@Override public int compare(final ReadFeature o1, final ReadFeature o2) { return o1.getPosition() - o2.getPosition(); } };
var Padding = function(pleft, ptop, pright, pbottom) { this.top = (ptop != null) ? ptop : 20; this.left = (pleft!= null) ? pleft: 1; this.right = (pright!= null) ? pright: 0; this.bottom = (pbottom!= null) ? pbottom: 0; }; function testPadding() { var p; p = new Padding(91, 92, 93, 94); alert(p.left.toString() + "," + p.top.toString() + "," + p.right.toString() + "," + p.bottom.toString()); } testPadding(); // ? testPadding(); // ? testPadding(); // ?
/** * Build an array of substitution frequencies for the given CRAM records. * * @param records * CRAM records to scan * @return a 2D array of frequencies, see * {@link htsjdk.samtools.cram.structure.SubstitutionMatrix} */ static long[][] buildFrequencies(final List<CramCompressionRecord> records) { final long[][] frequencies = new long[BYTE_SPACE_SIZE][BYTE_SPACE_SIZE]; for (final CramCompressionRecord record : records) { if (record.readFeatures != null) { for (final ReadFeature readFeature : record.readFeatures) { if (readFeature.getOperator() == Substitution.operator) { final Substitution substitution = ((Substitution) readFeature); final byte refBase = substitution.getReferenceBase(); final byte base = substitution.getBase(); frequencies[refBase][base]++; } } } } return frequencies; }
/** * Given the records update the substitution matrix with actual substitution * codes. * * @param records * CRAM records * @param substitutionMatrix * the matrix to be updated */ static void updateSubstitutionCodes(final List<CramCompressionRecord> records, final SubstitutionMatrix substitutionMatrix) { for (final CramCompressionRecord record : records) { if (record.readFeatures != null) { for (final ReadFeature recordFeature : record.readFeatures) { if (recordFeature.getOperator() == Substitution.operator) { final Substitution substitution = ((Substitution) recordFeature); if (substitution.getCode() == Substitution.NO_CODE) { final byte refBase = substitution.getReferenceBase(); final byte base = substitution.getBase(); substitution.setCode(substitutionMatrix.code(refBase, base)); } } } } } }
void calculateAlignmentBoundaries() { if (isSegmentUnmapped()) { alignmentSpan = 0; alignmentEnd = SAMRecord.NO_ALIGNMENT_START; } else if (readFeatures == null || readFeatures.isEmpty()) { alignmentSpan = readLength; alignmentEnd = alignmentStart + alignmentSpan - 1; } else { alignmentSpan = readLength; for (final ReadFeature readFeature : readFeatures) { switch (readFeature.getOperator()) { case InsertBase.operator: alignmentSpan--; break; case Insertion.operator: alignmentSpan -= ((Insertion) readFeature).getSequence().length; break; case SoftClip.operator: alignmentSpan -= ((SoftClip) readFeature).getSequence().length; break; case Deletion.operator: alignmentSpan += ((Deletion) readFeature).getLength(); break; default: break; } } alignmentEnd = alignmentStart + alignmentSpan - 1; } }
@Test public void faultyEquality() { final Bases b1 = new Bases(0, new byte[] {}); final Bases b2 = new Bases(0, new byte[] {}); Assert.assertEquals(b1, b2); final Scores s1 = new Scores(0, new byte[] {}); final Scores s2 = new Scores(0, new byte[] {}); Assert.assertEquals(s1, s2); final SoftClip sc1 = new SoftClip(0, new byte[] {}); final SoftClip sc2 = new SoftClip(0, new byte[] {}); Assert.assertEquals(sc1, sc2); } }
private void addInsertion(final List<ReadFeature> features, final int zeroBasedPositionInRead, final int cigarElementLength, final byte[] bases) { final byte[] insertedBases = Arrays.copyOfRange(bases, zeroBasedPositionInRead, zeroBasedPositionInRead + cigarElementLength); for (int i = 0; i < insertedBases.length; i++) { // single base insertion: final InsertBase insertBase = new InsertBase(); insertBase.setPosition(zeroBasedPositionInRead + 1 + i); insertBase.setBase(insertedBases[i]); features.add(insertBase); } }
public static void main(String args[]) { Scores s1 = new Scores(); GameEntry e1 = new GameEntry("Paul", 750); s1.add(e1); GameEntry e2 = new GameEntry("John", 770); s1.add(e2); system.out.println(s1.toString()); e1 = new GameEntry("Sam", 600); s1.add(e1); e2 = new GameEntry("Raj", 800); s1.add(e2); system.out.println(s1.toString()); e1 = new GameEntry("Gobi", 550); s1.add(e1); e2 = new GameEntry("Raj", 580); s1.add(e2); system.out.println(s1.toString()); }
