logger.warn("unexpected event kmers out of order between read anchor kmers: " + read.getReadString() + " Offending kmer offsets: " + readVertexKmerOffset.get(leftAnchorVertex) + " " + readVertexKmerOffset.get(rightAnchorVertex) + " sequences: " + read.getReadString().substring(readVertexKmerOffset.get(leftAnchorVertex), haplotypeGraph.getKmerSize() + readVertexKmerOffset.get(leftAnchorVertex)) + " " + read.getReadString().substring(readVertexKmerOffset.get(rightAnchorVertex), haplotypeGraph.getKmerSize() + readVertexKmerOffset.get(rightAnchorVertex)) + " Reference haplotype: " + haplotypeGraph.getReferenceHaplotype().getBaseString()); return Collections.emptyMap();
@SuppressWarnings("unused") public GATKSAMRecord readFromString(final String readSequence) { if (readBySequence == null) { final List<GATKSAMRecord> readList = readList(); readBySequence = new HashMap<>(readList.size()); for (final GATKSAMRecord r : readList) readBySequence.put(r.getReadString(),r); } return readBySequence.get(readSequence); }
String bases = read.getReadString(); Matcher match = pattern.matcher(bases);
Assert.assertEquals(r.getReadString(),haplotypes.get(hapNumber).getBaseString().substring(offset,offset+readLength)); if (as.getReference().indexOf(r.getReadString()) == -1) { hapReadsNotInReference[hapNumber]++;
correctedRead.setIsStrandless(inputRead.isStrandless()); correctedRead.setReadBases(inputRead.getReadBases()); correctedRead.setReadString(inputRead.getReadString()); correctedRead.setReadGroup(inputRead.getReadGroup()); return correctedRead;