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Searched refs:adaptorBoundary (Results 1 – 3 of 3) sorted by relevance

/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/transformers/
H A DPalindromeArtifactClipReadTransformer.java70 final int adaptorBoundary = read.getAdaptorBoundary(); in apply() local
71 … if (!read.isProperlyPaired() || adaptorBoundary == ReadUtils.CANNOT_COMPUTE_ADAPTOR_BOUNDARY) { in apply()
93 …final int refStart = readIsUpstreamOfMate ? adaptorBoundary - numBasesToCompare : adaptorBoundary … in apply()
94 …final int refEnd = readIsUpstreamOfMate ? adaptorBoundary - 1 : adaptorBoundary + numBasesToCompar… in apply()
/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/utils/clipping/
H A DReadClipper.java356 final int adaptorBoundary = read.getAdaptorBoundary(); in hardClipAdaptorSequence() local
358 …if (adaptorBoundary == ReadUtils.CANNOT_COMPUTE_ADAPTOR_BOUNDARY || !ReadUtils.isInsideRead(read, … in hardClipAdaptorSequence()
362 …hardClipByReferenceCoordinatesLeftTail(adaptorBoundary) : hardClipByReferenceCoordinatesRightTail(… in hardClipAdaptorSequence()
/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/utils/read/
H A DReadUtils.java1065 final int adaptorBoundary = read.getAdaptorBoundary(); in isBaseInsideAdaptor() local
1066 …if (adaptorBoundary == CANNOT_COMPUTE_ADAPTOR_BOUNDARY || read.getFragmentLength() > DEFAULT_ADAPT… in isBaseInsideAdaptor()
1069 return read.isReverseStrand() ? basePos <= adaptorBoundary : basePos >= adaptorBoundary; in isBaseInsideAdaptor()