Merge branch 'master' into master_fixes

NEWS

@@ -1,3 +1,44 @@
+Release 0.7.3a (15 March, 2013)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+In 0.7.3, the wrong CIGAR bug was only fixed in one scenario, but not fixed
+in another corner case.
+
+(0.7.3a: 15 March 2013, r367)
+
+
+
+Release 0.7.3 (15 March, 2013)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Changes to BWA-MEM:
+
+ * Bugfix: pairing score is inaccurate when option -A does not take the default
+   value. This is a very minor issue even if it happens.
+
+ * Bugfix: occasionally wrong CIGAR. This happens when in the alignment there
+   is a 1bp deletion and a 1bp insertion which are close to the end of the
+   reads, and there are no other substitutions or indels. BWA-MEM would not do
+   a gapped alignment due to the bug.
+
+ * New feature: output other non-overlapping alignments in the XP tag such that
+   we can see the entire picture of alignment from one SAM line. XP gives the
+   position, CIGAR, NM and mapQ of each aligned subsequence of the query.
+
+BWA-MEM has been used to align ~300Gbp 100-700bp SE/PE reads. SNP/indel calling
+has also been evaluated on part of these data. BWA-MEM generally gives better
+pre-filtered SNP calls than BWA. No significant issues have been observed since
+0.7.2, though minor improvements or bugs (e.g. the bug fixed in this release)
+are still possible. If you find potential issues, please send bug reports to
+<bio-bwa-help@lists.sourceforge.net> (free registration required).
+
+In addition, more detailed description of the BWA-MEM algorithm can be found at
+<https://github.com/lh3/mem-paper>.
+
+(0.7.3: 15 March 2013, r366)
+
+
+
 Release 0.7.2 (9 March, 2013)
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 

bwa.1

@@ -1,4 +1,4 @@
-.TH bwa 1 "13 March 2013" "bwa-0.7.3" "Bioinformatics tools"
+.TH bwa 1 "15 March 2013" "bwa-0.7.3a" "Bioinformatics tools"
 .SH NAME
 .PP
 bwa - Burrows-Wheeler Alignment Tool
@@ -580,7 +580,7 @@ XS	Suboptimal alignment score
 XF	Support from forward/reverse alignment
 XE	Number of supporting seeds
 _
-XP	Alt primary hits; format: /(chr,pos,CIGAR;mapQ,NM;)+/
+XP	Alt primary hits; format: /(chr,pos,CIGAR,mapQ,NM;)+/
 .TE
 
 .PP

bwamem.c

@@ -542,7 +542,7 @@ void mem_chain2aln(const mem_opt_t *opt, int64_t l_pac, const uint8_t *pac, int
 		a = kv_pushp(mem_alnreg_t, *av);
 		memset(a, 0, sizeof(mem_alnreg_t));
 		a->w = aw[0] = aw[1] = opt->w;
-		a->score = -1;
+		a->score = a->truesc = -1;
 
 		if (s->qbeg) { // left extension
 			uint8_t *rs, *qs;
@@ -556,14 +556,19 @@ void mem_chain2aln(const mem_opt_t *opt, int64_t l_pac, const uint8_t *pac, int
 				int prev = a->score;
 				aw[0] = opt->w << i;
 				a->score = ksw_extend(s->qbeg, qs, tmp, rs, 5, opt->mat, opt->q, opt->r, aw[0], opt->zdrop, s->len * opt->a, &qle, &tle, &gtle, &gscore, &max_off[0]);
-				if (bwa_verbose >= 4) printf("L\t%d < %d; w=%d; max_off=%d\n", prev, a->score, aw[0], max_off[0]); fflush(stdout);
+				if (bwa_verbose >= 4) { printf("L\t%d < %d; w=%d; max_off=%d\n", prev, a->score, aw[0], max_off[0]); fflush(stdout); }
 				if (a->score == prev || max_off[0] < (aw[0]>>1) + (aw[0]>>2)) break;
 			}
 			// check whether we prefer to reach the end of the query
-			if (gscore <= 0 || gscore <= a->score - opt->pen_clip) a->qb = s->qbeg - qle, a->rb = s->rbeg - tle; // local hits
+			if (gscore <= 0 || gscore <= a->score - opt->pen_clip) { // local extension
-			else a->qb = 0, a->rb = s->rbeg - gtle; // reach the end
+				a->qb = s->qbeg - qle, a->rb = s->rbeg - tle;
+				a->truesc = a->score;
+			} else { // to-end extension
+				a->qb = 0, a->rb = s->rbeg - gtle;
+				a->truesc = gscore;
+			}
 			free(qs); free(rs);
-		} else a->score = s->len * opt->a, a->qb = 0, a->rb = s->rbeg;
+		} else a->score = a->truesc = s->len * opt->a, a->qb = 0, a->rb = s->rbeg;
 
