bamcheck:bamcheck.o
$(CC) $(CFLAGS) -o $@ bamcheck.o -lm -lz -L.. -lbam
+bamcheck.o:bamcheck.c ../faidx.h ../khash.h ../sam.h ../razf.h
+ $(CC) $(CFLAGS) -c -I.. -o $@ bamcheck.c
+
ace2sam:ace2sam.o
$(CC) $(CFLAGS) -o $@ ace2sam.o -lz
considered, even small overlap is good enough to include the read in the stats.
*/
-#define BAMCHECK_VERSION "2012-03-22"
+#define BAMCHECK_VERSION "2012-03-29"
#define _ISOC99_SOURCE
#define _GNU_SOURCE
{
if ( stats->regions )
{
- if ( bam_line->core.tid >= stats->nregions ) continue;
+ if ( bam_line->core.tid >= stats->nregions || bam_line->core.tid<0 ) continue;
if ( !stats->is_sorted ) error("The BAM must be sorted in order for -t to work.\n");
regions_t *reg = &stats->regions[bam_line->core.tid];