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

/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/spark/sv/discovery/
H A DBreakEndVariantType.java157 …tAllele(final String refBase, final String insertedSequence, final SimpleInterval novelAdjRefLoc) { in constructAltAllele() argument
158 …rn Allele.create(refBase + insertedSequence + "]" + novelAdjRefLoc.getContig() + ":" + novelAdjRef… in constructAltAllele()
190 …return Allele.create("[" + novelAdjRefLoc.getContig() + ":" + novelAdjRefLoc.getEnd() + "[" + inse… in constructAltAllele()
222 …AltAllele(final String refBase, final String insertedSequence, final SimpleInterval novelAdjRefLoc, in constructAltAllele() argument
225 …return Allele.create("]" + novelAdjRefLoc.getContig() + ":" + novelAdjRefLoc.getEnd() + "]" + inse… in constructAltAllele()
227 …rn Allele.create(refBase + insertedSequence + "[" + novelAdjRefLoc.getContig() + ":" + novelAdjRef… in constructAltAllele()
263 …final SimpleInterval novelAdjRefLoc = forUpstreamLoc ? narl.getLeftJustifiedRightRefLoc() : narl.g… in constructAltAllele() local
270 …rn Allele.create(refBase + insertedSequence + "[" + novelAdjRefLoc.getContig() + ":" + novelAdjRef… in constructAltAllele()
272 …return Allele.create("]" + novelAdjRefLoc.getContig() + ":" + novelAdjRefLoc.getStart() + "]" + in… in constructAltAllele()
275 …rn Allele.create(refBase + insertedSequence + "]" + novelAdjRefLoc.getContig() + ":" + novelAdjRef… in constructAltAllele()
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