteDB_->addSpliceSite(*rd2, *rs2);
            }
		}
	}

protected:

	/**
	 * Append a single per-mate alignment result to the given output
	 * stream.  If the alignment is part of a pair, information about
	 * the opposite mate and its alignment are given in rdo/rso.
	 */
	void appendMate(
		BTString&     o,
		StackedAln&   staln,
		const Read&   rd,
		const Read*   rdo,
		const TReadId rdid,
		AlnRes* rs,
		AlnRes* rso,
		const AlnSetSumm& summ,
		const SeedAlSumm& ssm,
		const SeedAlSumm& ssmo,
		const AlnFlags& flags,
		const PerReadMetrics& prm, // per-read metrics
		const Mapq& mapq,          // MAPQ calculator
		const Scoring& sc);        // scoring scheme

	const SamConfig<index_t>& samc_;    // settings & routines for SAM output
	BTDnaString               dseq_;    // buffer for decoded read sequence
	BTString                  dqual_;   // buffer for decoded quality sequence
};

static inline std::ostream& printPct(
							  std::ostream& os,
							  uint64_t num,
							  uint64_t denom)
{
	double pct = 0.0f;
	if(denom != 0) { pct = 100.0 * (double)num / (double)denom; }
	os << fixed << setprecision(2) << pct << '%';
	return os;
}

/**
 * Print a friendly summary of:
 *
 *  1. How many reads were aligned and had one or more alignments
 *     reported
 *  2. How many reads exceeded the -m or -M ceiling and therefore had
 *     their alignments suppressed or sampled
 *  3. How many reads failed to align entirely
 *
 * Optionally print a series of Hadoop streaming-style counter updates
 * with similar information.
 */
template <typename index_t>
void AlnSink<index_t>::printAlSumm(
                                   ostream& out,
								   const ReportingMetrics& met,
								   size_t repThresh,   // threshold for uniqueness, or max if no thresh
								   bool discord,       // looked for discordant alignments
								   bool mixed,         // looked for unpaired alignments where paired failed?
                                   bool newSummary,    // alignment summary in a new style
								   bool hadoopOut)     // output Hadoop counters?
{
	// NOTE: there's a filtering step at the very beginning, so everything
	// being reported here is post filtering
	
	bool canRep = repThresh != MAX_SIZE_T;
    if(hadoopOut) {
        out << "reporter:counter:HISAT2,Reads processed," << met.nread << endl;
    }
    uint64_t totread = met.nread;
    uint64_t totpair = met.npaired;
    uint64_t totunpair = met.nunpaired;
    uint64_t tot_al_cand = totunpair + totpair*2;
    uint64_t tot_al = (met.nconcord_uni + met.nconcord_rep) * 2 + (met.ndiscord) * 2 + met.nunp_0_uni + met.nunp_0_rep + met.nunp_uni + met.nunp_rep;
    assert_leq(tot_al, tot_al_cand);
    if(newSummary) {
        out << "HISAT2 summary stats:" << endl;
        if(totpair > 0) {
            uint64_t ncondiscord_0 = met.nconcord_0 - met.ndiscord;
            out << "\tTotal pairs: " << totpair << endl;
            out << "\t\tAligned concordantly or discordantly 0 time: " << ncondiscord_0 << " ("; printPct(out, ncondiscord_0, met.npaired); out << ")" << endl;
            out << "\t\tAligned concordantly 1 time: " << met.nconcord_uni1 << " ("; printPct(out, met.nconcord_uni1, met.npaired); out << ")" << endl;
            out << "\t\tAligned concordantly >1 times: " << met.nconcord_uni2 << " ("; printPct(out, met.nconcord_uni2, met.npaired); out << ")" << endl;
            out << "\t\tAligned discordantly 1 time: " << met.ndiscord << " ("; printPct(out, met.ndiscord, met.npaired); out << ")" << endl;
            
            out << "\tTotal unpaired reads: " << ncondiscord_0 * 2 << endl;
            out << "\t\tAligned 0 time: " << met.nunp_0_0 << " ("; printPct(out, met.nunp_0_0, ncondiscord_0 * 2); out << ")" << endl;
            out << "\t\tAligned 1 time: " << met.nunp_0_uni1 << " ("; printPct(out, met.nunp_0_uni1, ncondiscord_0 * 2); out << ")" << endl;
            out << "\t\tAligned >1 times: " << met.nunp_0_uni2 << " ("; printPct(out, met.nunp_0_uni2, ncondiscord_0 * 2); out << ")" << endl;
        } else {
            out << "\tTotal reads: " << totread << endl;
            out << "\t\tAligned 0 time: " << met.nunp_0 << " ("; printPct(out, met.nunp_0, met.nunpaired); out << ")" << endl;
            out << "\t\tAligned 1 time: " << met.nunp_uni1 << " ("; printPct(out, met.nunp_uni1, met.nunpaired); out << ")" << endl;
            out << "\t\tAligned >1 times: " << met.nunp_uni2 << " ("; printPct(out, met.nunp_uni2, met.nunpaired); out << ")" << endl;
        }
        out << "\tOverall alignment rate: "; printPct(out, tot_al, tot_al_cand); out << endl;
        
    } else {
        if(totread > 0) {
            out << "" << totread << " reads; of these:" << endl;
        } else {
            assert_eq(0, met.npaired);
            assert_eq(0, met.nunpaired);
            out << "" << totread << " reads" << endl;
        }
        if(totpair > 0) {
            // Paired output
            out << "  " << totpair << " (";
            printPct(out, totpair, totread);
            out << ") were paired; of these:" << endl;
            
            // Concordants
            out << "    " << met.nconcord_0 << " (";
            printPct(out, met.nconcord_0, met.npaired);
            out << ") aligned concordantly 0 times" << endl;
            if(canRep) {
                // Print the number that aligned concordantly exactly once
                assert_eq(met.nconcord_uni, met.nconcord_uni1+met.nconcord_uni2);
                out << "    " << met.nconcord_uni1 << " (";
                printPct(out, met.nconcord_uni1, met.npaired);
                out << ") aligned concordantly exactly 1 time" << endl;
                
                // Print the number that aligned concordantly more than once but
                // fewer times than the limit
                
                out << "    " << met.nconcord_uni2+met.nconcord_rep << " (";
                printPct(out, met.nconcord_uni2+met.nconcord_rep, met.npaired);
                out << ") aligned concordantly >1 times" << endl;
            } else {
                // Print the number that aligned concordantly exactly once
                assert_eq(met.nconcord_uni, met.nconcord_uni1+met.nconcord_uni2);
                out << "    " << met.nconcord_uni1 << " (";
                printPct(out, met.nconcord_uni1, met.npaired);
                out << ") aligned concordantly exactly 1 time" << endl;
                
                // Print the number that aligned concordantly more than once
                out << "    " << met.nconcord_uni2 << " (";
                printPct(out, met.nconcord_uni2, met.npaired);
                out << ") aligned concordantly >1 times" << endl;
            }
            if(discord) {
                // TODO: what about discoardant and on separate chromosomes?
                
