# Install bcftools, its manpage, bcf-fix.pl, vcfutils.pl, and new examples.

[samtools.git] / bam.c

diff --git a/bam.c b/bam.c
index 94b0aa8bb85bef4ae4a787af3337f1765ed8899e..521c1dda7897aa2b4489b103e1ee1a84129d6c63 100644 (file)
--- 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);
@@ -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)
 {