 		if (s->qbeg + s->len != l_query) { // right extension
 			int qle, tle, qe, re, gtle, gscore, sc0 = a->score;
@@ -574,12 +579,17 @@ void mem_chain2aln(const mem_opt_t *opt, int64_t l_pac, const uint8_t *pac, int
 				int prev = a->score;
 				aw[1] = opt->w << i;
 				a->score = ksw_extend(l_query - qe, query + qe, rmax[1] - rmax[0] - re, rseq + re, 5, opt->mat, opt->q, opt->r, aw[1], opt->zdrop, sc0, &qle, &tle, &gtle, &gscore, &max_off[1]);
-				if (bwa_verbose >= 4) printf("R\t%d < %d; w=%d; max_off=%d\n", prev, a->score, aw[1], max_off[1]); fflush(stdout);
+				if (bwa_verbose >= 4) { printf("R\t%d < %d; w=%d; max_off=%d\n", prev, a->score, aw[1], max_off[1]); fflush(stdout); }
 				if (a->score == prev || max_off[1] < (aw[1]>>1) + (aw[1]>>2)) break;
 			}
 			// similar to the above
-			if (gscore <= 0 || gscore <= a->score - opt->pen_clip) a->qe = qe + qle, a->re = rmax[0] + re + tle;
+			if (gscore <= 0 || gscore <= a->score - opt->pen_clip) { // local extension
-			else a->qe = l_query, a->re = rmax[0] + re + gtle;
+				a->qe = qe + qle, a->re = rmax[0] + re + tle;
+				a->truesc += a->score - sc0;
+			} else { // to-end extension
+				a->qe = l_query, a->re = rmax[0] + re + gtle;
+				a->truesc += gscore - sc0;
+			}
 		} else a->qe = l_query, a->re = s->rbeg + s->len;
 		if (bwa_verbose >= 4) { printf("[%d]\taw={%d,%d}\tscore=%d\t[%d,%d) <=> [%ld,%ld)\n", k, aw[0], aw[1], a->score, a->qb, a->qe, (long)a->rb, (long)a->re); fflush(stdout); }
 
@@ -601,7 +611,7 @@ void mem_chain2aln(const mem_opt_t *opt, int64_t l_pac, const uint8_t *pac, int
 static inline int infer_bw(int l1, int l2, int score, int a, int q, int r)
 {
 	int w;
-	if (l1 == l2 && l1 * a - score < (q + r)<<1) return 0; // to get equal alignment length, we need at least two gaps
+	if (l1 == l2 && l1 * a - score < (q + r - a)<<1) return 0; // to get equal alignment length, we need at least two gaps
 	w = ((double)((l1 < l2? l1 : l2) * a - score - q) / r + 1.);
 	if (w < abs(l1 - l2)) w = abs(l1 - l2);
 	return w;
@@ -839,7 +849,7 @@ mem_aln_t mem_reg2aln(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *
 	a.mapq = ar->secondary < 0? mem_approx_mapq_se(opt, ar) : 0;
 	if (ar->secondary >= 0) a.flag |= 0x20000;
 	bwa_fix_xref(opt->mat, opt->q, opt->r, opt->w, bns, pac, (uint8_t*)query, &qb, &qe, &rb, &re);
-	w2 = infer_bw(qe - qb, re - rb, ar->score, opt->a, opt->q, opt->r);
+	w2 = infer_bw(qe - qb, re - rb, ar->truesc, opt->a, opt->q, opt->r);
 	w2 = w2 < opt->w? w2 : opt->w;
 	a.cigar = bwa_gen_cigar(opt->mat, opt->q, opt->r, w2, bns->l_pac, pac, qe - qb, (uint8_t*)&query[qb], rb, re, &score, &a.n_cigar, &NM);
 	a.NM = NM;

bwamem.h

@@ -43,7 +43,8 @@ typedef struct {
 typedef struct {
 	int64_t rb, re; // [rb,re): reference sequence in the alignment
 	int qb, qe;     // [qb,qe): query sequence in the alignment
-	int score;      // best SW score
+	int score;      // best local SW score
+	int truesc;     // actual score corresponding to the aligned region; possibly smaller than $score
 	int sub;        // 2nd best SW score
 	int csub;       // SW score of a tandem hit
 	int sub_n;      // approximate number of suboptimal hits

bwamem_pair.c

@@ -201,7 +201,7 @@ int mem_pair(const mem_opt_t *opt, int64_t l_pac, const uint8_t *pac, const mem_
 				if (dist > pes[dir].high) break;
 				if (dist < pes[dir].low)  continue;
 				ns = (dist - pes[dir].avg) / pes[dir].std;
-				q = (int)((v.a[i].y>>32) + (v.a[k].y>>32) + .721 * log(2. * erfc(fabs(ns) * M_SQRT1_2)) + .499); // .721 = 1/log(4)
+				q = (int)((v.a[i].y>>32) + (v.a[k].y>>32) + .721 * log(2. * erfc(fabs(ns) * M_SQRT1_2)) * opt->a + .499); // .721 = 1/log(4)
 				if (q < 0) q = 0;
 				p = kv_pushp(pair64_t, u);
 				p->y = (uint64_t)k<<32 | i;

main.c

@@ -3,7 +3,7 @@
 #include "utils.h"
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.7.2-r363-beta"
+#define PACKAGE_VERSION "0.7.3a-r367"
 #endif
 
 int bwa_fa2pac(int argc, char *argv[]);