Searched refs:samFlags (Results 1 – 2 of 2) sorted by relevance
164 uint16_t samFlags = samRecord.getFlag(); in processFile() local166 if((!SamFlag::isMapped(samFlags)) || in processFile()167 (!SamFlag::isMateMapped(samFlags)) || in processFile()168 (!SamFlag::isPaired(samFlags)) || in processFile()169 (samFlags & SamFlag::SECONDARY_ALIGNMENT) || in processFile()170 (samFlags & SamFlag::SUPPLEMENTARY_ALIGNMENT) || in processFile()171 (SamFlag::isDuplicate(samFlags)) || in processFile()172 (SamFlag::isQCFailure(samFlags))) in processFile()216 if(checkFirst && !SamFlag::isFirstFragment(samFlags)) in processFile()220 if(checkStrand && SamFlag::isReverse(samFlags)) in processFile()[all …]
458 int samFlags = 0; in getSAMFlagsForRead() local461 samFlags |= SAM_READ_PAIRED_FLAG; in getSAMFlagsForRead()464 samFlags |= SAM_PROPER_PAIR_FLAG; in getSAMFlagsForRead()467 samFlags |= SAM_READ_UNMAPPED_FLAG; in getSAMFlagsForRead()470 samFlags |= SAM_MATE_UNMAPPED_FLAG; in getSAMFlagsForRead()473 samFlags |= SAM_READ_STRAND_FLAG; in getSAMFlagsForRead()476 samFlags |= SAM_MATE_STRAND_FLAG; in getSAMFlagsForRead()479 samFlags |= SAM_FIRST_OF_PAIR_FLAG; in getSAMFlagsForRead()482 samFlags |= SAM_SECOND_OF_PAIR_FLAG; in getSAMFlagsForRead()491 samFlags |= SAM_DUPLICATE_READ_FLAG; in getSAMFlagsForRead()[all …]