uint64_t nreads_unmapped;
uint64_t nreads_unpaired;
uint64_t nreads_paired;
+ uint64_t nreads_anomalous;
uint64_t nreads_mq0;
uint64_t nbases_mapped;
uint64_t nbases_mapped_cigar;
count_indels(stats,bam_line);
- // The insert size is tricky, because for long inserts the libraries are
- // prepared differently and the pairs point in other direction. BWA does
- // not set the paired flag for them. Similar thing is true also for 454
- // reads. Therefore, do the insert size stats for all mapped reads.
- int32_t isize = bam_line->core.isize;
- if ( isize<0 ) isize = -isize;
- if ( IS_PAIRED(bam_line) )
+ if ( !IS_PAIRED(bam_line) )
+ stats->nreads_unpaired++;
+ else
{
stats->nreads_paired++;
- if ( isize >= stats->nisize )
- isize=stats->nisize-1;
- int pos_fst = bam_line->core.mpos - bam_line->core.pos;
- int is_fst = IS_READ1(bam_line) ? 1 : -1;
- int is_fwd = IS_REVERSE(bam_line) ? -1 : 1;
- int is_mfwd = IS_MATE_REVERSE(bam_line) ? -1 : 1;
+ if ( bam_line->core.tid!=bam_line->core.mtid )
+ stats->nreads_anomalous++;
- if ( is_fwd*is_mfwd>0 )
- stats->isize_other[isize]++;
- else if ( is_fst*pos_fst>0 )
- {
- if ( is_fst*is_fwd>0 )
- stats->isize_inward[isize]++;
- else
- stats->isize_outward[isize]++;
- }
- else if ( is_fst*pos_fst<0 )
+ // The insert size is tricky, because for long inserts the libraries are
+ // prepared differently and the pairs point in other direction. BWA does
+ // not set the paired flag for them. Similar thing is true also for 454
+ // reads. Mates mapped to different chromosomes have isize==0.
+ int32_t isize = bam_line->core.isize;
+ if ( isize<0 ) isize = -isize;
+ if ( isize >= stats->nisize )
+ isize = stats->nisize-1;
+ if ( isize>0 || bam_line->core.tid==bam_line->core.mtid )
{
- if ( is_fst*is_fwd>0 )
- stats->isize_outward[isize]++;
- else
- stats->isize_inward[isize]++;
+ int pos_fst = bam_line->core.mpos - bam_line->core.pos;
+ int is_fst = IS_READ1(bam_line) ? 1 : -1;
+ int is_fwd = IS_REVERSE(bam_line) ? -1 : 1;
+ int is_mfwd = IS_MATE_REVERSE(bam_line) ? -1 : 1;
+
+ if ( is_fwd*is_mfwd>0 )
+ stats->isize_other[isize]++;
+ else if ( is_fst*pos_fst>0 )
+ {
+ if ( is_fst*is_fwd>0 )
+ stats->isize_inward[isize]++;
+ else
+ stats->isize_outward[isize]++;
+ }
+ else if ( is_fst*pos_fst<0 )
+ {
+ if ( is_fst*is_fwd>0 )
+ stats->isize_outward[isize]++;
+ else
+ stats->isize_inward[isize]++;
+ }
}
}
- else
- stats->nreads_unpaired++;
// Number of mismatches
uint8_t *nm = bam_aux_get(bam_line,"NM");
printf("SN\tinward oriented pairs:\t%ld\n", (long)nisize_inward);
printf("SN\toutward oriented pairs:\t%ld\n", (long)nisize_outward);
printf("SN\tpairs with other orientation:\t%ld\n", (long)nisize_other);
+ printf("SN\tpairs on different chromosomes:\t%ld\n", (long)stats->nreads_anomalous/2);
int ibase,iqual;
if ( stats->max_len<stats->nbases ) stats->max_len++;