                // Bring out the unaligned pair total so we can subtract discordants
                out << "    ----" << endl;
                out << "    " << met.nconcord_0
                << " pairs aligned concordantly 0 times; of these:" << endl;
                // Discordants
                out << "      " << met.ndiscord << " (";
                printPct(out, met.ndiscord, met.nconcord_0);
                out << ") aligned discordantly 1 time" << endl;
            }
            uint64_t ncondiscord_0 = met.nconcord_0 - met.ndiscord;
            if(mixed) {
                // Bring out the unaligned pair total so we can subtract discordants
                out << "    ----" << endl;
                out << "    " << ncondiscord_0
                    << " pairs aligned 0 times concordantly or discordantly; of these:" << endl;
                out << "      " << (ncondiscord_0 * 2) << " mates make up the pairs; of these:" << endl;
                out << "        " << met.nunp_0_0 << " " << "(";
                printPct(out, met.nunp_0_0, ncondiscord_0 * 2);
                out << ") aligned 0 times" << endl;
                if(canRep) {
                    // Print the number that aligned exactly once
                    assert_eq(met.nunp_0_uni, met.nunp_0_uni1+met.nunp_0_uni2);
                    out << "        " << met.nunp_0_uni1 << " (";
                    printPct(out, met.nunp_0_uni1, ncondiscord_0 * 2);
                    out << ") aligned exactly 1 time" << endl;
                    
                    // Print the number that aligned more than once but fewer times
                    // than the limit
                    out << "        " << met.nunp_0_uni2+met.nunp_0_rep << " (";
                    printPct(out, met.nunp_0_uni2+met.nunp_0_rep, ncondiscord_0 * 2);
                    out << ") aligned >1 times" << endl;
                } else {
                    // Print the number that aligned exactly once
                    assert_eq(met.nunp_0_uni, met.nunp_0_uni1+met.nunp_0_uni2);
                    out << "        " << met.nunp_0_uni1 << " (";
                    printPct(out, met.nunp_0_uni1, ncondiscord_0 * 2);
                    out << ") aligned exactly 1 time" << endl;
                    
                    // Print the number that aligned more than once but fewer times
                    // than the limit
                    out << "        " << met.nunp_0_uni2 << " (";
                    printPct(out, met.nunp_0_uni2, ncondiscord_0 * 2);
                    out << ") aligned >1 times" << endl;
                }
            }
        }
        if(totunpair > 0) {
            // Unpaired output
            out << "  " << totunpair << " (";
            printPct(out, totunpair, totread);
            out << ") were unpaired; of these:" << endl;
            
            out << "    " << met.nunp_0 << " (";
            printPct(out, met.nunp_0, met.nunpaired);
            out << ") aligned 0 times" << endl;
            if(hadoopOut) {
                out << "reporter:counter:HISAT 2,Unpaired reads with 0 alignments,"
                << met.nunpaired << endl;
            }
            
            if(canRep) {
                // Print the number that aligned exactly once
                assert_eq(met.nunp_uni, met.nunp_uni1+met.nunp_uni2);
                out << "    " << met.nunp_uni1 << " (";
                printPct(out, met.nunp_uni1, met.nunpaired);
                out << ") aligned exactly 1 time" << endl;
                
                // Print the number that aligned more than once but fewer times
                // than the limit
                out << "    " << met.nunp_uni2+met.nunp_rep << " (";
                printPct(out, met.nunp_uni2+met.nunp_rep, met.nunpaired);
                out << ") aligned >1 times" << endl;
            } else {
                // Print the number that aligned exactly once
                assert_eq(met.nunp_uni, met.nunp_uni1+met.nunp_uni2);
                out << "    " << met.nunp_uni1 << " (";
                printPct(out, met.nunp_uni1, met.nunpaired);
                out << ") aligned exactly 1 time" << endl;
                
                // Print the number that aligned more than once
                out << "    " << met.nunp_uni2 << " (";
                printPct(out, met.nunp_uni2, met.nunpaired);
                out << ") aligned >1 times" << endl;
            }
        }
        
        printPct(out, tot_al, tot_al_cand);
        out << " overall alignment rate" << endl;
    }
}

/**
 * Return true iff the read in rd1/rd2 matches the last read handled, which
 * should still be in rd1_/rd2_.
 */
template <typename index_t>
bool AlnSinkWrap<index_t>::sameRead(
									// One of the other of rd1, rd2 will = NULL if read is unpaired
									const Read* rd1,      // new mate #1
									const Read* rd2,      // new mate #2
									bool qualitiesMatter) // aln policy distinguishes b/t quals?
{
	bool same = false;
	if(rd1_ != NULL || rd2_ != NULL) {
		// This is not the first time the sink was initialized with
		// a read.  Check if new read/pair is identical to previous
		// read/pair
		if((rd1_ == NULL) == (rd1 == NULL) &&
		   (rd2_ == NULL) == (rd2 == NULL))
		{
			bool m1same = (rd1 == NULL && rd1_ == NULL);
			if(!m1same) {
				assert(rd1 != NULL);
				assert(rd1_ != NULL);
				m1same = Read::same(
									rd1->patFw,  // new seq
									rd1->qual,   // new quals
									rd1_->patFw, // old seq
									rd1_->qual,  // old quals
									qualitiesMatter);
			}
			if(m1same) {
				bool m2same = (rd2 == NULL && rd2_ == NULL);
				if(!m2same) {
					m2same = Read::same(
										rd2->patFw,  // new seq
										rd2->qual,   // new quals
										rd2_->patFw, // old seq
										rd2_->qual,  // old quals
										qualitiesMatter);
				}
				same = m2same;
			}
		}
	}
	return same;
}

/**
 * Initialize the wrapper with a new read pair and return an integer >= -1
 * indicating which stage the aligner should start at.  If -1 is returned, the
 * aligner can skip the read entirely.  Checks if the new read pair is
 * identical to the previous pair.  If it is, then we return the id of the
 * first stage to run.
 */
template <typename index_t>
int AlnSinkWrap<index_t>::nextRead(
								   // One of the other of rd1, rd2 will = NULL if read is unpaired
								   const Read* rd1,      // new mate #1
								   const Read* rd2,      // new mate #2
								   TReadId rdid,         // read ID for new pair
								   bool qualitiesMatter) // aln policy distinguishes b/t quals?
{
	assert(!init_);
	assert(rd1 != NULL || rd2 != NULL);
	init_ = true;
	// Keep copy of new read, so that we can compare it with the
	// next one
	if(rd1 != NULL) {
		rd1_ = rd1;
	} else rd1_ = NULL;
	if(rd2 != NULL) {
		rd2_ = rd2;
	} else rd2_ = NULL;
	rdid_ = rdid;
	// Caller must now align the read
	maxed1_ = false;
	maxed2_ = false;
	maxedOverall_ = false;
	bestPair_ = best2Pair_ =
	bestUnp1_ = best2Unp1_ =
	bestUnp2_ = best2Unp2_ = std::numeric_limits<THitInt>::min();
    bestSplicedPair_ = best2SplicedPair_ =
    bestSplicedUnp1_ = best2SplicedUnp1_ =
    bestSplicedUnp2_ = best2SplicedUnp2_ = 0;
	rs1_.clear();     // clear out paired-end alignments
	rs2_.clear();     // clear out paired-end alignments
	rs1u_.clear();    // clear out unpaired alignments for mate #1
	rs2u_.clear();    // clear out unpaired alignments for mate #2
	st_.nextRead(readIsPair()); // reset state
	assert(empty());
	assert(!maxed());
	// Start from the first stage
	return 0;
}

