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;
{
uint8_t qual = quals[iread] + 1;
if ( qual>=stats->nquals )
- error("TODO: quality too high %d>=%d\n", quals[iread],stats->nquals);
+ error("TODO: quality too high %d>=%d (%s %d %s)\n", qual,stats->nquals, stats->sam->header->target_name[bam_line->core.tid],bam_line->core.pos+1,bam1_qname(bam_line));
int idx = is_fwd ? icycle : read_len-icycle-1;
if ( idx>stats->max_len )
{
uint8_t qual = bam_quals[ reverse ? seq_len-i-1 : i];
if ( qual>=stats->nquals )
- error("TODO: quality too high %d>=%d\n", quals[i],stats->nquals);
+ error("TODO: quality too high %d>=%d (%s %d %s)\n", qual,stats->nquals,stats->sam->header->target_name[bam_line->core.tid],bam_line->core.pos+1,bam1_qname(bam_line));
if ( qual>stats->max_qual )
stats->max_qual = qual;
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) && isize!=0 )
+ 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");
// Calculate average insert size and standard deviation (from the main bulk data only)
int isize, ibulk=0;
uint64_t nisize=0, nisize_inward=0, nisize_outward=0, nisize_other=0;
- for (isize=1; isize<stats->nisize; isize++)
+ for (isize=0; isize<stats->nisize; isize++)
{
// Each pair was counted twice
stats->isize_inward[isize] *= 0.5;
}
double bulk=0, avg_isize=0, sd_isize=0;
- for (isize=1; isize<stats->nisize; isize++)
+ for (isize=0; isize<stats->nisize; isize++)
{
bulk += stats->isize_inward[isize] + stats->isize_outward[isize] + stats->isize_other[isize];
avg_isize += isize * (stats->isize_inward[isize] + stats->isize_outward[isize] + stats->isize_other[isize]);
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++;
printf("GCC\t%d\t%.2f\t%.2f\t%.2f\t%.2f\n", ibase,100.*ptr[0]/sum,100.*ptr[1]/sum,100.*ptr[2]/sum,100.*ptr[3]/sum);
}
printf("# Insert sizes. Use `grep ^IS | cut -f 2-` to extract this part. The columns are: pairs total, inward oriented pairs, outward oriented pairs, other pairs\n");
- for (isize=1; isize<ibulk; isize++)
+ for (isize=0; isize<ibulk; isize++)
printf("IS\t%d\t%ld\t%ld\t%ld\t%ld\n", isize, (long)(stats->isize_inward[isize]+stats->isize_outward[isize]+stats->isize_other[isize]),
(long)stats->isize_inward[isize], (long)stats->isize_outward[isize], (long)stats->isize_other[isize]);
}
printf("# Coverage distribution. Use `grep ^COV | cut -f 2-` to extract this part.\n");
- printf("COV\t[<%d]\t%d\t%ld\n",stats->cov_min,stats->cov_min-1, (long)stats->cov[0]);
+ if ( stats->cov[0] )
+ printf("COV\t[<%d]\t%d\t%ld\n",stats->cov_min,stats->cov_min-1, (long)stats->cov[0]);
int icov;
for (icov=1; icov<stats->ncov-1; icov++)
- printf("COV\t[%d-%d]\t%d\t%ld\n",stats->cov_min + (icov-1)*stats->cov_step, stats->cov_min + icov*stats->cov_step-1,stats->cov_min + icov*stats->cov_step-1, (long)stats->cov[icov]);
- printf("COV\t[%d<]\t%d\t%ld\n",stats->cov_min + (stats->ncov-2)*stats->cov_step-1,stats->cov_min + (stats->ncov-2)*stats->cov_step-1, (long)stats->cov[stats->ncov-1]);
-
+ if ( stats->cov[icov] )
+ printf("COV\t[%d-%d]\t%d\t%ld\n",stats->cov_min + (icov-1)*stats->cov_step, stats->cov_min + icov*stats->cov_step-1,stats->cov_min + icov*stats->cov_step-1, (long)stats->cov[icov]);
+ if ( stats->cov[stats->ncov-1] )
+ printf("COV\t[%d<]\t%d\t%ld\n",stats->cov_min + (stats->ncov-2)*stats->cov_step-1,stats->cov_min + (stats->ncov-2)*stats->cov_step-1, (long)stats->cov[stats->ncov-1]);
// Calculate average GC content, then sort by GC and depth
printf("# GC-depth. Use `grep ^GCD | cut -f 2-` to extract this part. The columns are: GC%%, unique sequence percentiles, 10th, 25th, 50th, 75th and 90th depth percentile\n");
stats_t *stats = calloc(1,sizeof(stats_t));
stats->ngc = 200;
- stats->nquals = 95;
+ stats->nquals = 256;
stats->nbases = 300;
stats->nisize = 8000;
stats->max_len = 30;
stats->gcd_bin_size = 20e3;
stats->gcd_ref_size = 4.2e9;
stats->rseq_pos = -1;
- stats->tid = stats->gcd_pos = stats->igcd = -1;
+ stats->tid = stats->gcd_pos = -1;
+ stats->igcd = 0;
stats->is_sorted = 1;
stats->cov_min = 1;
stats->cov_max = 1000;
projects / samtools.git / blobdiff