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;
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 )
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);