/**
 * Inform global, shared AlnSink object that we're finished with this read.
 * The global AlnSink is responsible for updating counters, creating the output
 * record, and delivering the record to the appropriate output stream.
 *
 * What gets reported for a paired-end alignment?
 *
 * 1. If there are reportable concordant alignments, report those and stop
 * 2. If there are reportable discordant alignments, report those and stop
 * 3. If unpaired alignments can be reported:
 *    3a. Report 
 #
 * Update metrics.  Only ambiguity is: what if a pair aligns repetitively and
 * one of its mates aligns uniquely?
 *
 * 	uint64_t al;   // # mates w/ >= 1 reported alignment
 *  uint64_t unal; // # mates w/ 0 alignments
 *  uint64_t max;  // # mates withheld for exceeding -M/-m ceiling
 *  uint64_t al_concord;  // # pairs w/ >= 1 concordant alignment
 *  uint64_t al_discord;  // # pairs w/ >= 1 discordant alignment
 *  uint64_t max_concord; // # pairs maxed out
 *  uint64_t unal_pair;   // # pairs where neither mate aligned
 */
template <typename index_t>
void AlnSinkWrap<index_t>::finishRead(
									  const SeedResults<index_t> *sr1, // seed alignment results for mate 1
									  const SeedResults<index_t> *sr2, // seed alignment results for mate 2
									  bool               exhaust1,     // mate 1 exhausted?
									  bool               exhaust2,     // mate 2 exhausted?
									  bool               nfilt1,       // mate 1 N-filtered?
									  bool               nfilt2,       // mate 2 N-filtered?
									  bool               scfilt1,      // mate 1 score-filtered?
									  bool               scfilt2,      // mate 2 score-filtered?
									  bool               lenfilt1,     // mate 1 length-filtered?
									  bool               lenfilt2,     // mate 2 length-filtered?
									  bool               qcfilt1,      // mate 1 qc-filtered?
									  bool               qcfilt2,      // mate 2 qc-filtered?
									  bool               sortByScore,  // prioritize alignments by score
									  RandomSource&      rnd,          // pseudo-random generator
									  ReportingMetrics&  met,          // reporting metrics
									  const PerReadMetrics& prm,       // per-read metrics
									  const Scoring& sc,               // scoring scheme
									  bool suppressSeedSummary,        // = true
                                      bool suppressAlignments,         // = false
                                      bool templateLenAdjustment)      // = true
{
	obuf_.clear();
	OutputQueueMark qqm(g_.outq(), obuf_, rdid_, threadid_);
	assert(init_);
	if(!suppressSeedSummary) {
		if(sr1 != NULL) {
			assert(rd1_ != NULL);
			// Mate exists and has non-empty SeedResults
			g_.reportSeedSummary(obuf_, *rd1_, rdid_, threadid_, *sr1, true);
		} else if(rd1_ != NULL) {
			// Mate exists but has NULL SeedResults
			g_.reportEmptySeedSummary(obuf_, *rd1_, rdid_, true);
		}
		if(sr2 != NULL) {
			assert(rd2_ != NULL);
			// Mate exists and has non-empty SeedResults
			g_.reportSeedSummary(obuf_, *rd2_, rdid_, threadid_, *sr2, true);
		} else if(rd2_ != NULL) {
			// Mate exists but has NULL SeedResults
			g_.reportEmptySeedSummary(obuf_, *rd2_, rdid_, true);
		}
	}
	if(!suppressAlignments) {
		// Ask the ReportingState what to report
		st_.finish();
		uint64_t nconcord = 0, ndiscord = 0, nunpair1 = 0, nunpair2 = 0;
		bool pairMax = false, unpair1Max = false, unpair2Max = false;
		st_.getReport(
					  nconcord,
					  ndiscord,
					  nunpair1,
					  nunpair2,
					  pairMax,
					  unpair1Max,
					  unpair2Max);
		assert_leq(nconcord, rs1_.size());
		assert_leq(nunpair1, rs1u_.size());
		assert_leq(nunpair2, rs2u_.size());
		assert_leq(ndiscord, 1);
		assert_gt(rp_.khits, 0);
		assert_gt(rp_.mhits, 0);
		assert(!pairMax    || rs1_.size()  >= (uint64_t)rp_.mhits);
		assert(!unpair1Max || rs1u_.size() >= (uint64_t)rp_.mhits);
		assert(!unpair2Max || rs2u_.size() >= (uint64_t)rp_.mhits);
		met.nread++;
		if(readIsPair()) {
			met.npaired++;
		} else {
			met.nunpaired++;
		}
		// Report concordant paired-end alignments if possible
		if(nconcord > 0) {
            AlnSetSumm concordSumm(
                                   rd1_, rd2_, &rs1_, &rs2_, &rs1u_, &rs2u_,
                                   exhaust1, exhaust2, -1, -1);
            
			// Possibly select a random subset
			size_t off;
			if(sortByScore) {
				// Sort by score then pick from low to high
				off = selectByScore(&rs1_, &rs2_, nconcord, select1_, rnd);
			} else {
				// Select subset randomly
				off = selectAlnsToReport(rs1_, nconcord, select1_, rnd);
			}
            
            concordSumm.numAlnsPaired(select1_.size());
            
