From: Heng Li <lh3@live.co.uk>
Date: Thu, 16 Sep 2010 20:54:48 +0000 (+0000)
Subject:  * fixed a bug in capQ
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=cdfe59776873444748f34af06bed3ade0bd2aee2;hp=2cbbde8535bbb29daa4088db10d0c534fd275aec;p=samtools.git

 * fixed a bug in capQ
 * valgrind identifies a use of uninitialised value, but I have not fixed it.
---

diff --git a/bam.c b/bam.c
index 94b0aa8..41850ba 100644
--- a/bam.c
+++ b/bam.c
@@ -245,7 +245,11 @@ char *bam_format1_core(const bam_header_t *header, const bam1_t *b, int of)
 		kputc('\t', &str);
 	}
 	if (c->tid < 0) kputsn("*\t", 2, &str);
-	else { kputs(header->target_name[c->tid], &str); kputc('\t', &str); }
+	else {
+		if (header) kputs(header->target_name[c->tid] , &str);
+		else kputw(c->tid, &str);
+		kputc('\t', &str);
+	}
 	kputw(c->pos + 1, &str); kputc('\t', &str); kputw(c->qual, &str); kputc('\t', &str);
 	if (c->n_cigar == 0) kputc('*', &str);
 	else {
@@ -257,7 +261,11 @@ char *bam_format1_core(const bam_header_t *header, const bam1_t *b, int of)
 	kputc('\t', &str);
 	if (c->mtid < 0) kputsn("*\t", 2, &str);
 	else if (c->mtid == c->tid) kputsn("=\t", 2, &str);
-	else { kputs(header->target_name[c->mtid], &str); kputc('\t', &str); }
+	else {
+		if (header) kputs(header->target_name[c->mtid], &str);
+		else kputw(c->mtid, &str);
+		kputc('\t', &str);
+	}
 	kputw(c->mpos + 1, &str); kputc('\t', &str); kputw(c->isize, &str); kputc('\t', &str);
 	if (c->l_qseq) {
 		for (i = 0; i < c->l_qseq; ++i) kputc(bam_nt16_rev_table[bam1_seqi(s, i)], &str);
diff --git a/bam_md.c b/bam_md.c
index d2c84dc..f3f7e22 100644
--- a/bam_md.c
+++ b/bam_md.c
@@ -200,7 +200,7 @@ int bam_realn(bam1_t *b, const char *ref)
 		} else if (op == BAM_CSOFT_CLIP) y += ol;
 		else if (op == BAM_CREF_SKIP) x += ol;
 	}
-	if (score < 0) return -1; // no high scoring segments
+	if (q[1] < 0) return -1; // no high scoring segments
 	endx = x - 1;
 	// find the left boundary
 	for (k = c->n_cigar - 1, score = max = 0, x = x-1, y = y-1; k >= 0; --k) {
@@ -229,7 +229,7 @@ int bam_realn(bam1_t *b, const char *ref)
 		} else if (op == BAM_CSOFT_CLIP) y -= ol;
 		else if (op == BAM_CREF_SKIP) x -= ol;
 	}
-	if (q[1] - q[0] < 15) return -1; // the high-scoring segment is too short
+	if (q[0] < 0 || q[1] - q[0] < 15) return -1; // the high-scoring segment is too short
 	// modify CIGAR
 	n_cigar = 0;
 	cigar = calloc(c->n_cigar + 4, 4);
diff --git a/bam_pileup.c b/bam_pileup.c
index db170e8..266b966 100644
--- a/bam_pileup.c
+++ b/bam_pileup.c
@@ -391,7 +391,7 @@ int bam_mplp_auto(bam_mplp_t iter, int *_tid, int *_pos, int *n_plp, const bam_p
 	if (new_min == (uint64_t)-1) return 0;
 	*_tid = new_min>>32; *_pos = (uint32_t)new_min;
 	for (i = 0; i < iter->n; ++i) {
-		if (iter->pos[i] == iter->min) {
+		if (iter->pos[i] == iter->min) { // FIXME: valgrind reports "uninitialised value(s) at this line"
 			n_plp[i] = iter->n_plp[i], plp[i] = iter->plp[i];
 			++ret;
 		} else n_plp[i] = 0, plp[i] = 0;