File: aligner_bt.cpp

package info (click to toggle)
centrifuge 1.0.3-2
  • links: PTS, VCS
  • area: main
  • in suites: bullseye, buster, sid
  • size: 11,864 kB
  • sloc: cpp: 51,936; perl: 1,919; python: 1,538; makefile: 618; sh: 352
file content (1773 lines) | stat: -rw-r--r-- 53,941 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
/*
 * 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/>.
 */

#include "aligner_bt.h"
#include "mask.h"

using namespace std;

#define CHECK_ROW_COL(rowc, colc) \
	if(rowc >= 0 && colc >= 0) { \
		if(!sawcell_[colc].insert(rowc)) { \
			/* was already in there */ \
			abort = true; \
			return; \
		} \
		assert(local || prob_.cper_->debugCell(rowc, colc, hefc)); \
	}

/**
 * Fill in a triangle of the DP table and backtrace from the given cell to
 * a cell in the previous checkpoint, or to the terminal cell.
 */
void BtBranchTracer::triangleFill(
	int64_t rw,          // row of cell to backtrace from
	int64_t cl,          // column of cell to backtrace from
	int hef,             // cell to backtrace from is H (0), E (1), or F (2)
	TAlScore targ,       // score of cell to backtrace from
	TAlScore targ_final, // score of alignment we're looking for
	RandomSource& rnd,   // pseudo-random generator
	int64_t& row_new,    // out: row we ended up in after backtrace
	int64_t& col_new,    // out: column we ended up in after backtrace
	int& hef_new,        // out: H/E/F after backtrace
	TAlScore& targ_new,  // out: score up to cell we ended up in
	bool& done,          // out: finished tracing out an alignment?
	bool& abort)         // out: aborted b/c cell was seen before?
{
	assert_geq(rw, 0);
	assert_geq(cl, 0);
	assert_range(0, 2, hef);
	assert_lt(rw, (int64_t)prob_.qrylen_);
	assert_lt(cl, (int64_t)prob_.reflen_);
	assert(prob_.usecp_ && prob_.fill_);
	int64_t row = rw, col = cl;
	const int64_t colmin = 0;
	const int64_t rowmin = 0;
	const int64_t colmax = prob_.reflen_ - 1;
	const int64_t rowmax = prob_.qrylen_ - 1;
	assert_leq(prob_.reflen_, (TRefOff)sawcell_.size());
	assert_leq(col, (int64_t)prob_.cper_->hicol());
	assert_geq(col, (int64_t)prob_.cper_->locol());
	assert_geq(prob_.cper_->per(), 2);
	size_t mod = (row + col) & prob_.cper_->lomask();
	assert_lt(mod, prob_.cper_->per());
	// Allocate room for diags
	size_t depth = mod+1;
	assert_leq(depth, prob_.cper_->per());
	size_t breadth = depth;
	tri_.resize(depth);
	// Allocate room for each diag
	for(size_t i = 0; i < depth; i++) {
		tri_[i].resize(breadth - i);
	}
	bool upperleft = false;
	size_t off = (row + col) >> prob_.cper_->perpow2();
	if(off == 0) {
		upperleft = true;
	} else {
		off--;
	}
	const TAlScore sc_rdo = prob_.sc_->readGapOpen();
	const TAlScore sc_rde = prob_.sc_->readGapExtend();
	const TAlScore sc_rfo = prob_.sc_->refGapOpen();
	const TAlScore sc_rfe = prob_.sc_->refGapExtend();
	const bool local = !prob_.sc_->monotone;
	int64_t row_lo = row - (int64_t)mod;
	const CpQuad *prev2 = NULL, *prev1 = NULL;
	if(!upperleft) {
		// Read-only pointer to cells in diagonal -2.  Start one row above the
		// target row.
		prev2 = prob_.cper_->qdiag1sPtr() + (off * prob_.cper_->nrow() + row_lo - 1);
		// Read-only pointer to cells in diagonal -1.  Start one row above the
		// target row
		prev1 = prob_.cper_->qdiag2sPtr() + (off * prob_.cper_->nrow() + row_lo - 1);
#ifndef NDEBUG
		if(row >= (int64_t)mod) {
			size_t rowc = row - mod, colc = col;
			if(rowc > 0 && prob_.cper_->isCheckpointed(rowc-1, colc)) {
				TAlScore al = prev1[0].sc[0];
				if(al == MIN_I16) al = MIN_I64;
				assert_eq(prob_.cper_->scoreTriangle(rowc-1, colc, 0), al);
			}
			if(rowc > 0 && colc > 0 && prob_.cper_->isCheckpointed(rowc-1, colc-1)) {
				TAlScore al = prev2[0].sc[0];
				if(al == MIN_I16) al = MIN_I64;
				assert_eq(prob_.cper_->scoreTriangle(rowc-1, colc-1, 0), al);
			}
		}
#endif
	}
	// Pointer to cells in current diagonal
	// For each diagonal we need to fill in
	for(size_t i = 0; i < depth; i++) {
		CpQuad * cur = tri_[i].ptr();
		CpQuad * curc = cur;
		size_t doff = mod - i; // # diagonals we are away from target diag
		//assert_geq(row, (int64_t)doff);
		int64_t rowc = row - doff;
		int64_t colc = col;
		size_t neval = 0; // # cells evaluated in this diag
		ASSERT_ONLY(const CpQuad *last = NULL);
		// Fill this diagonal from upper right to lower left
		for(size_t j = 0; j < breadth; j++) {
			if(rowc >= rowmin && rowc <= rowmax &&
			   colc >= colmin && colc <= colmax)
			{
				neval++;
				int64_t fromend = prob_.qrylen_ - rowc - 1;
				bool allowGaps = fromend >= prob_.sc_->gapbar && rowc >= prob_.sc_->gapbar;
				// Fill this cell
				// Some things we might want to calculate about this cell up front:
				// 1. How many matches are possible from this cell to the cell in
				//    row, col, in case this allows us to prune
				// Get character from read
				int qc = prob_.qry_[rowc];
				// Get quality value from read
				int qq = prob_.qual_[rowc];
				assert_geq(qq, 33);
				// Get character from reference
				int rc = prob_.ref_[colc];
				assert_range(0, 16, rc);
				int16_t sc_diag = prob_.sc_->score(qc, rc, qq - 33);
				int16_t sc_h_up = MIN_I16;
				int16_t sc_f_up = MIN_I16;
				int16_t sc_h_lf = MIN_I16;
				int16_t sc_e_lf = MIN_I16;
				if(allowGaps) {
					if(rowc > 0) {
						assert(local || prev1[j+0].sc[2] < 0);
						if(prev1[j+0].sc[0] > MIN_I16) {
							sc_h_up = prev1[j+0].sc[0] - sc_rfo;
							if(local) sc_h_up = max<int16_t>(sc_h_up, 0);
						}
						if(prev1[j+0].sc[2] > MIN_I16) {
							sc_f_up = prev1[j+0].sc[2] - sc_rfe;
							if(local) sc_f_up = max<int16_t>(sc_f_up, 0);
						}
#ifndef NDEBUG
						TAlScore hup = prev1[j+0].sc[0];
						TAlScore fup = prev1[j+0].sc[2];
						if(hup == MIN_I16) hup = MIN_I64;
						if(fup == MIN_I16) fup = MIN_I64;
						if(local) {
							hup = max<int16_t>(hup, 0);
