Searched refs:novelAdjRefLoc (Results 1 – 1 of 1) sorted by relevance
157 …tAllele(final String refBase, final String insertedSequence, final SimpleInterval novelAdjRefLoc) { in constructAltAllele() argument158 …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() argument225 …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() local270 …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()[all …]