private byte adjustBase(byte base) { if (complement) return SequenceUtil.complement(base); return base; } private class ReadKmerIterator extends AbstractIterator<ReadKmer> {
public static void reverseComplement(final byte[] bases, final int offset, final int len) { final int lastIndex = len - 1; int i, j; for (i = offset, j = offset + lastIndex; i < j; ++i, --j) { final byte tmp = complement(bases[i]); bases[i] = complement(bases[j]); bases[j] = tmp; } if (len % 2 == 1) { bases[i] = complement(bases[i]); } }
public static void reverseComplement(final byte[] bases, final int offset, final int len) { final int lastIndex = len - 1; int i, j; for (i = offset, j = offset + lastIndex; i < j; ++i, --j) { final byte tmp = complement(bases[i]); bases[i] = complement(bases[j]); bases[j] = tmp; } if (len % 2 == 1) { bases[i] = complement(bases[i]); } }
public static void complement(byte[] bases) { final int lastIndex = bases.length; for (int i = 0; i < lastIndex; i++) { bases[i] = SequenceUtil.complement(bases[i]); } }
/** Reverses and complements the bases in place. */ public static void reverseComplement(final byte[] bases) { final int lastIndex = bases.length - 1; int i, j; for (i=0, j=lastIndex; i<j; ++i, --j) { final byte tmp = complement(bases[i]); bases[i] = complement(bases[j]); bases[j] = tmp; } if (bases.length % 2 == 1) { bases[i] = complement(bases[i]); } }
/** * Return the complementary transition. Both ref and call must be complemented. */ public Transition complement() { return transitionOf((char) SequenceUtil.complement((byte) this.ref), (char) SequenceUtil.complement((byte) this.call)); }
/** * Return the complementary transition. Both ref and call must be complemented. */ public Transition complement() { return transitionOf((char) SequenceUtil.complement((byte) this.ref), (char) SequenceUtil.complement((byte) this.call)); }
private static char stratifySequenceBase(final byte input, final Boolean getComplement) { return (char) SequenceUtil.upperCase(getComplement ? SequenceUtil.complement(input) : input); }
private static char stratifySequenceBase(final byte input, final Boolean getComplement) { return (char) SequenceUtil.upperCase(getComplement ? SequenceUtil.complement(input) : input); }
private static boolean matchesAdapterSequence(String adapter, byte[] read, int readStartOffset, int readDirection, boolean complementAdapter) { boolean nonzeroSize = false; for (int i = 0; readStartOffset + i * readDirection < read.length && readStartOffset + i * readDirection >= 0 && i < adapter.length(); i++) { byte readBase = read[readStartOffset + i * readDirection]; byte adapterBase = (byte)adapter.charAt(i); if (complementAdapter) adapterBase = SequenceUtil.complement(adapterBase); if (SequenceUtil.isValidBase(readBase) && readBase != adapterBase) { return false; } nonzeroSize = true; } return nonzeroSize; // no bases compared = no adapter match } }
public static char complement(char character) { byte base = htsjdk.samtools.util.StringUtil.charToByte(character); base = SequenceUtil.complement(base); return htsjdk.samtools.util.StringUtil.byteToChar(base); }
if (cons[i] == 'N') { int seqOffset = negativeStrand ? seq.length - 1 - i : i; cons[i] = negativeStrand ? SequenceUtil.complement(seq[seqOffset]) : seq[seqOffset];
in.forEach(m -> { if (m.REF_BASE == 'G' || m.REF_BASE == 'T') { m.REF_BASE = (char) SequenceUtil.complement((byte) m.REF_BASE); m.ALT_BASE = (char) SequenceUtil.complement((byte) m.ALT_BASE);
in.forEach(m -> { if (m.REF_BASE == 'G' || m.REF_BASE == 'T') { m.REF_BASE = (char) SequenceUtil.complement((byte) m.REF_BASE); m.ALT_BASE = (char) SequenceUtil.complement((byte) m.ALT_BASE);
private static int homologyLength(ReferenceLookup lookup, int referenceIndex, int referencePosition, int referenceStep, byte[] seq, int seqPosition, int seqStep) { SAMSequenceRecord refSeq = lookup.getSequenceDictionary().getSequence(referenceIndex); int homlen = 0; boolean complement = referenceStep != seqStep; while (seqPosition >= 0 && seqPosition < seq.length && // next step must still be on the contig referencePosition >= 1 && referencePosition <= refSeq.getSequenceLength()) { byte base = seq[seqPosition]; if (complement) { base = SequenceUtil.complement(base); } if (SequenceUtil.basesEqual(base, lookup.getBase(referenceIndex, referencePosition)) && !SequenceUtil.basesEqual(base, SequenceUtil.N)) { referencePosition += referenceStep; seqPosition += seqStep; homlen++; } else { break; } } return homlen; }
final byte baseAsRead = samrec.getReadNegativeStrandFlag() ? SequenceUtil.complement(base) : base; final int read = samrec.getReadPairedFlag() && samrec.getSecondOfPairFlag() ? 2 : 1;
final byte baseAsRead = samrec.getReadNegativeStrandFlag() ? SequenceUtil.complement(base) : base; final int read = samrec.getReadPairedFlag() && samrec.getSecondOfPairFlag() ? 2 : 1;