			assert_lt(off, rs1_.size());
			const AlnRes *rs1 = &rs1_[off];
			const AlnRes *rs2 = &rs2_[off];
			AlnFlags flags1(
							ALN_FLAG_PAIR_CONCORD_MATE1,
							st_.params().mhitsSet(),
							unpair1Max,
							pairMax,
							nfilt1,
							scfilt1,
							lenfilt1,
							qcfilt1,
							st_.params().mixed,
							true,       // primary
							true,       // opp aligned
							rs2->fw()); // opp fw
			AlnFlags flags2(
							ALN_FLAG_PAIR_CONCORD_MATE2,
							st_.params().mhitsSet(),
							unpair2Max,
							pairMax,
							nfilt2,
							scfilt2,
							lenfilt2,
							qcfilt2,
							st_.params().mixed,
							false,      // primary
							true,       // opp aligned
							rs1->fw()); // opp fw
			// Issue: we only set the flags once, but some of the flags might
			// vary from pair to pair among the pairs we're reporting.  For
			// instance, whether a given mate aligns to the forward strand.
			SeedAlSumm ssm1, ssm2;
            if(sr1 != NULL && sr2 != NULL) {
                sr1->toSeedAlSumm(ssm1);
                sr2->toSeedAlSumm(ssm2);
            }
			for(size_t i = 0; i < rs1_.size(); i++) {
                spliceSites_.clear();
                if(templateLenAdjustment) {
                    rs1_[i].setMateParams(ALN_RES_TYPE_MATE1, &rs2_[i], flags1, ssdb_, threads_rids_mindist_, &spliceSites_);
                    rs2_[i].setMateParams(ALN_RES_TYPE_MATE2, &rs1_[i], flags2, ssdb_, threads_rids_mindist_, &spliceSites_);
                } else {
                    rs1_[i].setMateParams(ALN_RES_TYPE_MATE1, &rs2_[i], flags1);
                    rs2_[i].setMateParams(ALN_RES_TYPE_MATE2, &rs1_[i], flags2);
                }
				assert_eq(abs(rs1_[i].fragmentLength()), abs(rs2_[i].fragmentLength()));
			}
			assert(!select1_.empty());
			g_.reportHits(
						  obuf_,
						  staln_,
						  threadid_,
						  rd1_,
						  rd2_,
						  rdid_,
						  select1_,
						  NULL,
						  &rs1_,
						  &rs2_,
						  pairMax,
						  concordSumm,
						  ssm1,
						  ssm2,
						  &flags1,
						  &flags2,
						  prm,
						  mapq_,
						  sc);
			if(pairMax) {
				met.nconcord_rep++;
			} else {
				met.nconcord_uni++;
				assert(!rs1_.empty());
				if(select1_.size() == 1) {
					met.nconcord_uni1++;
				} else {
					met.nconcord_uni2++;
				}
			}
			init_ = false;
			//g_.outq().finishRead(obuf_, rdid_, threadid_);
			return;
		}
		// Report concordant paired-end alignments if possible
		else if(ndiscord > 0) {
			ASSERT_ONLY(bool ret =) prepareDiscordants();
			assert(ret);
			assert_eq(1, rs1_.size());
			assert_eq(1, rs2_.size());
			AlnSetSumm discordSumm(
								   rd1_, rd2_, &rs1_, &rs2_, &rs1u_, &rs2u_,
								   exhaust1, exhaust2, -1, -1);
			const AlnRes *rs1 = &rs1_[0];
			const AlnRes *rs2 = &rs2_[0];
			AlnFlags flags1(
							ALN_FLAG_PAIR_DISCORD_MATE1,
							st_.params().mhitsSet(),
							false,
							pairMax,
							nfilt1,
							scfilt1,
							lenfilt1,
							qcfilt1,
							st_.params().mixed,
							true,       // primary
							true,       // opp aligned
							rs2->fw()); // opp fw
			AlnFlags flags2(
							ALN_FLAG_PAIR_DISCORD_MATE2,
							st_.params().mhitsSet(),
							false,
							pairMax,
							nfilt2,
							scfilt2,
							lenfilt2,
							qcfilt2,
							st_.params().mixed,
							false,      // primary
							true,       // opp aligned
							rs1->fw()); // opp fw
			SeedAlSumm ssm1, ssm2;
            if(sr1 != NULL) sr1->toSeedAlSumm(ssm1);
			if(sr2 != NULL) sr2->toSeedAlSumm(ssm2);
			for(size_t i = 0; i < rs1_.size(); i++) {
				rs1_[i].setMateParams(ALN_RES_TYPE_MATE1, &rs2_[i], flags1);
				rs2_[i].setMateParams(ALN_RES_TYPE_MATE2, &rs1_[i], flags2);
				assert(rs1_[i].isFraglenSet() == rs2_[i].isFraglenSet());
				assert(!rs1_[i].isFraglenSet() || abs(rs1_[i].fragmentLength()) == abs(rs2_[i].fragmentLength()));
			}
			ASSERT_ONLY(size_t off);
			if(sortByScore) {
				// Sort by score then pick from low to high
				ASSERT_ONLY(off =) selectByScore(&rs1_, &rs2_, ndiscord, select1_, rnd);
			} else {
				// Select subset randomly
				ASSERT_ONLY(off =) selectAlnsToReport(rs1_, ndiscord, select1_, rnd);
			}
			assert_eq(0, off);
			assert(!select1_.empty());
			g_.reportHits(
						  obuf_,
						  staln_,
						  threadid_,
						  rd1_,
						  rd2_,
						  rdid_,
						  select1_,
						  NULL,
						  &rs1_,
						  &rs2_,
						  pairMax,
						  discordSumm,
						  ssm1,
						  ssm2,
						  &flags1,
						  &flags2,
						  prm,
						  mapq_,
						  sc);
			met.nconcord_0++;
			met.ndiscord++;
			init_ = false;
			//g_.outq().finishRead(obuf_, rdid_, threadid_);
			return;
		}
		// If we're at this point, at least one mate failed to align.
		// BTL: That's not true.  It could be that there are no concordant
		// alignments but both mates have unpaired alignments, with one of
		// the mates having more than one.
		//assert(nunpair1 == 0 || nunpair2 == 0);
		assert(!pairMax);
			
		const AlnRes *repRs1 = NULL, *repRs2 = NULL;
		AlnSetSumm summ1, summ2;
		AlnFlags flags1, flags2;
		TRefId refid = -1; TRefOff refoff = -1;
		bool rep1 = rd1_ != NULL && nunpair1 > 0;
		bool rep2 = rd2_ != NULL && nunpair2 > 0;
		
		// This is the preliminary if statement for mate 1 - here we're
		// gathering some preliminary information, making it possible to call
		// g_.reportHits(...) with information about both mates potentially
		if(rep1) {
			// Mate 1 aligned at least once
            if(rep2) {
                summ1.init(
					   rd1_, rd2_, NULL, NULL, &rs1u_, &rs2u_,
					   exhaust1, exhaust2, -1, -1);
            } else {
                summ1.init(
                           rd1_, NULL, NULL, NULL, &rs1u_, NULL,
                           exhaust1, exhaust2, -1, -1);
            }
			size_t off;
			if(sortByScore) {
				// Sort by score then pick from low to high
				off = selectByScore(&rs1u_, NULL, nunpair1, select1_, rnd);
			} else {
				// Select subset randomly
				off = selectAlnsToReport(rs1u_, nunpair1, select1_, rnd);
			}
            summ1.numAlns1(select1_.size());
            summ2.numAlns1(select1_.size());
			repRs1 = &rs1u_[off];
		} else if(rd1_ != NULL) {
			// Mate 1 failed to align - don't do anything yet.  First we want
			// to collect information on mate 2 in case that factors into the
			// summary
			assert(!unpair1Max);
		}
		
		if(rep2) {
            if(rep1) {
                summ2.init(
                           rd1_, rd2_, NULL, NULL, &rs1u_, &rs2u_,
                           exhaust1, exhaust2, -1, -1);
            } else {
                summ2.init(
                           NULL, rd2_, NULL, NULL, NULL, &rs2u_,
                           exhaust1, exhaust2, -1, -1);
            }
			size_t off;
			if(sortByScore) {
				// Sort by score then pick from low to high
				off = selectByScore(&rs2u_, NULL, nunpair2, select2_, rnd);
			} else {
				// Select subset randomly
				off = selectAlnsToReport(rs2u_, nunpair2, select2_, rnd);
			}
			repRs2 = &rs2u_[off];
            summ1.numAlns2(select2_.size());
            summ2.numAlns2(select2_.size());
		} else if(rd2_ != NULL) {
			// Mate 2 failed to align - don't do anything yet.  First we want
			// to collect information on mate 1 in case that factors into the
			// summary
			assert(!unpair2Max);
		}
        