							fup = max<int16_t>(fup, 0);
						}
						if(prob_.cper_->isCheckpointed(rowc-1, colc)) {
							assert_eq(hup, prob_.cper_->scoreTriangle(rowc-1, colc, 0));
							assert_eq(fup, prob_.cper_->scoreTriangle(rowc-1, colc, 2));
						}
#endif
					}
					if(colc > 0) {
						assert(local || prev1[j+1].sc[1] < 0);
						if(prev1[j+1].sc[0] > MIN_I16) {
							sc_h_lf = prev1[j+1].sc[0] - sc_rdo;
							if(local) sc_h_lf = max<int16_t>(sc_h_lf, 0);
						}
						if(prev1[j+1].sc[1] > MIN_I16) {
							sc_e_lf = prev1[j+1].sc[1] - sc_rde;
							if(local) sc_e_lf = max<int16_t>(sc_e_lf, 0);
						}
#ifndef NDEBUG
						TAlScore hlf = prev1[j+1].sc[0];
						TAlScore elf = prev1[j+1].sc[1];
						if(hlf == MIN_I16) hlf = MIN_I64;
						if(elf == MIN_I16) elf = MIN_I64;
						if(local) {
							hlf = max<int16_t>(hlf, 0);
							elf = max<int16_t>(elf, 0);
						}
						if(prob_.cper_->isCheckpointed(rowc, colc-1)) {
							assert_eq(hlf, prob_.cper_->scoreTriangle(rowc, colc-1, 0));
							assert_eq(elf, prob_.cper_->scoreTriangle(rowc, colc-1, 1));
						}
#endif
					}
				}
				assert(rowc <= 1 || colc <= 0 || prev2 != NULL);
				int16_t sc_h_dg = ((rowc > 0 && colc > 0) ? prev2[j+0].sc[0] : 0);
				if(colc == 0 && rowc > 0 && !local) {
					sc_h_dg = MIN_I16;
				}
				if(sc_h_dg > MIN_I16) {
					sc_h_dg += sc_diag;
				}
				if(local) sc_h_dg = max<int16_t>(sc_h_dg, 0);
				// cerr << sc_diag << " " << sc_h_dg << " " << sc_h_up << " " << sc_f_up << " " << sc_h_lf << " " << sc_e_lf << endl;
				int mask = 0;
				// Calculate best ways into H, E, F cells starting with H.
				// Mask bits:
				// H: 1=diag, 2=hhoriz, 4=ehoriz, 8=hvert, 16=fvert
				// E: 32=hhoriz, 64=ehoriz
				// F: 128=hvert, 256=fvert
				int16_t sc_best = sc_h_dg;
				if(sc_h_dg > MIN_I64) {
					mask = 1;
				}
				if(colc > 0 && sc_h_lf >= sc_best && sc_h_lf > MIN_I64) {
					if(sc_h_lf > sc_best) mask = 0;
					mask |= 2;
					sc_best = sc_h_lf;
				}
				if(colc > 0 && sc_e_lf >= sc_best && sc_e_lf > MIN_I64) {
					if(sc_e_lf > sc_best) mask = 0;
					mask |= 4;
					sc_best = sc_e_lf;
				}
				if(rowc > 0 && sc_h_up >= sc_best && sc_h_up > MIN_I64) {
					if(sc_h_up > sc_best) mask = 0;
					mask |= 8;
					sc_best = sc_h_up;
				}
				if(rowc > 0 && sc_f_up >= sc_best && sc_f_up > MIN_I64) {
					if(sc_f_up > sc_best) mask = 0;
					mask |= 16;
					sc_best = sc_f_up;
				}
				// Calculate best way into E cell
				int16_t sc_e_best = sc_h_lf;
				if(colc > 0) {
					if(sc_h_lf >= sc_e_lf && sc_h_lf > MIN_I64) {
						if(sc_h_lf == sc_e_lf) {
							mask |= 64;
						}
						mask |= 32;
					} else if(sc_e_lf > MIN_I64) {
						sc_e_best = sc_e_lf;
						mask |= 64;
					}
				}
				if(sc_e_best > sc_best) {
					sc_best = sc_e_best;
					mask &= ~31; // don't go diagonal
				}
				// Calculate best way into F cell
				int16_t sc_f_best = sc_h_up;
				if(rowc > 0) {
					if(sc_h_up >= sc_f_up && sc_h_up > MIN_I64) {
						if(sc_h_up == sc_f_up) {
							mask |= 256;
						}
						mask |= 128;
					} else if(sc_f_up > MIN_I64) {
						sc_f_best = sc_f_up;
						mask |= 256;
					}
				}
				if(sc_f_best > sc_best) {
					sc_best = sc_f_best;
					mask &= ~127; // don't go horizontal or diagonal
				}
				// Install results in cur
				assert(!prob_.sc_->monotone || sc_best <= 0);
				assert(!prob_.sc_->monotone || sc_e_best <= 0);
				assert(!prob_.sc_->monotone || sc_f_best <= 0);
				curc->sc[0] = sc_best;
				assert( local || sc_e_best < 0);
				assert( local || sc_f_best < 0);
				assert(!local || sc_e_best >= 0 || sc_e_best == MIN_I16);
				assert(!local || sc_f_best >= 0 || sc_f_best == MIN_I16);
				curc->sc[1] = sc_e_best;
				curc->sc[2] = sc_f_best;
				curc->sc[3] = mask;
				// cerr << curc->sc[0] << " " << curc->sc[1] << " " << curc->sc[2] << " " << curc->sc[3] << endl;
				ASSERT_ONLY(last = curc);
#ifndef NDEBUG
				if(prob_.cper_->isCheckpointed(rowc, colc)) {
					if(local) {
						sc_e_best = max<int16_t>(sc_e_best, 0);
						sc_f_best = max<int16_t>(sc_f_best, 0);
					}
					TAlScore sc_best64   = sc_best;   if(sc_best   == MIN_I16) sc_best64   = MIN_I64;
					TAlScore sc_e_best64 = sc_e_best; if(sc_e_best == MIN_I16) sc_e_best64 = MIN_I64;
					TAlScore sc_f_best64 = sc_f_best; if(sc_f_best == MIN_I16) sc_f_best64 = MIN_I64;
					assert_eq(prob_.cper_->scoreTriangle(rowc, colc, 0), sc_best64);
					assert_eq(prob_.cper_->scoreTriangle(rowc, colc, 1), sc_e_best64);
					assert_eq(prob_.cper_->scoreTriangle(rowc, colc, 2), sc_f_best64);
				}
#endif
			}
			// Update row, col
			assert_lt(rowc, (int64_t)prob_.qrylen_);
			rowc++;
			colc--;
			curc++;
		} // for(size_t j = 0; j < breadth; j++)
		if(i == depth-1) {
			// Final iteration
			assert(last != NULL);
			assert_eq(1, neval);
			assert_neq(0, last->sc[3]);
			assert_eq(targ, last->sc[hef]);
		} else {
			breadth--;
			prev2 = prev1 + 1;
			prev1 = cur;
		}
	} // for(size_t i = 0; i < depth; i++)
	//
	// Now backtrack through the triangle.  Abort as soon as we enter a cell
	// that was visited by a previous backtrace.
	//
	int64_t rowc = row, colc = col;
	size_t curid;
	int hefc = hef;
	if(bs_.empty()) {
		// Start an initial branch
		CHECK_ROW_COL(rowc, colc);
		curid = bs_.alloc();
		assert_eq(0, curid);
		Edit e;
		bs_[curid].init(
			prob_,
			0,      // parent ID
			0,      // penalty
			0,      // score_en
			rowc,   // row
			colc,   // col
			e,      // edit
			0,      // hef
			true,   // I am the root
			false); // don't try to extend with exact matches
		bs_[curid].len_ = 0;
	} else {
		curid = bs_.size()-1;
	}
	size_t idx_orig = (row + col) >> prob_.cper_->perpow2();
	while(true) {
		// What depth are we?
		size_t mod = (rowc + colc) & prob_.cper_->lomask();
		assert_lt(mod, prob_.cper_->per());
		CpQuad * cur = tri_[mod].ptr();
		int64_t row_off = rowc - row_lo - mod;
