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Searched refs:samFlags (Results 1 – 2 of 2) sorted by relevance

/dports/biology/bamutil/bamUtil-1.0.15/src/
H A DGapInfo.cpp164 uint16_t samFlags = samRecord.getFlag(); in processFile() local
166 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()
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/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/utils/read/
H A DReadUtils.java458 int samFlags = 0; in getSAMFlagsForRead() local
461 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()
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