        // Update counters given that one mate didn't align
        if(readIsPair()) {
            met.nconcord_0++;
        }
        if(rd1_ != NULL) {
            if(nunpair1 > 0) {
                // Update counters
                if(readIsPair()) {
                    if(unpair1Max) met.nunp_0_rep++;
                    else {
                        met.nunp_0_uni++;
                        assert(!rs1u_.empty());
                        if(select1_.size() == 1) {
                            met.nunp_0_uni1++;
                        } else {
                            met.nunp_0_uni2++;
                        }
                    }
                } else {
                    if(unpair1Max) met.nunp_rep++;
                    else {
                        met.nunp_uni++;
                        assert(!rs1u_.empty());
                        if(select1_.size() == 1) {
                            met.nunp_uni1++;
                        } else {
                            met.nunp_uni2++;
                        }
                    }
                }
            } else if(unpair1Max) {
                // Update counters
                if(readIsPair())   met.nunp_0_rep++;
                else               met.nunp_rep++;
            } else {
                // Update counters
                if(readIsPair())   met.nunp_0_0++;
                else               met.nunp_0++;
            }
        }
        if(rd2_ != NULL) {
            if(nunpair2 > 0) {
                // Update counters
                if(readIsPair()) {
                    if(unpair2Max) met.nunp_0_rep++;
                    else {
                        assert(!rs2u_.empty());
                        met.nunp_0_uni++;
                        if(select2_.size() == 1) {
                            met.nunp_0_uni1++;
                        } else {
                            met.nunp_0_uni2++;
                        }
                    }
                } else {
                    if(unpair2Max) met.nunp_rep++;
                    else {
                        assert(!rs2u_.empty());
                        met.nunp_uni++;
                        if(select2_.size() == 1) {
                            met.nunp_uni1++;
                        } else {
                            met.nunp_uni2++;
                        }
                    }
                }
            } else if(unpair2Max) {
                // Update counters
                if(readIsPair())   met.nunp_0_rep++;
                else               met.nunp_rep++;
            } else {
                // Update counters
                if(readIsPair())   met.nunp_0_0++;
                else               met.nunp_0++;
            }
        }
		
		// Now set up flags
		if(rep1) {
			// Initialize flags.  Note: We want to have information about how
			// the other mate aligned (if it did) at this point
			flags1.init(
						readIsPair() ?
						ALN_FLAG_PAIR_UNPAIRED_MATE1 :
						ALN_FLAG_PAIR_UNPAIRED,
						st_.params().mhitsSet(),
						unpair1Max,
						pairMax,
						nfilt1,
						scfilt1,
						lenfilt1,
						qcfilt1,
						st_.params().mixed,
						true,   // primary
						repRs2 != NULL,                    // opp aligned
						repRs2 == NULL || repRs2->fw());   // opp fw
			for(size_t i = 0; i < rs1u_.size(); i++) {
				rs1u_[i].setMateParams(ALN_RES_TYPE_UNPAIRED_MATE1, NULL, flags1);
			}
		}
		if(rep2) {
			// Initialize flags.  Note: We want to have information about how
			// the other mate aligned (if it did) at this point
			flags2.init(
						readIsPair() ?
						ALN_FLAG_PAIR_UNPAIRED_MATE2 :
						ALN_FLAG_PAIR_UNPAIRED,
						st_.params().mhitsSet(),
						unpair2Max,
						pairMax,
						nfilt2,
						scfilt2,
						lenfilt2,
						qcfilt2,
						st_.params().mixed,
						true,   // primary
						repRs1 != NULL,                  // opp aligned
						repRs1 == NULL || repRs1->fw()); // opp fw
			for(size_t i = 0; i < rs2u_.size(); i++) {
				rs2u_[i].setMateParams(ALN_RES_TYPE_UNPAIRED_MATE2, NULL, flags2);
			}
		}
		
		// Now report mate 1
		if(rep1) {
			SeedAlSumm ssm1, ssm2;
			if(sr1 != NULL) sr1->toSeedAlSumm(ssm1);
			if(sr2 != NULL) sr2->toSeedAlSumm(ssm2);
			assert(!select1_.empty());
			g_.reportHits(
						  obuf_,
						  staln_,
						  threadid_,
						  rd1_,
						  repRs2 != NULL ? rd2_ : NULL,
						  rdid_,
						  select1_,
						  repRs2 != NULL ? &select2_ : NULL,
						  &rs1u_,
						  repRs2 != NULL ? &rs2u_ : NULL,
						  unpair1Max,
						  summ1,
						  ssm1,
						  ssm2,
						  &flags1,
						  repRs2 != NULL ? &flags2 : NULL,
						  prm,
						  mapq_,
						  sc);
			assert_lt(select1_[0], rs1u_.size());
			refid = rs1u_[select1_[0]].refid();
			refoff = rs1u_[select1_[0]].refoff();
		}
		
		// Now report mate 2
		if(rep2 && !rep1) {
			SeedAlSumm ssm1, ssm2;
			if(sr1 != NULL) sr1->toSeedAlSumm(ssm1);
			if(sr2 != NULL) sr2->toSeedAlSumm(ssm2);
			assert(!select2_.empty());
			g_.reportHits(
						  obuf_,
						  staln_,
						  threadid_,
						  rd2_,
						  repRs1 != NULL ? rd1_ : NULL,
						  rdid_,
						  select2_,
						  repRs1 != NULL ? &select1_ : NULL,
						  &rs2u_,
						  repRs1 != NULL ? &rs1u_ : NULL,
						  unpair2Max,
						  summ2,
						  ssm1,
						  ssm2,
						  &flags2,
						  repRs1 != NULL ? &flags1 : NULL,
						  prm,
						  mapq_,
						  sc);
			assert_lt(select2_[0], rs2u_.size());
			refid = rs2u_[select2_[0]].refid();
			refoff = rs2u_[select2_[0]].refoff();
		}
		
		if(rd1_ != NULL && nunpair1 == 0) {
			if(nunpair2 > 0) {
				assert_neq(-1, refid);
				summ1.init(
						   rd1_, NULL, NULL, NULL, NULL, NULL,
						   exhaust1, exhaust2, refid, refoff);
			} else {
				summ1.init(
						   rd1_, NULL, NULL, NULL, NULL, NULL,
						   exhaust1, exhaust2, -1, -1);
			}
			SeedAlSumm ssm1, ssm2;
			if(sr1 != NULL) sr1->toSeedAlSumm(ssm1);
			if(sr2 != NULL) sr2->toSeedAlSumm(ssm2);
			flags1.init(
						readIsPair() ?
						ALN_FLAG_PAIR_UNPAIRED_MATE1 :
						ALN_FLAG_PAIR_UNPAIRED,
						st_.params().mhitsSet(),
						false,
						false,
						nfilt1,
						scfilt1,
						lenfilt1,
						qcfilt1,
						st_.params().mixed,
						true,           // primary
						repRs2 != NULL, // opp aligned
						(repRs2 != NULL) ? repRs2->fw() : false); // opp fw
			g_.reportUnaligned(
							   obuf_,      // string to write output to
							   staln_,
							   threadid_,
							   rd1_,    // read 1
							   NULL,    // read 2
							   rdid_,   // read id
							   summ1,   // summ
							   ssm1,    // 
							   ssm2,
							   &flags1, // flags 1
							   NULL,    // flags 2
							   prm,     // per-read metrics
							   mapq_,   // MAPQ calculator
							   sc,      // scoring scheme
							   true);   // get lock?
		}
		if(rd2_ != NULL && nunpair2 == 0) {
			if(nunpair1 > 0) {
				assert_neq(-1, refid);
				summ2.init(
						   NULL, rd2_, NULL, NULL, NULL, NULL,
						   exhaust1, exhaust2, refid, refoff);
			} else {
				summ2.init(
						   NULL, rd2_, NULL, NULL, NULL, NULL,
						   exhaust1, exhaust2, -1, -1);
			}
			SeedAlSumm ssm1, ssm2;
			if(sr1 != NULL) sr1->toSeedAlSumm(ssm1);
			if(sr2 != NULL) sr2->toSeedAlSumm(ssm2);
			flags2.init(
						readIsPair() ?
						ALN_FLAG_PAIR_UNPAIRED_MATE2 :
						ALN_FLAG_PAIR_UNPAIRED,
						st_.params().mhitsSet(),
						false,
						false,
						nfilt2,
						scfilt2,
						lenfilt2,
						qcfilt2,
						st_.params().mixed,
						true,           // primary
						repRs1 != NULL, // opp aligned
						(repRs1 != NULL) ? repRs1->fw() : false); // opp fw
			g_.reportUnaligned(
							   obuf_,      // string to write output to
							   staln_,
							   threadid_,
							   rd2_,    // read 1
							   NULL,    // read 2
							   rdid_,   // read id
							   summ2,   // summ
							   ssm1,
							   ssm2,
							   &flags2, // flags 1
							   NULL,    // flags 2
							   prm,     // per-read metrics
							   mapq_,   // MAPQ calculator
							   sc,      // scoring scheme
							   true);   // get lock?
		}
	} // if(suppress alignments)
	init_ = false;
	return;
}