		assert(!local || cur[row_off].sc[0] > 0);
		assert_geq(row_off, 0);
		int mask = cur[row_off].sc[3];
		assert_gt(mask, 0);
		int sel = -1;
		// Select what type of move to make, which depends on whether we're
		// currently in H, E, F:
		if(hefc == 0) {
			if(       (mask & 1) != 0) {
				// diagonal
				sel = 0;
			} else if((mask & 8) != 0) {
				// up to H
				sel = 3;
			} else if((mask & 16) != 0) {
				// up to F
				sel = 4;
			} else if((mask & 2) != 0) {
				// left to H
				sel = 1;
			} else if((mask & 4) != 0) {
				// left to E
				sel = 2;
			}
		} else if(hefc == 1) {
			if(       (mask & 32) != 0) {
				// left to H
				sel = 5;
			} else if((mask & 64) != 0) {
				// left to E
				sel = 6;
			}
		} else {
			assert_eq(2, hefc);
			if(       (mask & 128) != 0) {
				// up to H
				sel = 7;
			} else if((mask & 256) != 0) {
				// up to F
				sel = 8;
			}
		}
		assert_geq(sel, 0);
		// Get character from read
		int qc = prob_.qry_[rowc], qq = prob_.qual_[rowc];
		// Get character from reference
		int rc = prob_.ref_[colc];
		assert_range(0, 16, rc);
		// Now that we know what type of move to make, make it, updating our
		// row and column and moving updating the branch.
		if(sel == 0) {
			assert_geq(rowc, 0);
			assert_geq(colc, 0);
			TAlScore scd = prob_.sc_->score(qc, rc, qq - 33);
			if((rc & (1 << qc)) == 0) {
				// Mismatch
				size_t id = curid;
				// Check if the previous branch was the initial (bottommost)
				// branch with no matches.  If so, the mismatch should be added
				// to the initial branch, instead of starting a new branch.
				bool empty = (bs_[curid].len_ == 0 && curid == 0);
				if(!empty) {
					id = bs_.alloc();
				}
				Edit e((int)rowc, mask2dna[rc], "ACGTN"[qc], EDIT_TYPE_MM);
				assert_lt(scd, 0);
				TAlScore score_en = bs_[curid].score_st_ + scd;
				bs_[id].init(
					prob_,
					curid,    // parent ID
					-scd,     // penalty
					score_en, // score_en
					rowc,     // row
					colc,     // col
					e,        // edit
					hefc,     // hef
					empty,    // root?
					false);   // don't try to extend with exact matches
				//assert(!local || bs_[id].score_st_ >= 0);
				curid = id;
			} else {
				// Match
				bs_[curid].score_st_ += prob_.sc_->match();
				bs_[curid].len_++;
				assert_leq((int64_t)bs_[curid].len_, bs_[curid].row_ + 1);
			}
			rowc--;
			colc--;
			assert(local || bs_[curid].score_st_ >= targ_final);
			hefc = 0;
		} else if((sel >= 1 && sel <= 2) || (sel >= 5 && sel <= 6)) {
			assert_gt(colc, 0);
			// Read gap
			size_t id = bs_.alloc();
			Edit e((int)rowc+1, mask2dna[rc], '-', EDIT_TYPE_READ_GAP);
			TAlScore gapp = prob_.sc_->readGapOpen();
			if(bs_[curid].len_ == 0 && bs_[curid].e_.inited() && bs_[curid].e_.isReadGap()) {
				gapp = prob_.sc_->readGapExtend();
			}
			TAlScore score_en = bs_[curid].score_st_ - gapp;
			bs_[id].init(
				prob_,
				curid,    // parent ID
				gapp,     // penalty
				score_en, // score_en
				rowc,     // row
				colc-1,   // col
				e,        // edit
				hefc,     // hef
				false,    // root?
				false);   // don't try to extend with exact matches
			colc--;
			curid = id;
			assert( local || bs_[curid].score_st_ >= targ_final);
			//assert(!local || bs_[curid].score_st_ >= 0);
			if(sel == 1 || sel == 5) {
				hefc = 0;
			} else {
				hefc = 1;
			}
		} else {
			assert_gt(rowc, 0);
			// Reference gap
			size_t id = bs_.alloc();
			Edit e((int)rowc, '-', "ACGTN"[qc], EDIT_TYPE_REF_GAP);
			TAlScore gapp = prob_.sc_->refGapOpen();
			if(bs_[curid].len_ == 0 && bs_[curid].e_.inited() && bs_[curid].e_.isRefGap()) {
				gapp = prob_.sc_->refGapExtend();
			}
			TAlScore score_en = bs_[curid].score_st_ - gapp;
			bs_[id].init(
				prob_,
				curid,    // parent ID
				gapp,     // penalty
				score_en, // score_en
				rowc-1,   // row
				colc,     // col
				e,        // edit
				hefc,     // hef
				false,    // root?
				false);   // don't try to extend with exact matches
			rowc--;
			curid = id;
			//assert(!local || bs_[curid].score_st_ >= 0);
			if(sel == 3 || sel == 7) {
				hefc = 0;
			} else {
				hefc = 2;
			}
		}
		CHECK_ROW_COL(rowc, colc);
		size_t mod_new = (rowc + colc) & prob_.cper_->lomask();
		size_t idx = (rowc + colc) >> prob_.cper_->perpow2();
		assert_lt(mod_new, prob_.cper_->per());
		int64_t row_off_new = rowc - row_lo - mod_new;
		CpQuad * cur_new = NULL;
		if(colc >= 0 && rowc >= 0 && idx == idx_orig) {
			cur_new = tri_[mod_new].ptr();
		}
		bool hit_new_tri = (idx < idx_orig && colc >= 0 && rowc >= 0);
		// Check whether we made it to the top row or to a cell with score 0
		if(colc < 0 || rowc < 0 ||
		   (cur_new != NULL && (local && cur_new[row_off_new].sc[0] == 0)))
		{
			done = true;
			assert(bs_[curid].isSolution(prob_));
			addSolution(curid);
#ifndef NDEBUG
			// A check to see if any two adjacent branches in the backtrace
			// overlap.  If they do, the whole alignment will be filtered out
			// in trySolution(...)
			size_t cur = curid;
			if(!bs_[cur].root_) {
				size_t next = bs_[cur].parentId_;
				while(!bs_[next].root_) {
					assert_neq(cur, next);
					if(bs_[next].len_ != 0 || bs_[cur].len_ == 0) {
						assert(!bs_[cur].overlap(prob_, bs_[next]));
					}
					cur = next;
					next = bs_[cur].parentId_;
				}
			}
#endif
			return;
		}
		if(hit_new_tri) {
			assert(rowc < 0 || colc < 0 || prob_.cper_->isCheckpointed(rowc, colc));
			row_new = rowc; col_new = colc;
			hef_new = hefc;
			done = false;
			if(rowc < 0 || colc < 0) {
				assert(local);
				targ_new = 0;
			} else {
				targ_new = prob_.cper_->scoreTriangle(rowc, colc, hefc);
			}
			if(local && targ_new == 0) {
				done = true;
				assert(bs_[curid].isSolution(prob_));
				addSolution(curid);
			}
			assert((row_new >= 0 && col_new >= 0) || done);
			return;
		}
	}
	assert(false);
}

