* samtools-0.1.5-32 (r449)

[samtools.git] / bam_import.c

diff --git a/bam_import.c b/bam_import.c
index 19cd75f4352f2d144b1d0a36ed0925cab6a50cc8..1dc906eb49f36428460be547b1582ab52432f651 100644 (file)
--- a/bam_import.c
+++ b/bam_import.c
@@ -374,7 +374,10 @@ int sam_read1(tamFile fp, bam_header_t *header, bam1_t *b)
                        c->bin = bam_reg2bin(c->pos, bam_calend(c, bam1_cigar(b)));
                        doff += c->n_cigar * 4;
                } else {
-                       if (!(c->flag&BAM_FUNMAP)) parse_error(fp->n_lines, "mapped sequence without CIGAR");
+                       if (!(c->flag&BAM_FUNMAP)) {
+                               fprintf(stderr, "Parse warning at line %lld: mapped sequence without CIGAR\n", (long long)fp->n_lines);
+                               c->flag |= BAM_FUNMAP;
+                       }
                        c->bin = bam_reg2bin(c->pos, c->pos + 1);
                }
        }