/**
 * Called by the aligner when a new unpaired or paired alignment is
 * discovered in the given stage.  This function checks whether the
 * addition of this alignment causes the reporting policy to be
 * violated (by meeting or exceeding the limits set by -k, -m, -M),
 * in which case true is returned immediately and the aligner is
 * short circuited.  Otherwise, the alignment is tallied and false
 * is returned.
 */
template <typename index_t>
bool AlnSinkWrap<index_t>::report(
								  int stage,
								  const AlnRes* rs1,
								  const AlnRes* rs2)
{
	assert(init_);
	assert(rs1 != NULL || rs2 != NULL);
	assert(rs1 == NULL || !rs1->empty());
	assert(rs2 == NULL || !rs2->empty());
	assert(rs1 == NULL || rs1->repOk());
	assert(rs2 == NULL || rs2->repOk());
	bool paired = (rs1 != NULL && rs2 != NULL);
	bool one = (rs1 != NULL);
	const AlnRes* rsa = one ? rs1 : rs2;
	const AlnRes* rsb = one ? rs2 : rs1;
	if(paired) {
		assert(readIsPair());
		st_.foundConcordant();
		rs1_.push_back(*rs1);
		rs2_.push_back(*rs2);
	} else {
        st_.foundUnpaired(one);
		if(one) {
			rs1u_.push_back(*rs1);
  		} else {
			rs2u_.push_back(*rs2);
		}
	}
	// Tally overall alignment score
	TAlScore score = rsa->score().score();
	if(rsb != NULL) score += rsb->score().score();
    index_t num_spliced = (index_t)rsa->num_spliced();
    if(rsb != NULL) num_spliced += (index_t)rsb->num_spliced();
	// Update best score so far
	if(paired) {
		if(score > bestPair_) {
			best2Pair_ = bestPair_;
			bestPair_ = score;
            best2SplicedPair_ = bestSplicedPair_;
            bestSplicedPair_ = num_spliced;
		} else if(score > best2Pair_) {
			best2Pair_ = score;
            best2SplicedPair_ = num_spliced;
		}
	} else {
		if(one) {
			if(score > bestUnp1_) {
				best2Unp1_ = bestUnp1_;
				bestUnp1_ = score;
                best2SplicedUnp1_ = bestSplicedUnp1_;
                bestSplicedUnp1_ = num_spliced;
			} else if(score > best2Unp1_) {
				best2Unp1_ = score;
                best2SplicedUnp1_ = num_spliced;
			}
		} else {
			if(score > bestUnp2_) {
				best2Unp2_ = bestUnp2_;
				bestUnp2_ = score;
                best2SplicedUnp2_ = bestSplicedUnp2_;
                bestSplicedUnp2_ = num_spliced;
			} else if(score > best2Unp2_) {
				best2Unp2_ = score;
                best2SplicedUnp1_ = num_spliced;
			}
		}
	}
	return st_.done();
}

/**
 * If there is a configuration of unpaired alignments that fits our
 * criteria for there being one or more discordant alignments, then
 * shift the discordant alignments over to the rs1_/rs2_ lists, clear the
 * rs1u_/rs2u_ lists and return true.  Otherwise, return false.
 */
template <typename index_t>
bool AlnSinkWrap<index_t>::prepareDiscordants() {
	if(rs1u_.size() == 1 && rs2u_.size() == 1) {
		assert(rs1_.empty());
		assert(rs2_.empty());
		rs1_.push_back(rs1u_[0]);
		rs2_.push_back(rs2u_[0]);
		return true;
	}
	return false;
}

/**
 * rs1 (possibly together with rs2 if reads are paired) are populated with
 * alignments.  Here we prioritize them according to alignment score, and
 * some randomness to break ties.  Priorities are returned in the 'select'
 * list.
 */
template <typename index_t>
size_t AlnSinkWrap<index_t>::selectByScore(
										   const EList<AlnRes>* rs1,    // alignments to select from (mate 1)
										   const EList<AlnRes>* rs2,    // alignments to select from (mate 2, or NULL)
										   uint64_t             num,    // number of alignments to select
										   EList<size_t>&       select, // prioritized list to put results in
										   RandomSource&        rnd)
const
{
	assert(init_);
	assert(repOk());
	assert_gt(num, 0);
	assert(rs1 != NULL);
	size_t sz = rs1->size(); // sz = # alignments found
	assert_leq(num, sz);
	if(sz < num) {
		num = sz;
	}
	// num = # to select
	if(sz < 1) {
		return 0;
	}
	select.resize((size_t)num);
	// Use 'selectBuf_' as a temporary list for sorting purposes
	EList<std::pair<TAlScore, size_t> >& buf =
	const_cast<EList<std::pair<TAlScore, size_t> >& >(selectBuf_);
	buf.resize(sz);
	// Sort by score.  If reads are pairs, sort by sum of mate scores.
	for(size_t i = 0; i < sz; i++) {
		buf[i].first = (*rs1)[i].score().hisat2_score();
		if(rs2 != NULL) {
			buf[i].first += (*rs2)[i].score().hisat2_score();
		}
		buf[i].second = i; // original offset
	}
	buf.sort(); buf.reverse(); // sort in descending order by score
	
	// Randomize streaks of alignments that are equal by score
	size_t streak = 0;
	for(size_t i = 1; i < buf.size(); i++) {
		if(buf[i].first == buf[i-1].first) {
			if(streak == 0) { streak = 1; }
			streak++;
		} else {
			if(streak > 1) {
				assert_geq(i, streak);
				buf.shufflePortion(i-streak, streak, rnd);
			}
			streak = 0;
		}
	}
	if(streak > 1) {
		buf.shufflePortion(buf.size() - streak, streak, rnd);
	}
	
	for(size_t i = 0; i < num; i++) { select[i] = buf[i].second; }
    
    if(!secondary_) {
        assert_geq(buf.size(), select.size());
        for(size_t i = 0; i + 1 < select.size(); i++) {
            if(buf[i].first != buf[i+1].first) {
                select.resize(i+1);
                break;
            }
        }
    }
    
	// Returns index of the representative alignment, but in 'select' also
	// returns the indexes of the next best selected alignments in order by
	// score.
	return selectBuf_[0].second;
}