#ifndef NDEBUG
#define DEBUG_CHECK(ss, row, col, hef) { \
	if(prob_.cper_->debug() && row >= 0 && col >= 0) { \
		TAlScore s = ss; \
		if(s == MIN_I16) s = MIN_I64; \
		if(local && s < 0) s = 0; \
		TAlScore deb = prob_.cper_->debugCell(row, col, hef); \
		if(local && deb < 0) deb = 0; \
		assert_eq(s, deb); \
	} \
}
#else
#define DEBUG_CHECK(ss, row, col, hef)
#endif


/**
 * Fill in a square of the DP table and backtrace from the given cell to
 * a cell in the previous checkpoint, or to the terminal cell.
 */
void BtBranchTracer::squareFill(
	int64_t rw,          // row of cell to backtrace from
	int64_t cl,          // column of cell to backtrace from
	int hef,             // cell to backtrace from is H (0), E (1), or F (2)
	TAlScore targ,       // score of cell to backtrace from
	TAlScore targ_final, // score of alignment we're looking for
	RandomSource& rnd,   // pseudo-random generator
	int64_t& row_new,    // out: row we ended up in after backtrace
	int64_t& col_new,    // out: column we ended up in after backtrace
	int& hef_new,        // out: H/E/F after backtrace
	TAlScore& targ_new,  // out: score up to cell we ended up in
	bool& done,          // out: finished tracing out an alignment?
	bool& abort)         // out: aborted b/c cell was seen before?
{
	assert_geq(rw, 0);
	assert_geq(cl, 0);
	assert_range(0, 2, hef);
	assert_lt(rw, (int64_t)prob_.qrylen_);
	assert_lt(cl, (int64_t)prob_.reflen_);
	assert(prob_.usecp_ && prob_.fill_);
	const bool is8_ = prob_.cper_->is8_;
	int64_t row = rw, col = cl;
	assert_leq(prob_.reflen_, (TRefOff)sawcell_.size());
	assert_leq(col, (int64_t)prob_.cper_->hicol());
	assert_geq(col, (int64_t)prob_.cper_->locol());
	assert_geq(prob_.cper_->per(), 2);
	size_t xmod = col & prob_.cper_->lomask();
	size_t ymod = row & prob_.cper_->lomask();
	size_t xdiv = col >> prob_.cper_->perpow2();
	size_t ydiv = row >> prob_.cper_->perpow2();
	size_t sq_ncol = xmod+1, sq_nrow = ymod+1;
	sq_.resize(sq_ncol * sq_nrow);
	bool upper = ydiv == 0;
	bool left  = xdiv == 0;
	const TAlScore sc_rdo = prob_.sc_->readGapOpen();
	const TAlScore sc_rde = prob_.sc_->readGapExtend();
	const TAlScore sc_rfo = prob_.sc_->refGapOpen();
	const TAlScore sc_rfe = prob_.sc_->refGapExtend();
	const bool local = !prob_.sc_->monotone;
	const CpQuad *qup = NULL;
	const __m128i *qlf = NULL;
	size_t per = prob_.cper_->per_;
	ASSERT_ONLY(size_t nrow = prob_.cper_->nrow());
	size_t ncol = prob_.cper_->ncol();
	assert_eq(prob_.qrylen_, nrow);
	assert_eq(prob_.reflen_, (TRefOff)ncol);
	size_t niter = prob_.cper_->niter_;
	if(!upper) {
		qup = prob_.cper_->qrows_.ptr() + (ncol * (ydiv-1)) + xdiv * per;
	}
	if(!left) {
		// Set up the column pointers to point to the first __m128i word in the
		// relevant column
		size_t off = (niter << 2) * (xdiv-1);
		qlf = prob_.cper_->qcols_.ptr() + off;
	}
	size_t xedge = xdiv * per; // absolute offset of leftmost cell in square
	size_t yedge = ydiv * per; // absolute offset of topmost cell in square
	size_t xi = xedge, yi = yedge; // iterators for columns, rows
	size_t ii = 0; // iterator into packed square
	// Iterate over rows, then over columns
	size_t m128mod = yi % prob_.cper_->niter_;
	size_t m128div = yi / prob_.cper_->niter_;
	int16_t sc_h_dg_lastrow = MIN_I16;
	for(size_t i = 0; i <= ymod; i++, yi++) {
		assert_lt(yi, nrow);
 		xi = xedge;
		// Handling for first column is done outside the loop
		size_t fromend = prob_.qrylen_ - yi - 1;
		bool allowGaps = fromend >= (size_t)prob_.sc_->gapbar && yi >= (size_t)prob_.sc_->gapbar;
		// Get character, quality from read
		int qc = prob_.qry_[yi], qq = prob_.qual_[yi];
		assert_geq(qq, 33);
		int16_t sc_h_lf_last = MIN_I16;
		int16_t sc_e_lf_last = MIN_I16;
		for(size_t j = 0; j <= xmod; j++, xi++) {
			assert_lt(xi, ncol);
			// Get character from reference
			int rc = prob_.ref_[xi];
			assert_range(0, 16, rc);
			int16_t sc_diag = prob_.sc_->score(qc, rc, qq - 33);
			int16_t sc_h_up = MIN_I16, sc_f_up = MIN_I16,
			        sc_h_lf = MIN_I16, sc_e_lf = MIN_I16,
					sc_h_dg = MIN_I16;
			int16_t sc_h_up_c = MIN_I16, sc_f_up_c = MIN_I16,
			        sc_h_lf_c = MIN_I16, sc_e_lf_c = MIN_I16,
					sc_h_dg_c = MIN_I16;
			if(yi == 0) {
				// If I'm in the first first row or column set it to 0
				sc_h_dg = 0;
			} else if(xi == 0) {
				// Do nothing; leave it at min
				if(local) {
					sc_h_dg = 0;
				}
			} else if(i == 0 && j == 0) {
				// Otherwise, if I'm in the upper-left square corner, I can get
				// it from the checkpoint 
				sc_h_dg = qup[-1].sc[0];
			} else if(j == 0) {
				// Otherwise, if I'm in the leftmost cell of this row, I can
				// get it from sc_h_lf in first column of previous row
				sc_h_dg = sc_h_dg_lastrow;
			} else {
				// Otherwise, I can get it from qup
				sc_h_dg = qup[j-1].sc[0];
			}
			if(yi > 0 && xi > 0) DEBUG_CHECK(sc_h_dg, yi-1, xi-1, 2);
			
			// If we're in the leftmost column, calculate sc_h_lf regardless of
			// allowGaps.
			if(j == 0 && xi > 0) {
				// Get values for left neighbors from the checkpoint
				if(is8_) {
					size_t vecoff = (m128mod << 6) + m128div;
					sc_e_lf = ((uint8_t*)(qlf + 0))[vecoff];
					sc_h_lf = ((uint8_t*)(qlf + 2))[vecoff];
					if(local) {
						// No adjustment
					} else {
						if(sc_h_lf == 0) sc_h_lf = MIN_I16;
						else sc_h_lf -= 0xff;
						if(sc_e_lf == 0) sc_e_lf = MIN_I16;
						else sc_e_lf -= 0xff;
					}
				} else {
					size_t vecoff = (m128mod << 5) + m128div;
					sc_e_lf = ((int16_t*)(qlf + 0))[vecoff];
					sc_h_lf = ((int16_t*)(qlf + 2))[vecoff];
					if(local) {
						sc_h_lf += 0x8000; assert_geq(sc_h_lf, 0);
						sc_e_lf += 0x8000; assert_geq(sc_e_lf, 0);
					} else {
						if(sc_h_lf != MIN_I16) sc_h_lf -= 0x7fff;
						if(sc_e_lf != MIN_I16) sc_e_lf -= 0x7fff;
					}
				}
				DEBUG_CHECK(sc_e_lf, yi, xi-1, 0);
				DEBUG_CHECK(sc_h_lf, yi, xi-1, 2);
				sc_h_dg_lastrow = sc_h_lf;
			}
			
			if(allowGaps) {
				if(j == 0 /* at left edge */ && xi > 0 /* not extreme */) {
					sc_h_lf_c = sc_h_lf;
					sc_e_lf_c = sc_e_lf;
					if(sc_h_lf_c != MIN_I16) sc_h_lf_c -= sc_rdo;
					if(sc_e_lf_c != MIN_I16) sc_e_lf_c -= sc_rde;
					assert_leq(sc_h_lf_c, prob_.cper_->perf_);
					assert_leq(sc_e_lf_c, prob_.cper_->perf_);
				} else if(xi > 0) {
					// Get values for left neighbors from the previous iteration
					if(sc_h_lf_last != MIN_I16) {
						sc_h_lf = sc_h_lf_last;
						sc_h_lf_c = sc_h_lf - sc_rdo;
					}
					if(sc_e_lf_last != MIN_I16) {
						sc_e_lf = sc_e_lf_last;
						sc_e_lf_c = sc_e_lf - sc_rde;
					}
				}
				if(yi > 0 /* not extreme */) {
					// Get column values
					assert(qup != NULL);
					assert(local || qup[j].sc[2] < 0);
					if(qup[j].sc[0] > MIN_I16) {
						DEBUG_CHECK(qup[j].sc[0], yi-1, xi, 2);
						sc_h_up = qup[j].sc[0];
						sc_h_up_c = sc_h_up - sc_rfo;
					}
					if(qup[j].sc[2] > MIN_I16) {
						DEBUG_CHECK(qup[j].sc[2], yi-1, xi, 1);
						sc_f_up = qup[j].sc[2];
						sc_f_up_c = sc_f_up - sc_rfe;
					}
				}
				if(local) {
					sc_h_up_c = max<int16_t>(sc_h_up_c, 0);
					sc_f_up_c = max<int16_t>(sc_f_up_c, 0);
					sc_h_lf_c = max<int16_t>(sc_h_lf_c, 0);
					sc_e_lf_c = max<int16_t>(sc_e_lf_c, 0);
				}
			}
			
			if(sc_h_dg > MIN_I16) {
				sc_h_dg_c = sc_h_dg + sc_diag;
			}
			if(local) sc_h_dg_c = max<int16_t>(sc_h_dg_c, 0);
			
