Add bam_validate1().

[samtools.git] / bam.c

diff --git a/bam.c b/bam.c
index 41850bab46e190f33c0b279ec20e4bec663bb86f..521c1dda7897aa2b4489b103e1ee1a84129d6c63 100644 (file)
--- a/bam.c
+++ b/bam.c
@@ -305,6 +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)
 {