/**
 * Given that rs is already populated with alignments, consider the
 * alignment policy and make random selections where necessary.  E.g. if we
 * found 10 alignments and the policy is -k 2 -m 20, select 2 alignments at
 * random.  We "select" an alignment by setting the parallel entry in the
 * 'select' list to true.
 *
 * Return the "representative" alignment.  This is simply the first one
 * selected.  That will also be what SAM calls the "primary" alignment.
 */
template <typename index_t>
size_t AlnSinkWrap<index_t>::selectAlnsToReport(
												const EList<AlnRes>& rs,     // alignments to select from
												uint64_t             num,    // number of alignments to select
												EList<size_t>&       select, // list to put results in
												RandomSource&        rnd)
const
{
	assert(init_);
	assert(repOk());
	assert_gt(num, 0);
	size_t sz = rs.size();
	if(sz < num) {
		num = sz;
	}
	if(sz < 1) {
		return 0;
	}
	select.resize((size_t)num);
	if(sz == 1) {
		assert_eq(1, num);
		select[0] = 0;
		return 0;
	}
	// Select a random offset into the list of alignments
	uint32_t off = rnd.nextU32() % (uint32_t)sz;
	uint32_t offOrig = off;
	// Now take elements starting at that offset, wrapping around to 0 if
	// necessary.  Leave the rest.
	for(size_t i = 0; i < num; i++) {
		select[i] = off;
		off++;
		if(off == sz) {
			off = 0;
		}
	}
	return offOrig;
}

#define NOT_SUPPRESSED !suppress_[field++]
#define BEGIN_FIELD { \
if(firstfield) firstfield = false; \
else o.append('\t'); \
}
#define WRITE_TAB { \
if(firstfield) firstfield = false; \
else o.append('\t'); \
}
#define WRITE_NUM(o, x) { \
itoa10(x, buf); \
o.append(buf); \
}

/**
 * Print a seed summary to the first output stream in the outs_ list.
 */
template <typename index_t>
void AlnSink<index_t>::reportSeedSummary(
										 BTString&          o,
										 const Read&        rd,
										 TReadId            rdid,
										 size_t             threadId,
										 const SeedResults<index_t>& rs,
										 bool               getLock)
{
	appendSeedSummary(
					  o,                     // string to write to
					  rd,                    // read
					  rdid,                  // read id
					  rs.numOffs()*2,        // # seeds tried
					  rs.nonzeroOffsets(),   // # seeds with non-empty results
					  rs.numRanges(),        // # ranges for all seed hits
					  rs.numElts(),          // # elements for all seed hits
					  rs.numOffs(),          // # seeds tried from fw read
					  rs.nonzeroOffsetsFw(), // # seeds with non-empty results from fw read
					  rs.numRangesFw(),      // # ranges for seed hits from fw read
					  rs.numEltsFw(),        // # elements for seed hits from fw read
					  rs.numOffs(),          // # seeds tried from rc read
					  rs.nonzeroOffsetsRc(), // # seeds with non-empty results from fw read
					  rs.numRangesRc(),      // # ranges for seed hits from fw read
					  rs.numEltsRc());       // # elements for seed hits from fw read
}

/**
 * Print an empty seed summary to the first output stream in the outs_ list.
 */
template <typename index_t>
void AlnSink<index_t>::reportEmptySeedSummary(
											  BTString&          o,
											  const Read&        rd,
											  TReadId            rdid,
											  size_t             threadId,
											  bool               getLock)
{
	appendSeedSummary(
					  o,                     // string to append to
					  rd,                    // read
					  rdid,                  // read id
					  0,                     // # seeds tried
					  0,                     // # seeds with non-empty results
					  0,                     // # ranges for all seed hits
					  0,                     // # elements for all seed hits
					  0,                     // # seeds tried from fw read
					  0,                     // # seeds with non-empty results from fw read
					  0,                     // # ranges for seed hits from fw read
					  0,                     // # elements for seed hits from fw read
					  0,                     // # seeds tried from rc read
					  0,                     // # seeds with non-empty results from fw read
					  0,                     // # ranges for seed hits from fw read
					  0);                    // # elements for seed hits from fw read
}

/**
 * Print the given string.  If ws = true, print only up to and not
 * including the first space or tab.  Useful for printing reference
 * names.
 */
template<typename T>
static inline void printUptoWs(
							   BTString& s,
							   const T& str,
							   bool chopws)
{
	size_t len = str.length();
	for(size_t i = 0; i < len; i++) {
		if(!chopws || (str[i] != ' ' && str[i] != '\t')) {
			s.append(str[i]);
		} else {
			break;
		}
	}
}

/**
 * Append a batch of unresolved seed alignment summary results (i.e.
 * seed alignments where all we know is the reference sequence aligned
 * to and its SA range, not where it falls in the reference
 * sequence) to the given output stream in Bowtie's seed-sumamry
 * verbose-mode format.
 *
 * The seed summary format is:
 *
 *  - One line per read
 *  - A typical line consists of a set of tab-delimited fields:
 *
 *    1. Read name
 *    2. Total number of seeds extracted from the read
 *    3. Total number of seeds that aligned to the reference at
 *       least once (always <= field 2)
 *    4. Total number of distinct BW ranges found in all seed hits
 *       (always >= field 3)
 *    5. Total number of distinct BW elements found in all seed
 *       hits (always >= field 4)
 *    6-9.:   Like 2-5. but just for seeds extracted from the
 *            forward representation of the read
 *    10-13.: Like 2-5. but just for seeds extracted from the
 *            reverse-complement representation of the read
 *
 *    Note that fields 6 and 10 should add to field 2, 7 and 11
 *    should add to 3, etc.
 *
 *  - Lines for reads that are filtered out for any reason (e.g. too
 *    many Ns) have columns 2 through 13 set to 0.
 */
template <typename index_t>
void AlnSink<index_t>::appendSeedSummary(
										 BTString&     o,
										 const Read&   rd,
										 const TReadId rdid,
										 size_t        seedsTried,
										 size_t        nonzero,
										 size_t        ranges,
										 size_t        elts,
										 size_t        seedsTriedFw,
										 size_t        nonzeroFw,
										 size_t        rangesFw,
										 size_t        eltsFw,
										 size_t        seedsTriedRc,
										 size_t        nonzeroRc,
										 size_t        rangesRc,
										 size_t        eltsRc)
{
	char buf[1024];
	bool firstfield = true;
	//
	// Read name
	//
	BEGIN_FIELD;
	printUptoWs(o, rd.name, true);
	
	//
	// Total number of seeds tried
	//
	BEGIN_FIELD;
	WRITE_NUM(o, seedsTried);
	
	//
	// Total number of seeds tried where at least one range was found.
	//
	BEGIN_FIELD;
	WRITE_NUM(o, nonzero);
	
	//
	// Total number of ranges found
	//
	BEGIN_FIELD;
	WRITE_NUM(o, ranges);
	
	//
	// Total number of elements found
	//
	BEGIN_FIELD;
	WRITE_NUM(o, elts);
	
	//
	// The same four numbers, but only for seeds extracted from the
	// forward read representation.
	//
	BEGIN_FIELD;
	WRITE_NUM(o, seedsTriedFw);
	
	BEGIN_FIELD;
	WRITE_NUM(o, nonzeroFw);
	
	BEGIN_FIELD;
	WRITE_NUM(o, rangesFw);
	
	BEGIN_FIELD;
	WRITE_NUM(o, eltsFw);
	
	//
	// The same four numbers, but only for seeds extracted from the
	// reverse complement read representation.
	//
	BEGIN_FIELD;
	WRITE_NUM(o, seedsTriedRc);
	
	BEGIN_FIELD;
	WRITE_NUM(o, nonzeroRc);
	
	BEGIN_FIELD;
	WRITE_NUM(o, rangesRc);
	