			int mask = 0;
			// Calculate best ways into H, E, F cells starting with H.
			// Mask bits:
			// H: 1=diag, 2=hhoriz, 4=ehoriz, 8=hvert, 16=fvert
			// E: 32=hhoriz, 64=ehoriz
			// F: 128=hvert, 256=fvert
			int16_t sc_best = sc_h_dg_c;
			if(sc_h_dg_c > MIN_I64) {
				mask = 1;
			}
			if(xi > 0 && sc_h_lf_c >= sc_best && sc_h_lf_c > MIN_I64) {
				if(sc_h_lf_c > sc_best) mask = 0;
				mask |= 2;
				sc_best = sc_h_lf_c;
			}
			if(xi > 0 && sc_e_lf_c >= sc_best && sc_e_lf_c > MIN_I64) {
				if(sc_e_lf_c > sc_best) mask = 0;
				mask |= 4;
				sc_best = sc_e_lf_c;
			}
			if(yi > 0 && sc_h_up_c >= sc_best && sc_h_up_c > MIN_I64) {
				if(sc_h_up_c > sc_best) mask = 0;
				mask |= 8;
				sc_best = sc_h_up_c;
			}
			if(yi > 0 && sc_f_up_c >= sc_best && sc_f_up_c > MIN_I64) {
				if(sc_f_up_c > sc_best) mask = 0;
				mask |= 16;
				sc_best = sc_f_up_c;
			}
			// Calculate best way into E cell
			int16_t sc_e_best = sc_h_lf_c;
			if(xi > 0) {
				if(sc_h_lf_c >= sc_e_lf_c && sc_h_lf_c > MIN_I64) {
					if(sc_h_lf_c == sc_e_lf_c) {
						mask |= 64;
					}
					mask |= 32;
				} else if(sc_e_lf_c > MIN_I64) {
					sc_e_best = sc_e_lf_c;
					mask |= 64;
				}
			}
			if(sc_e_best > sc_best) {
				sc_best = sc_e_best;
				mask &= ~31; // don't go diagonal
			}
			// Calculate best way into F cell
			int16_t sc_f_best = sc_h_up_c;
			if(yi > 0) {
				if(sc_h_up_c >= sc_f_up_c && sc_h_up_c > MIN_I64) {
					if(sc_h_up_c == sc_f_up_c) {
						mask |= 256;
					}
					mask |= 128;
				} else if(sc_f_up_c > MIN_I64) {
					sc_f_best = sc_f_up_c;
					mask |= 256;
				}
			}
			if(sc_f_best > sc_best) {
				sc_best = sc_f_best;
				mask &= ~127; // don't go horizontal or diagonal
			}
			// Install results in cur
			assert( local || sc_best <= 0);
			sq_[ii+j].sc[0] = sc_best;
			assert( local || sc_e_best < 0);
			assert( local || sc_f_best < 0);
			assert(!local || sc_e_best >= 0 || sc_e_best == MIN_I16);
			assert(!local || sc_f_best >= 0 || sc_f_best == MIN_I16);
			sq_[ii+j].sc[1] = sc_e_best;
			sq_[ii+j].sc[2] = sc_f_best;
			sq_[ii+j].sc[3] = mask;
			DEBUG_CHECK(sq_[ii+j].sc[0], yi, xi, 2); // H
			DEBUG_CHECK(sq_[ii+j].sc[1], yi, xi, 0); // E
			DEBUG_CHECK(sq_[ii+j].sc[2], yi, xi, 1); // F
			// Update sc_h_lf_last, sc_e_lf_last
			sc_h_lf_last = sc_best;
			sc_e_lf_last = sc_e_best;
		}
		// Update m128mod, m128div
		m128mod++;
		if(m128mod == prob_.cper_->niter_) {
			m128mod = 0;
			m128div++;
		}
		// update qup
		ii += sq_ncol;
		// dimensions of sq_
		qup = sq_.ptr() + sq_ncol * i;
	}
	assert_eq(targ, sq_[ymod * sq_ncol + xmod].sc[hef]);
	//
	// Now backtrack through the triangle.  Abort as soon as we enter a cell
	// that was visited by a previous backtrace.
	//
	int64_t rowc = row, colc = col;
	size_t curid;
	int hefc = hef;
	if(bs_.empty()) {
		// Start an initial branch
		CHECK_ROW_COL(rowc, colc);
		curid = bs_.alloc();
		assert_eq(0, curid);
		Edit e;
		bs_[curid].init(
			prob_,
			0,      // parent ID
			0,      // penalty
			0,      // score_en
			rowc,   // row
			colc,   // col
			e,      // edit
			0,      // hef
			true,   // root?
			false); // don't try to extend with exact matches
		bs_[curid].len_ = 0;
	} else {
		curid = bs_.size()-1;
	}
	size_t ymodTimesNcol = ymod * sq_ncol;
	while(true) {
		// What depth are we?
		assert_eq(ymodTimesNcol, ymod * sq_ncol);
		CpQuad * cur = sq_.ptr() + ymodTimesNcol + xmod;
		int mask = cur->sc[3];
		assert_gt(mask, 0);
		int sel = -1;
		// Select what type of move to make, which depends on whether we're
		// currently in H, E, F:
		if(hefc == 0) {
			if(       (mask & 1) != 0) {
				// diagonal
				sel = 0;
			} else if((mask & 8) != 0) {
				// up to H
				sel = 3;
			} else if((mask & 16) != 0) {
				// up to F
				sel = 4;
			} else if((mask & 2) != 0) {
				// left to H
				sel = 1;
			} else if((mask & 4) != 0) {
				// left to E
				sel = 2;
			}
		} else if(hefc == 1) {
			if(       (mask & 32) != 0) {
				// left to H
				sel = 5;
			} else if((mask & 64) != 0) {
				// left to E
				sel = 6;
			}
		} else {
			assert_eq(2, hefc);
			if(       (mask & 128) != 0) {
				// up to H
				sel = 7;
			} else if((mask & 256) != 0) {
				// up to F
				sel = 8;
			}
		}
		assert_geq(sel, 0);
		// Get character from read
		int qc = prob_.qry_[rowc], qq = prob_.qual_[rowc];
		// Get character from reference
		int rc = prob_.ref_[colc];
		assert_range(0, 16, rc);
		bool xexit = false, yexit = false;
		// Now that we know what type of move to make, make it, updating our
		// row and column and moving updating the branch.
		if(sel == 0) {
			assert_geq(rowc, 0);
			assert_geq(colc, 0);
			TAlScore scd = prob_.sc_->score(qc, rc, qq - 33);
			if((rc & (1 << qc)) == 0) {
				// Mismatch
				size_t id = curid;
				// Check if the previous branch was the initial (bottommost)
				// branch with no matches.  If so, the mismatch should be added
				// to the initial branch, instead of starting a new branch.
				bool empty = (bs_[curid].len_ == 0 && curid == 0);
				if(!empty) {
					id = bs_.alloc();
				}
				Edit e((int)rowc, mask2dna[rc], "ACGTN"[qc], EDIT_TYPE_MM);
				assert_lt(scd, 0);
				TAlScore score_en = bs_[curid].score_st_ + scd;
				bs_[id].init(
					prob_,
					curid,    // parent ID
					-scd,     // penalty
					score_en, // score_en
					rowc,     // row
					colc,     // col
					e,        // edit
					hefc,     // hef
					empty,    // root?
					false);   // don't try to extend with exact matches
				curid = id;
				//assert(!local || bs_[curid].score_st_ >= 0);
			} else {
				// Match
				bs_[curid].score_st_ += prob_.sc_->match();
				bs_[curid].len_++;
				assert_leq((int64_t)bs_[curid].len_, bs_[curid].row_ + 1);
			}
			if(xmod == 0) xexit = true;
			if(ymod == 0) yexit = true;
			rowc--; ymod--; ymodTimesNcol -= sq_ncol;
			colc--; xmod--;
			assert(local || bs_[curid].score_st_ >= targ_final);
			hefc = 0;
		} else if((sel >= 1 && sel <= 2) || (sel >= 5 && sel <= 6)) {
			assert_gt(colc, 0);
			// Read gap
			size_t id = bs_.alloc();
			Edit e((int)rowc+1, mask2dna[rc], '-', EDIT_TYPE_READ_GAP);
			TAlScore gapp = prob_.sc_->readGapOpen();
			if(bs_[curid].len_ == 0 && bs_[curid].e_.inited() && bs_[curid].e_.isReadGap()) {
				gapp = prob_.sc_->readGapExtend();
			}
			//assert(!local || bs_[curid].score_st_ >= gapp);
			TAlScore score_en = bs_[curid].score_st_ - gapp;
			bs_[id].init(
				prob_,
				curid,    // parent ID
				gapp,     // penalty
				score_en, // score_en
				rowc,     // row
				colc-1,   // col
				e,        // edit
				hefc,     // hef
				false,    // root?
				false);   // don't try to extend with exact matches
			if(xmod == 0) xexit = true;
			colc--; xmod--;
			curid = id;
			assert( local || bs_[curid].score_st_ >= targ_final);
			//assert(!local || bs_[curid].score_st_ >= 0);
			if(sel == 1 || sel == 5) {
				hefc = 0;
			} else {
				hefc = 1;
			}
		} else {
			assert_gt(rowc, 0);
			// Reference gap
			size_t id = bs_.alloc();
			Edit e((int)rowc, '-', "ACGTN"[qc], EDIT_TYPE_REF_GAP);
			TAlScore gapp = prob_.sc_->refGapOpen();
			if(bs_[curid].len_ == 0 && bs_[curid].e_.inited() && bs_[curid].e_.isRefGap()) {
				gapp = prob_.sc_->refGapExtend();
			}
			//assert(!local || bs_[curid].score_st_ >= gapp);
			TAlScore score_en = bs_[curid].score_st_ - gapp;
			bs_[id].init(
				prob_,
				curid,    // parent ID
				gapp,     // penalty
				score_en, // score_en
				rowc-1,   // row
				colc,     // col
				e,        // edit
				hefc,     // hef
				false,    // root?
				false);   // don't try to extend with exact matches
			if(ymod == 0) yexit = true;
			rowc--; ymod--; ymodTimesNcol -= sq_ncol;
			curid = id;
			assert( local || bs_[curid].score_st_ >= targ_final);
			//assert(!local || bs_[curid].score_st_ >= 0);
			if(sel == 3 || sel == 7) {
				hefc = 0;
			} else {
				hefc = 2;
			}
		}
		CHECK_ROW_COL(rowc, colc);
		CpQuad * cur_new = NULL;
		if(!xexit && !yexit) {
			cur_new = sq_.ptr() + ymodTimesNcol + xmod;
		}
		// Check whether we made it to the top row or to a cell with score 0
		if(colc < 0 || rowc < 0 ||
		   (cur_new != NULL && local && cur_new->sc[0] == 0))
		{
			done = true;
			assert(bs_[curid].isSolution(prob_));
			addSolution(curid);
#ifndef NDEBUG
			// A check to see if any two adjacent branches in the backtrace
			// overlap.  If they do, the whole alignment will be filtered out
			// in trySolution(...)
			size_t cur = curid;
			if(!bs_[cur].root_) {
				size_t next = bs_[cur].parentId_;
				while(!bs_[next].root_) {
					assert_neq(cur, next);
					if(bs_[next].len_ != 0 || bs_[cur].len_ == 0) {
						assert(!bs_[cur].overlap(prob_, bs_[next]));
					}
					cur = next;
					next = bs_[cur].parentId_;
				}
			}
#endif
			return;
		}
		assert(!xexit || hefc == 0 || hefc == 1);
		assert(!yexit || hefc == 0 || hefc == 2);
		if(xexit || yexit) {
			//assert(rowc < 0 || colc < 0 || prob_.cper_->isCheckpointed(rowc, colc));
			row_new = rowc; col_new = colc;
			hef_new = hefc;
			done = false;
			if(rowc < 0 || colc < 0) {
				assert(local);
				targ_new = 0;
			} else {
				// TODO: Don't use scoreSquare
				targ_new = prob_.cper_->scoreSquare(rowc, colc, hefc);
				assert(local || targ_new >= targ);
				assert(local || targ_new >= targ_final);
			}
			if(local && targ_new == 0) {
				assert_eq(0, hefc);
				done = true;
				assert(bs_[curid].isSolution(prob_));
				addSolution(curid);
			}
			assert((row_new >= 0 && col_new >= 0) || done);
			return;
		}
	}
	assert(false);
}

