uint64_t total_len_dup;
uint64_t nreads_1st;
uint64_t nreads_2nd;
+ uint64_t nreads_filtered;
uint64_t nreads_dup;
uint64_t nreads_unmapped;
uint64_t nreads_unpaired;
uint64_t nbases_mapped_cigar;
uint64_t nbases_trimmed; // bwa trimmed bases
uint64_t nmismatches;
+ uint64_t nreads_QCfailed, nreads_secondary;
// GC-depth related data
uint32_t ngcd, igcd; // The maximum number of GC depth bins and index of the current bin
if ( k == kh_end(stats->rg_hash) ) return;
}
if ( stats->flag_require && (bam_line->core.flag & stats->flag_require)!=stats->flag_require )
+ {
+ stats->nreads_filtered++;
return;
+ }
if ( stats->flag_filter && (bam_line->core.flag & stats->flag_filter) )
+ {
+ stats->nreads_filtered++;
return;
-
+ }
if ( !is_in_regions(bam_line,stats) )
return;
+ if ( stats->filter_readlen!=-1 && bam_line->core.l_qseq!=stats->filter_readlen )
+ return;
+
+ if ( bam_line->core.flag & BAM_FQCFAIL ) stats->nreads_QCfailed++;
+ if ( bam_line->core.flag & BAM_FSECONDARY ) stats->nreads_secondary++;
int seq_len = bam_line->core.l_qseq;
if ( !seq_len ) return;
- if ( stats->filter_readlen!=-1 && seq_len!=stats->filter_readlen ) return;
+
if ( seq_len >= stats->nbases )
realloc_buffers(stats,seq_len);
if ( stats->max_len<seq_len )
printf(" %s",stats->argv[i]);
printf("\n");
printf("# Summary Numbers. Use `grep ^SN | cut -f 2-` to extract this part.\n");
+ printf("SN\traw total sequences:\t%ld\n", (long)(stats->nreads_filtered+stats->nreads_1st+stats->nreads_2nd));
+ printf("SN\tfiltered sequences:\t%ld\n", (long)stats->nreads_filtered);
printf("SN\tsequences:\t%ld\n", (long)(stats->nreads_1st+stats->nreads_2nd));
printf("SN\tis paired:\t%d\n", stats->nreads_1st&&stats->nreads_2nd ? 1 : 0);
printf("SN\tis sorted:\t%d\n", stats->is_sorted ? 1 : 0);
printf("SN\treads paired:\t%ld\n", (long)stats->nreads_paired);
printf("SN\treads duplicated:\t%ld\n", (long)stats->nreads_dup);
printf("SN\treads MQ0:\t%ld\n", (long)stats->nreads_mq0);
+ printf("SN\treads QC failed:\t%ld\n", (long)stats->nreads_QCfailed);
+ printf("SN\tnon-primary alignments:\t%ld\n", (long)stats->nreads_secondary);
printf("SN\ttotal length:\t%ld\n", (long)stats->total_len);
printf("SN\tbases mapped:\t%ld\n", (long)stats->nbases_mapped);
printf("SN\tbases mapped (cigar):\t%ld\n", (long)stats->nbases_mapped_cigar);