/** * * @return Sequence index for the given sequence name, or -1 if the name is not found. */ public int getSequenceIndex(final String sequenceName) { return mSequenceDictionary.getSequenceIndex(sequenceName); }
/** * * @return Sequence index for the given sequence name, or -1 if the name is not found. */ public int getSequenceIndex(final String sequenceName) { return mSequenceDictionary.getSequenceIndex(sequenceName); }
/** * * @return Sequence index for the given sequence name, or -1 if the name is not found. */ public int getSequenceIndex(final String sequenceName) { return mSequenceDictionary.getSequenceIndex(sequenceName); }
/** * Convert contig to its index in the dict, or throw an exception if it's not found or is null * @param chr the contig */ private int getIndex(final String chr) { if ( chr == null ) throw new IllegalArgumentException("chr is null"); final int index = dict.getSequenceIndex(chr); if ( index == -1 ) throw new IllegalArgumentException("Unknown contig " + chr); return index; } }
@Override public int getSequenceIndex(String sequenceName) { int index = super.getSequenceIndex(sequenceName); if (index < 0) { addSequence(new SAMSequenceRecord(sequenceName, 0)); } return super.getSequenceIndex(sequenceName); } }
@Override public ReferenceSequence getSubsequenceAt(final String name, final long start, final long stop) { final int index = getSequenceDictionary().getSequenceIndex(name); final byte[] bases = Arrays.copyOfRange(sequences.get(index), (int) start, (int) stop + 1); return new ReferenceSequence(name, index, bases); }
@Override public ReferenceSequence getSubsequenceAt(final String name, final long start, final long stop) { final int index = getSequenceDictionary().getSequenceIndex(name); final byte[] bases = Arrays.copyOfRange(sequences.get(index), (int) start, (int) stop + 1); return new ReferenceSequence(name, index, bases); }
@Override public ReferenceSequence getSubsequenceAt(String name, long start, long stop) { int index = getSequenceDictionary().getSequenceIndex(name); byte[] bases = Arrays.copyOfRange(sequences.get(index), (int) start, (int) stop + 1); return new ReferenceSequence(name, index, bases); }
@Override public ReferenceSequence getSequence(final String name) { final int index = getSequenceDictionary().getSequenceIndex(name); return new ReferenceSequence(name, index, sequences.get(index)); }
@Override public ReferenceSequence getSequence(final String name) { final int index = getSequenceDictionary().getSequenceIndex(name); return new ReferenceSequence(name, index, sequences.get(index)); }
@Override public ReferenceSequence getSequence(String name) { int index = getSequenceDictionary().getSequenceIndex(name); return new ReferenceSequence(name, index, sequences.get(index)); }
VariantContextSet(final SAMSequenceDictionary dict) { super((lhs, rhs) -> { final int lhsContig = dict.getSequenceIndex(lhs.getContig()); final int rhsContig = dict.getSequenceIndex(rhs.getContig()); final int retval = lhsContig - rhsContig; if (retval != 0) return retval; return lhs.getStart() - rhs.getStart(); }); } }
@Override public long getLinearCoordinate(String chr, long pos) { return getLinearCoordinate(getDictionary().getSequenceIndex(chr), pos); } /* (non-Javadoc)
VariantContextSet(final SAMSequenceDictionary dict) { super((lhs, rhs) -> { final int lhsContig = dict.getSequenceIndex(lhs.getContig()); final int rhsContig = dict.getSequenceIndex(rhs.getContig()); final int retval = lhsContig - rhsContig; if (retval != 0) return retval; return lhs.getStart() - rhs.getStart(); }); } }
/** * @return reference index for the given sequence name, or -1 if the variant is not on a reference contig */ public static int getReferenceIndex(GenomicProcessingContext processContext, VariantContext variant) { return processContext.getDictionary().getSequenceIndex(variant.getContig()); } /**
public void addSequence(final String name, final byte[] bases) { final SAMSequenceRecord r = new SAMSequenceRecord(name, bases.length); dictionary.addSequence(r); final int index = getSequenceDictionary().getSequenceIndex(name); sequences.put(index, bases); }
public void addSequence(final String name, final byte[] bases) { final SAMSequenceRecord r = new SAMSequenceRecord(name, bases.length); dictionary.addSequence(r); final int index = getSequenceDictionary().getSequenceIndex(name); sequences.put(index, bases); }
public void addSequence(String name, byte[] bases) { SAMSequenceRecord r = new SAMSequenceRecord(name, bases.length); dictionary.addSequence(r); int index = getSequenceDictionary().getSequenceIndex(name); sequences.put(index, bases); }
public long[] getBAMIndexPointers(File indexFile, SAMSequenceDictionary dictionary, String sequenceName, int alignmentStart, int alignmentEnd) { long[] filePointers = new long[0]; final int referenceIndex = dictionary.getSequenceIndex(sequenceName); if (referenceIndex != -1) { final BAMIndex fileIndex = BAMIndexFactory.SHARED_INSTANCE.createCachingIndex(indexFile, dictionary); final BAMFileSpan fileSpan = fileIndex.getSpanOverlapping(referenceIndex, alignmentStart, alignmentEnd); filePointers = fileSpan != null ? fileSpan.toCoordinateArray() : null; } return filePointers; } }
protected GATKSAMRecord buildSAMRecord(final String readName, final String contig, final int alignmentStart) { GATKSAMRecord record = new GATKSAMRecord(header); record.setReadName(readName); record.setReferenceIndex(dictionary.getSequenceIndex(contig)); record.setAlignmentStart(alignmentStart); record.setCigarString("1M"); record.setReadString("A"); record.setBaseQualityString("A"); record.setReadGroup(readGroup); return record; }