/**
 * Caller gives us score_en, row and col.  We figure out score_st and len_
 * by comparing characters from the strings.
 *
 * If this branch comes after a mismatch, (row, col) describe the cell that the
 * mismatch occurs in.  len_ is initially set to 1, and the next cell we test
 * is the next cell up and to the left (row-1, col-1).
 *
 * If this branch comes after a read gap, (row, col) describe the leftmost cell
 * involved in the gap.  len_ is initially set to 0, and the next cell we test
 * is the current cell (row, col).
 *
 * If this branch comes after a reference gap, (row, col) describe the upper
 * cell involved in the gap.  len_ is initially set to 0, and the next cell we
 * test is the current cell (row, col).
 */
void BtBranch::init(
	const BtBranchProblem& prob,
	size_t parentId,
	TAlScore penalty,
	TAlScore score_en,
	int64_t row,
	int64_t col,
	Edit e,
	int hef,
	bool root,
	bool extend)
{
	score_en_ = score_en;
	penalty_ = penalty;
	score_st_ = score_en_;
	row_ = row;
	col_ = col;
	parentId_ = parentId;
	e_ = e;
	root_ = root;
	assert(!root_ || parentId == 0);
	assert_lt(row, (int64_t)prob.qrylen_);
	assert_lt(col, (int64_t)prob.reflen_);
	// First match to check is diagonally above and to the left of the cell
	// where the edit occurs
	int64_t rowc = row;
	int64_t colc = col;
	len_ = 0;
	if(e.inited() && e.isMismatch()) {
		rowc--; colc--;
		len_ = 1;
	}
	int64_t match = prob.sc_->match();
	bool cp = prob.usecp_;
	size_t iters = 0;
	curtailed_ = false;
	if(extend) {
		while(rowc >= 0 && colc >= 0) {
			int rfm = prob.ref_[colc];
			assert_range(0, 16, rfm);
			int rdc = prob.qry_[rowc];
			bool matches = (rfm & (1 << rdc)) != 0;
			if(!matches) {
				// What's the mismatch penalty?
				break;
			}
			// Get score from checkpointer
			score_st_ += match;
			if(cp && rowc - 1 >= 0 && colc - 1 >= 0 &&
			   prob.cper_->isCheckpointed(rowc - 1, colc - 1))
			{
				// Possibly prune
				int16_t cpsc;
				cpsc = prob.cper_->scoreTriangle(rowc - 1, colc - 1, hef);
				if(cpsc + score_st_ < prob.targ_) {
					curtailed_ = true;
					break;
				}
			}
			iters++;
			rowc--; colc--;
		}
	}
	assert_geq(rowc, -1);
	assert_geq(colc, -1);
	len_ = (int64_t)row - rowc;
	assert_leq((int64_t)len_, row_+1);
	assert_leq((int64_t)len_, col_+1);
	assert_leq((int64_t)score_st_, (int64_t)prob.qrylen_ * match);
}

/**
 * Given a potential branch to add to the queue, see if we can follow the
 * branch a little further first.  If it's still valid, or if we reach a
 * choice between valid outgoing paths, go ahead and add it to the queue.
 */
void BtBranchTracer::examineBranch(
	int64_t row,
	int64_t col,
	const Edit& e,
	TAlScore pen,  // penalty associated with edit
	TAlScore sc,
	size_t parentId)
{
	size_t id = bs_.alloc();
	bs_[id].init(prob_, parentId, pen, sc, row, col, e, 0, false, true);
	if(bs_[id].isSolution(prob_)) {
		assert(bs_[id].isValid(prob_));
		addSolution(id);
	} else {
		// Check if this branch is legit
		if(bs_[id].isValid(prob_)) {
			add(id);
		} else {
			bs_.pop();
		}
	}
}