	BEGIN_FIELD;
	WRITE_NUM(o, eltsRc);
	
	o.append('\n');
}

/**
 * Append a single hit to the given output stream in Bowtie's
 * verbose-mode format.
 */
template <typename index_t>
void AlnSinkSam<index_t>::appendMate(
									 BTString&     o,           // append to this string
									 StackedAln&   staln,       // store stacked alignment struct here
									 const Read&   rd,
									 const Read*   rdo,
									 const TReadId rdid,
									 AlnRes* rs,
									 AlnRes* rso,
									 const AlnSetSumm& summ,
									 const SeedAlSumm& ssm,
									 const SeedAlSumm& ssmo,
									 const AlnFlags& flags,
									 const PerReadMetrics& prm,
									 const Mapq& mapqCalc,
									 const Scoring& sc)
{
	if(rs == NULL && samc_.omitUnalignedReads()) {
		return;
	}
	char buf[1024];
	char mapqInps[1024];
	if(rs != NULL) {
		staln.reset();
		rs->initStacked(rd, staln);
		staln.leftAlign(false /* not past MMs */);
	}
	int offAdj = 0;
	// QNAME
	samc_.printReadName(o, rd.name, flags.partOfPair());
	o.append('\t');
	// FLAG
	int fl = 0;
	if(flags.partOfPair()) {
		fl |= SAM_FLAG_PAIRED;
		if(flags.alignedConcordant()) {
			fl |= SAM_FLAG_MAPPED_PAIRED;
 		}
		if(!flags.mateAligned()) {
			// Other fragment is unmapped
			fl |= SAM_FLAG_MATE_UNMAPPED;
		}
		fl |= (flags.readMate1() ?
			   SAM_FLAG_FIRST_IN_PAIR : SAM_FLAG_SECOND_IN_PAIR);
		if(flags.mateAligned() && rso != NULL) {
			if(!rso->fw()) {
				fl |= SAM_FLAG_MATE_STRAND;
			}
		}
	}
	if(!flags.isPrimary()) {
		fl |= SAM_FLAG_NOT_PRIMARY;
	}
	if(rs != NULL && !rs->fw()) {
		fl |= SAM_FLAG_QUERY_STRAND;
	}
	if(rs == NULL) {
		// Failed to align
		fl |= SAM_FLAG_UNMAPPED;
	}
	itoa10<int>(fl, buf);
	o.append(buf);
	o.append('\t');
	// RNAME
	if(rs != NULL) {
		samc_.printRefNameFromIndex(o, (size_t)rs->refid());
		o.append('\t');
	} else {
		if(summ.orefid() != -1) {
			// Opposite mate aligned but this one didn't - print the opposite
			// mate's RNAME and POS as is customary
			assert(flags.partOfPair());
			samc_.printRefNameFromIndex(o, (size_t)summ.orefid());
		} else {		
			// No alignment
			o.append('*');
		}
		o.append('\t');
	}
	// POS
	// Note: POS is *after* soft clipping.  I.e. POS points to the
	// upstream-most character *involved in the clipped alignment*.
	if(rs != NULL) {
		itoa10<int64_t>(rs->refoff()+1+offAdj, buf);
		o.append(buf);
		o.append('\t');
	} else {
		if(summ.orefid() != -1) {
			// Opposite mate aligned but this one didn't - print the opposite
			// mate's RNAME and POS as is customary
			assert(flags.partOfPair());
			itoa10<int64_t>(summ.orefoff()+1+offAdj, buf);
			o.append(buf);
		} else {
			// No alignment
			o.append('0');
		}
		o.append('\t');
	}
	// MAPQ
	mapqInps[0] = '\0';
	if(rs != NULL) {
		itoa10<TMapq>(mapqCalc.mapq(
									summ, flags, rd.mate < 2, rd.length(),
									rdo == NULL ? 0 : rdo->length(), mapqInps), buf);
		o.append(buf);
		o.append('\t');
	} else {
		// No alignment
		o.append("0\t");
	}
	// CIGAR
	if(rs != NULL) {
		staln.buildCigar(false);
		staln.writeCigar(&o, NULL);
		o.append('\t');
	} else {
		// No alignment
		o.append("*\t");
	}
	// RNEXT
	if(rs != NULL && flags.partOfPair()) {
		if(rso != NULL && rs->refid() != rso->refid()) {
			samc_.printRefNameFromIndex(o, (size_t)rso->refid());
			o.append('\t');
		} else {
			o.append("=\t");
		}
	} else if(summ.orefid() != -1) {
		// The convention if this mate fails to align but the other doesn't is
		// to copy the mate's details into here
		o.append("=\t");
	} else {
		o.append("*\t");
	}
	// PNEXT
	if(rs != NULL && flags.partOfPair()) {
		if(rso != NULL) {
			itoa10<int64_t>(rso->refoff()+1, buf);
			o.append(buf);
			o.append('\t');
		} else {
			// The convenstion is that if this mate aligns but the opposite
			// doesn't, we print this mate's offset here
			itoa10<int64_t>(rs->refoff()+1, buf);
			o.append(buf);
			o.append('\t');
		}
	} else if(summ.orefid() != -1) {
		// The convention if this mate fails to align but the other doesn't is
		// to copy the mate's details into here
		itoa10<int64_t>(summ.orefoff()+1, buf);
		o.append(buf);
		o.append('\t');
	} else {
		o.append("0\t");
	}
	// ISIZE
	if(rs != NULL && rs->isFraglenSet()) {
		itoa10<int64_t>(rs->fragmentLength(), buf);
		o.append(buf);
		o.append('\t');
	} else {
		// No fragment
		o.append("0\t");
	}
	// SEQ
	if(!flags.isPrimary() && samc_.omitSecondarySeqQual()) {
		o.append('*');
	} else {
		// Print the read
		if(rd.patFw.length() == 0) {
			o.append('*');
		} else {
			if(rs == NULL || rs->fw()) {
				o.append(rd.patFw.toZBuf());
			} else {
				o.append(rd.patRc.toZBuf());
			}
		}
	}
	o.append('\t');
	// QUAL
	if(!flags.isPrimary() && samc_.omitSecondarySeqQual()) {
		o.append('*');
	} else {
		// Print the quals
		if(rd.qual.length() == 0) {
			o.append('*');
		} else {
			if(rs == NULL || rs->fw()) {
				o.append(rd.qual.toZBuf());
			} else {
				o.append(rd.qualRev.toZBuf());
			}
		}
	}
	o.append('\t');
	//
	// Optional fields
	//
	if(rs != NULL) {
		samc_.printAlignedOptFlags(
								   o,           // output buffer
								   true,        // first opt flag printed is first overall?
								   rd,          // read
								   *rs,         // individual alignment result
								   staln,       // stacked alignment
								   flags,       // alignment flags
								   summ,        // summary of alignments for this read
								   ssm,         // seed alignment summary
								   prm,         // per-read metrics
								   sc,          // scoring scheme
								   mapqInps,    // inputs to MAPQ calculation
                                   this->altdb_);
	} else {
		samc_.printEmptyOptFlags(
								 o,           // output buffer
								 true,        // first opt flag printed is first overall?
								 rd,          // read
								 flags,       // alignment flags
								 summ,        // summary of alignments for this read
								 ssm,         // seed alignment summary
								 prm,         // per-read metrics
								 sc);         // scoring scheme
	}
	o.append('\n');
}

#endif /*ndef ALN_SINK_H_*/