X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=samtools.git;a=blobdiff_plain;f=bam.c;h=96aace21c7ab7c261380ee2136e283022e9c834d;hp=94b0aa8bb85bef4ae4a787af3337f1765ed8899e;hb=ced7709f121a00d5049d99ee8576037994aab1d1;hpb=67801bf17aa6495879da63ce77a2014759fabc16

diff --git a/bam.c b/bam.c
index 94b0aa8..96aace2 100644
--- a/bam.c
+++ b/bam.c
@@ -79,7 +79,7 @@ bam_header_t *bam_header_read(bamFile fp)
 		// with ESPIPE.  Suppress the error message in this case.
 		if (errno != ESPIPE) perror("[bam_header_read] bgzf_check_EOF");
 	}
-	else if (i == 0) fprintf(stderr, "[bam_header_read] EOF marker is absent.\n");
+	else if (i == 0) fprintf(stderr, "[bam_header_read] EOF marker is absent. The input is probably truncated.\n");
 	// read "BAM1"
 	magic_len = bam_read(fp, buf, 4);
 	if (magic_len != 4 || strncmp(buf, "BAM\001", 4) != 0) {
@@ -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);
@@ -297,6 +305,22 @@ void bam_view1(const bam_header_t *header, const bam1_t *b)
 	free(s);
 }
 
+int bam_validate1(const bam_header_t *header, const bam1_t *b)
+{
+	char *s;
+
+	if (b->core.tid < -1 || b->core.mtid < -1) return 0;
+	if (header && (b->core.tid >= header->n_targets || b->core.mtid >= header->n_targets)) return 0;
+
+	if (b->data_len < b->core.l_qname) return 0;
+	s = memchr(bam1_qname(b), '\0', b->core.l_qname);
+	if (s != &bam1_qname(b)[b->core.l_qname-1]) return 0;
+
+	// FIXME: Other fields could also be checked, especially the auxiliary data
+
+	return 1;
+}
+
 // FIXME: we should also check the LB tag associated with each alignment
 const char *bam_get_library(bam_header_t *h, const bam1_t *b)
 {