/**
 * Take all possible ways of leaving the given branch and add them to the
 * branch queue.
 */
void BtBranchTracer::addOffshoots(size_t bid) {
	BtBranch& b = bs_[bid];
	TAlScore sc = b.score_en_;
	int64_t match = prob_.sc_->match();
	int64_t scoreFloor = prob_.sc_->monotone ? MIN_I64 : 0;
	bool cp = prob_.usecp_; // Are there are any checkpoints?
	ASSERT_ONLY(TAlScore perfectScore = prob_.sc_->perfectScore(prob_.qrylen_));
	assert_leq(prob_.targ_, perfectScore);
	// For each cell in the branch
	for(size_t i = 0 ; i < b.len_; i++) {
		assert_leq((int64_t)i, b.row_+1);
		assert_leq((int64_t)i, b.col_+1);
		int64_t row = b.row_ - i, col = b.col_ - i;
		int64_t bonusLeft = (row + 1) * match;
		int64_t fromend = prob_.qrylen_ - row - 1;
		bool allowGaps = fromend >= prob_.sc_->gapbar && row >= prob_.sc_->gapbar;
		if(allowGaps && row >= 0 && col >= 0) {
			if(col > 0) {
				// Try a read gap - it's either an extension or an open
				bool extend = b.e_.inited() && b.e_.isReadGap() && i == 0;
				TAlScore rdgapPen = extend ?
					prob_.sc_->readGapExtend() : prob_.sc_->readGapOpen();
				bool prune = false;
				assert_gt(rdgapPen, 0);
				if(cp && prob_.cper_->isCheckpointed(row, col - 1)) {
					// Possibly prune
					int16_t cpsc = (int16_t)prob_.cper_->scoreTriangle(row, col - 1, 0);
					assert_leq(cpsc, perfectScore);
					assert_geq(prob_.sc_->readGapOpen(), prob_.sc_->readGapExtend());
					TAlScore bonus = prob_.sc_->readGapOpen() - prob_.sc_->readGapExtend();
					assert_geq(bonus, 0);
					if(cpsc + bonus + sc - rdgapPen < prob_.targ_) {
						prune = true;
					}
				}
				if(prune) {
					if(extend) { nrdexPrune_++; } else { nrdopPrune_++; }
				} else if(sc - rdgapPen >= scoreFloor && sc - rdgapPen + bonusLeft >= prob_.targ_) {
					// Yes, we can introduce a read gap here
					Edit e((int)row + 1, mask2dna[(int)prob_.ref_[col]], '-', EDIT_TYPE_READ_GAP);
					assert(e.isReadGap());
					examineBranch(row, col - 1, e, rdgapPen, sc - rdgapPen, bid);
					if(extend) { nrdex_++; } else { nrdop_++; }
				}
			}
			if(row > 0) {
				// Try a reference gap - it's either an extension or an open
				bool extend = b.e_.inited() && b.e_.isRefGap() && i == 0;
				TAlScore rfgapPen = (b.e_.inited() && b.e_.isRefGap()) ?
					prob_.sc_->refGapExtend() : prob_.sc_->refGapOpen();
				bool prune = false;
				assert_gt(rfgapPen, 0);
				if(cp && prob_.cper_->isCheckpointed(row - 1, col)) {
					// Possibly prune
					int16_t cpsc = (int16_t)prob_.cper_->scoreTriangle(row - 1, col, 0);
					assert_leq(cpsc, perfectScore);
					assert_geq(prob_.sc_->refGapOpen(), prob_.sc_->refGapExtend());
					TAlScore bonus = prob_.sc_->refGapOpen() - prob_.sc_->refGapExtend();
					assert_geq(bonus, 0);
					if(cpsc + bonus + sc - rfgapPen < prob_.targ_) {
						prune = true;
					}
				}
				if(prune) {
					if(extend) { nrfexPrune_++; } else { nrfopPrune_++; }
				} else if(sc - rfgapPen >= scoreFloor && sc - rfgapPen + bonusLeft >= prob_.targ_) {
					// Yes, we can introduce a ref gap here
					Edit e((int)row, '-', "ACGTN"[(int)prob_.qry_[row]], EDIT_TYPE_REF_GAP);
					assert(e.isRefGap());
					examineBranch(row - 1, col, e, rfgapPen, sc - rfgapPen, bid);
					if(extend) { nrfex_++; } else { nrfop_++; }
				}
			}
		}
		// If we're at the top of the branch but not yet at the top of
		// the DP table, a mismatch branch is also possible.
		if(i == b.len_ && !b.curtailed_ && row >= 0 && col >= 0) {
			int rfm = prob_.ref_[col];
			assert_lt(row, (int64_t)prob_.qrylen_);
			int rdc = prob_.qry_[row];
			int rdq = prob_.qual_[row];
			int scdiff = prob_.sc_->score(rdc, rfm, rdq - 33);
			assert_lt(scdiff, 0); // at end of branch, so can't match
			bool prune = false;
			if(cp && row > 0 && col > 0 && prob_.cper_->isCheckpointed(row - 1, col - 1)) {
				// Possibly prune
				int16_t cpsc = prob_.cper_->scoreTriangle(row - 1, col - 1, 0);
				assert_leq(cpsc, perfectScore);
				assert_leq(cpsc + scdiff + sc, perfectScore);
				if(cpsc + scdiff + sc < prob_.targ_) {
					prune = true;
				}
			}
			if(prune) {
				nmm_++;
			} else  {
				// Yes, we can introduce a mismatch here
				if(sc + scdiff >= scoreFloor && sc + scdiff + bonusLeft >= prob_.targ_) {
					Edit e((int)row, mask2dna[rfm], "ACGTN"[rdc], EDIT_TYPE_MM);
					bool nmm = (mask2dna[rfm] == 'N' || rdc > 4);
					assert_neq(e.chr, e.qchr);
					assert_lt(scdiff, 0);
					examineBranch(row - 1, col - 1, e, -scdiff, sc + scdiff, bid);
					if(nmm) { nnmm_++; } else { nmm_++; }
				}
			}
		}
		sc += match;
	}
}

/**
 * Sort unsorted branches, merge them with master sorted list.
 */
void BtBranchTracer::flushUnsorted() {
	if(unsorted_.empty()) {
		return;
	}
	unsorted_.sort();
	unsorted_.reverse();
#ifndef NDEBUG
	for(size_t i = 1; i < unsorted_.size(); i++) {
		assert_leq(bs_[unsorted_[i].second].score_st_, bs_[unsorted_[i-1].second].score_st_);
	}
#endif
	EList<size_t> *src2 = sortedSel_ ? &sorted1_ : &sorted2_;
	EList<size_t> *dest = sortedSel_ ? &sorted2_ : &sorted1_;
	// Merge src1 and src2 into dest
	dest->clear();
	size_t cur1 = 0, cur2 = cur_;
	while(cur1 < unsorted_.size() || cur2 < src2->size()) {
		// Take from 1 or 2 next?
		bool take1 = true;
		if(cur1 == unsorted_.size()) {
			take1 = false;
		} else if(cur2 == src2->size()) {
			take1 = true;
		} else {
			assert_neq(unsorted_[cur1].second, (*src2)[cur2]);
			take1 = bs_[unsorted_[cur1].second] < bs_[(*src2)[cur2]];
		}
		if(take1) {
			dest->push_back(unsorted_[cur1++].second); // Take from list 1
		} else {
			dest->push_back((*src2)[cur2++]); // Take from list 2
		}
	}
	assert_eq(cur1, unsorted_.size());
	assert_eq(cur2, src2->size());
	sortedSel_ = !sortedSel_;
	cur_ = 0;
	unsorted_.clear();
}

/**
 * Try all the solutions accumulated so far.  Solutions might be rejected
 * if they, for instance, overlap a previous solution, have too many Ns,
 * fail to overlap a core diagonal, etc.
 */
bool BtBranchTracer::trySolutions(
	bool lookForOlap,
	SwResult& res,
	size_t& off,
	size_t& nrej,
	RandomSource& rnd,
	bool& success)
{
	if(solutions_.size() > 0) {
		for(size_t i = 0; i < solutions_.size(); i++) {
			int ret = trySolution(solutions_[i], lookForOlap, res, off, nrej, rnd);
			if(ret == BT_FOUND) {
				success = true;
				return true; // there were solutions and one was good
			}
		}
		solutions_.clear();
		success = false;
		return true; // there were solutions but none were good
	}
	return false; // there were no solutions to check
}

