# Uploaded samtools version 0.1.14-1.

[samtools.git] / bam.c

diff --git a/bam.c b/bam.c
index 94b0aa8bb85bef4ae4a787af3337f1765ed8899e..96aace21c7ab7c261380ee2136e283022e9c834d 100644 (file)
--- 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)
 {