Function get_pattern_code

scanForPairedEndReads.cpp:34–37

}

char get_pattern_code(uint32_t flag) {
  if (flag & BAM_FREAD1) return ((flag & BAM_FREVERSE) ? 1 : 0);
  else return ((flag & BAM_FREVERSE) ? 0 : 1);
}

bool less_than(bam1_t *a, bam1_t *b) {
	int32_t ap1 = min(a->core.pos, a->core.mpos);