/**
 * Given the id of a branch that completes a successful backtrace, turn the
 * chain of branches into 
 */
int BtBranchTracer::trySolution(
	size_t id,
	bool lookForOlap,
	SwResult& res,
	size_t& off,
	size_t& nrej,
	RandomSource& rnd)
{
#if 0
	AlnScore score;
	BtBranch *br = &bs_[id];
	// 'br' corresponds to the leftmost edit in a right-to-left
	// chain of edits.  
	EList<Edit>& ned = res.alres.ned();
	const BtBranch *cur = br, *prev = NULL;
	size_t ns = 0, nrefns = 0;
	size_t ngap = 0;
	while(true) {
		if(cur->e_.inited()) {
			if(cur->e_.isMismatch()) {
				if(cur->e_.qchr == 'N' || cur->e_.chr == 'N') {
					ns++;
				}
			} else if(cur->e_.isGap()) {
				ngap++;
			}
			if(cur->e_.chr == 'N') {
				nrefns++;
			}
			ned.push_back(cur->e_);
		}
		if(cur->root_) {
			break;
		}
		cur = &bs_[cur->parentId_];
	}
	if(ns > prob_.nceil_) {
		// Alignment has too many Ns in it!
		res.reset();
		assert(res.alres.ned().empty());
		nrej++;
		return BT_REJECTED_N;
	}
	// Update 'seenPaths_'
	cur = br;
	bool rejSeen = false; // set =true if we overlap prev path
	bool rejCore = true; // set =true if we don't touch core diag
	while(true) {
		// Consider row, col, len, then do something
		int64_t row = cur->row_, col = cur->col_;
		assert_lt(row, (int64_t)prob_.qrylen_);
		size_t fromend = prob_.qrylen_ - row - 1;
		size_t diag = fromend + col;
		// Calculate the diagonal within the *trimmed* rectangle,
		// i.e. the rectangle we dealt with in align, gather and
		// backtrack.
		int64_t diagi = col - row;
		// Now adjust to the diagonal within the *untrimmed*
		// rectangle by adding on the amount trimmed from the left.
		diagi += prob_.rect_->triml;
		assert_lt(diag, seenPaths_.size());
		// Does it overlap a core diagonal?
		if(diagi >= 0) {
			size_t diag = (size_t)diagi;
			if(diag >= prob_.rect_->corel &&
			   diag <= prob_.rect_->corer)
			{
				// Yes it does - it's OK
				rejCore = false;
			}
		}
		if(lookForOlap) {
			int64_t newlo, newhi;
			if(cur->len_ == 0) {
				if(prev != NULL && prev->len_ > 0) {
					// If there's a gap at the base of a non-0 length branch, the
					// gap will appear to overlap the branch if we give it length 1.
					newhi = newlo = 0;
				} else {
					// Read or ref gap with no matches coming off of it
					newlo = row;
					newhi = row + 1;
				}
			} else {
				// Diagonal with matches
				newlo = row - (cur->len_ - 1);
				newhi = row + 1;
			}
			assert_geq(newlo, 0);
			assert_geq(newhi, 0);
			// Does the diagonal cover cells?
			if(newhi > newlo) {
				// Check whether there is any overlap with previously traversed
				// cells
				bool added = false;
				const size_t sz = seenPaths_[diag].size();
				for(size_t i = 0; i < sz; i++) {
					// Does the new interval overlap this already-seen
					// interval?  Also of interest: does it abut this
					// already-seen interval?  If so, we should merge them.
					size_t lo = seenPaths_[diag][i].first;
					size_t hi = seenPaths_[diag][i].second;
					assert_lt(lo, hi);
					size_t lo_sm = newlo, hi_sm = newhi;
					if(hi - lo < hi_sm - lo_sm) {
						swap(lo, lo_sm);
						swap(hi, hi_sm);
					}
					if((lo <= lo_sm && hi > lo_sm) ||
					   (lo <  hi_sm && hi >= hi_sm))
					{
						// One or both of the shorter interval's end points
						// are contained in the longer interval - so they
						// overlap.
						rejSeen = true;
						// Merge them into one longer interval
						seenPaths_[diag][i].first = min(lo, lo_sm);
						seenPaths_[diag][i].second = max(hi, hi_sm);
#ifndef NDEBUG
						for(int64_t ii = seenPaths_[diag][i].first;
							ii < (int64_t)seenPaths_[diag][i].second;
							ii++)
						{
							//cerr << "trySolution rejected (" << ii << ", " << (ii + col - row) << ")" << endl;
						}
#endif
						added = true;
						break;
					} else if(hi == lo_sm || lo == hi_sm) {
						// Merge them into one longer interval
						seenPaths_[diag][i].first = min(lo, lo_sm);
						seenPaths_[diag][i].second = max(hi, hi_sm);
#ifndef NDEBUG
						for(int64_t ii = seenPaths_[diag][i].first;
							ii < (int64_t)seenPaths_[diag][i].second;
							ii++)
						{
							//cerr << "trySolution rejected (" << ii << ", " << (ii + col - row) << ")" << endl;
						}
#endif
						added = true;
						// Keep going in case it overlaps one of the other
						// intervals
					}
				}
				if(!added) {
					seenPaths_[diag].push_back(make_pair(newlo, newhi));
				}
			}
		}
		// After the merging that may have occurred above, it's no
		// longer guarnateed that all the overlapping intervals in
		// the list have been merged.  That's OK though.  We'll
		// still get correct answers to overlap queries.
		if(cur->root_) {
			assert_eq(0, cur->parentId_);
			break;
		}
		prev = cur;
		cur = &bs_[cur->parentId_];
	} // while(cur->e_.inited())
	if(rejSeen) {
		res.reset();
		assert(res.alres.ned().empty());
		nrej++;
		return BT_NOT_FOUND;
	}
	if(rejCore) {
		res.reset();
		assert(res.alres.ned().empty());
		nrej++;
		return BT_REJECTED_CORE_DIAG;
	}
	off = br->leftmostCol();
	score.score_ = prob_.targ_;
	score.ns_    = ns;
	score.gaps_  = ngap;
	res.alres.setScore(score);
	res.alres.setRefNs(nrefns);
	size_t trimBeg = br->uppermostRow();
	size_t trimEnd = prob_.qrylen_ - prob_.row_ - 1;
	assert_leq(trimBeg, prob_.qrylen_);
	assert_leq(trimEnd, prob_.qrylen_);
	TRefOff refoff = off + prob_.refoff_ + prob_.rect_->refl;
	res.alres.setShape(
		prob_.refid_,                   // ref id
		refoff,                         // 0-based ref offset
		prob_.treflen(),                // ref length
		prob_.fw_,                      // aligned to Watson?
		prob_.qrylen_,                  // read length
		true,                           // pretrim soft?
		0,                              // pretrim 5' end
		0,                              // pretrim 3' end
		true,                           // alignment trim soft?
		prob_.fw_ ? trimBeg : trimEnd,  // alignment trim 5' end
		prob_.fw_ ? trimEnd : trimBeg); // alignment trim 3' end
#endif
	return BT_FOUND;
}

/**
 * Get the next valid alignment given a backtrace problem.  Return false
 * if there is no valid solution.  Use a backtracking search to find the
 * solution.  This can be very slow.
 */
bool BtBranchTracer::nextAlignmentBacktrace(
	size_t maxiter,
	SwResult& res,
	size_t& off,
	size_t& nrej,
	size_t& niter,
	RandomSource& rnd)
{
	assert(!empty() || !emptySolution());
	assert(prob_.inited());
	// There's a subtle case where we might fail to backtracing in
	// local-alignment mode.  The basic fact to remember is that when we're
	// backtracing from the highest-scoring cell in the table, we're guaranteed
	// to be able to backtrace without ever dipping below 0.  But if we're
	// backtracing from a cell other than the highest-scoring cell in the
	// table, we might dip below 0.  Dipping below 0 implies that there's a
	// shorted local alignment with a better score.  In which case, it's
	// perfectly fair for us to abandon any path that dips below the floor, and
	// this might result in the queue becoming empty before we finish.
	bool result = false;
	niter = 0;
	while(!empty()) {
		if(trySolutions(true, res, off, nrej, rnd, result)) {
			return result;
		}
		if(niter++ >= maxiter) {
			break;
		}
		size_t brid = best(rnd); // put best branch in 'br'
		assert(!seen_.contains(brid));
		ASSERT_ONLY(seen_.insert(brid));
#if 0
		BtBranch *br = &bs_[brid];
		cerr << brid
		     << ": targ:" << prob_.targ_
		     << ", sc:" << br->score_st_
		     << ", row:" << br->uppermostRow()
			 << ", nmm:" << nmm_
			 << ", nnmm:" << nnmm_
			 << ", nrdop:" << nrdop_
			 << ", nrfop:" << nrfop_
			 << ", nrdex:" << nrdex_
			 << ", nrfex:" << nrfex_
			 << ", nrdop_pr: " << nrdopPrune_
			 << ", nrfop_pr: " << nrfopPrune_
			 << ", nrdex_pr: " << nrdexPrune_
			 << ", nrfex_pr: " << nrfexPrune_
			 << endl;
#endif
		addOffshoots(brid);
	}
	if(trySolutions(true, res, off, nrej, rnd, result)) {
		return result;
	}
	return false;
}

/**
 * Get the next valid alignment given a backtrace problem.  Return false
 * if there is no valid solution.  Use a triangle-fill backtrace to find
 * the solution.  This is usually fast (it's O(m + n)).
 */
bool BtBranchTracer::nextAlignmentFill(
	size_t maxiter,
	SwResult& res,
	size_t& off,
	size_t& nrej,
	size_t& niter,
	RandomSource& rnd)
{
	assert(prob_.inited());
	assert(!emptySolution());
	bool result = false;
	if(trySolutions(false, res, off, nrej, rnd, result)) {
		return result;
	}
	return false;
}

/**
 * Get the next valid alignment given the backtrace problem.  Return false
 * if there is no valid solution, e.g., if 
 */
bool BtBranchTracer::nextAlignment(
	size_t maxiter,
	SwResult& res,
	size_t& off,
	size_t& nrej,
	size_t& niter,
	RandomSource& rnd)
{
	if(prob_.fill_) {
		return nextAlignmentFill(
			maxiter,
			res,
			off,
			nrej,
			niter,
			rnd);
	} else {
		return nextAlignmentBacktrace(
			maxiter,
			res,
			off,
			nrej,
			niter,
			rnd);
	}
}

#ifdef MAIN_ALIGNER_BT

#include <iostream>

int main(int argc, char **argv) {
	size_t off = 0;
	RandomSource rnd(77);
	BtBranchTracer tr;
	Scoring sc = Scoring::base1();
	SwResult res;
	tr.init(
		"ACGTACGT", // in: read sequence
		"IIIIIIII", // in: quality sequence
		8,          // in: read sequence length
		"ACGTACGT", // in: reference sequence
		8,          // in: reference sequence length
		0,          // in: reference id
		0,          // in: reference offset
		true,       // in: orientation
		sc,         // in: scoring scheme
		0,          // in: N ceiling
		8,          // in: alignment score
		7,          // start in this row
		7,          // start in this column
		rnd);       // random gen, to choose among equal paths
	size_t nrej = 0;
	tr.nextAlignment(
		res,
		off,
		nrej,
		rnd);
}

#endif /*def MAIN_ALIGNER_BT*/