public static void reversePositionsInRead(CramCompressionRecord record) { if (record.readFeatures == null || record.readFeatures.isEmpty()) return; for (ReadFeature f : record.readFeatures) f.setPosition(record.readLength - f.getPosition() - 1); Collections.reverse(record.readFeatures); }
InsertionSort insertionSort; BubbleSort bubbleSort; void setup() { String url = sketchPath("numbers/512/"); insertion = new Insertion(); String[] stringData = null; int[] intData = null; runTest(stringData, intData, url, insertionSort); runTest(stringData, intData, url, bubbleSort); } void runTest(String[] text, int[] number, String url, SortingAlgorithm algorithm) { File directory = new File(url); File[] listOfFiles = directory.listFiles(); for (File file : listOfFiles) { //println(file.getName()); text = loadStrings(file); number = int(text); algorithm.sort(number); } }
private void addSoftClip(final List<ReadFeature> features, final int zeroBasedPositionInRead, final int cigarElementLength, final byte[] bases) { final byte[] insertedBases = Arrays.copyOfRange(bases, zeroBasedPositionInRead, zeroBasedPositionInRead + cigarElementLength); final SoftClip softClip = new SoftClip(zeroBasedPositionInRead + 1, insertedBases); features.add(softClip); }
private void addHardClip(final List<ReadFeature> features, final int zeroBasedPositionInRead, final int cigarElementLength, final byte[] bases) { final byte[] insertedBases = Arrays.copyOfRange(bases, zeroBasedPositionInRead, zeroBasedPositionInRead + cigarElementLength); final HardClip hardClip = new HardClip(zeroBasedPositionInRead + 1, insertedBases.length); features.add(hardClip); }
/** * Given the records update the substitution matrix with actual substitution * codes. * * @param records * CRAM records * @param substitutionMatrix * the matrix to be updated */ static void updateSubstitutionCodes(final List<CramCompressionRecord> records, final SubstitutionMatrix substitutionMatrix) { for (final CramCompressionRecord record : records) { if (record.readFeatures != null) { for (final ReadFeature recordFeature : record.readFeatures) { if (recordFeature.getOperator() == Substitution.operator) { final Substitution substitution = ((Substitution) recordFeature); if (substitution.getCode() == Substitution.NO_CODE) { final byte refBase = substitution.getReferenceBase(); final byte base = substitution.getBase(); substitution.setCode(substitutionMatrix.code(refBase, base)); } } } } } }
void calculateAlignmentBoundaries() { if (isSegmentUnmapped()) { alignmentSpan = 0; alignmentEnd = SAMRecord.NO_ALIGNMENT_START; } else if (readFeatures == null || readFeatures.isEmpty()) { alignmentSpan = readLength; alignmentEnd = alignmentStart + alignmentSpan - 1; } else { alignmentSpan = readLength; for (final ReadFeature readFeature : readFeatures) { switch (readFeature.getOperator()) { case InsertBase.operator: alignmentSpan--; break; case Insertion.operator: alignmentSpan -= ((Insertion) readFeature).getSequence().length; break; case SoftClip.operator: alignmentSpan -= ((SoftClip) readFeature).getSequence().length; break; case Deletion.operator: alignmentSpan += ((Deletion) readFeature).getLength(); break; default: break; } } alignmentEnd = alignmentStart + alignmentSpan - 1; } }
/** * Build an array of substitution frequencies for the given CRAM records. * * @param records * CRAM records to scan * @return a 2D array of frequencies, see * {@link htsjdk.samtools.cram.structure.SubstitutionMatrix} */ static long[][] buildFrequencies(final List<CramCompressionRecord> records) { final long[][] frequencies = new long[BYTE_SPACE_SIZE][BYTE_SPACE_SIZE]; for (final CramCompressionRecord record : records) { if (record.readFeatures != null) { for (final ReadFeature readFeature : record.readFeatures) { if (readFeature.getOperator() == Substitution.operator) { final Substitution substitution = ((Substitution) readFeature); final byte refBase = substitution.getReferenceBase(); final byte base = substitution.getBase(); frequencies[refBase][base]++; } } } } return frequencies; }
private void addInsertion(final List<ReadFeature> features, final int zeroBasedPositionInRead, final int cigarElementLength, final byte[] bases) { final byte[] insertedBases = Arrays.copyOfRange(bases, zeroBasedPositionInRead, zeroBasedPositionInRead + cigarElementLength); for (int i = 0; i < insertedBases.length; i++) { // single base insertion: final InsertBase insertBase = new InsertBase(); insertBase.setPosition(zeroBasedPositionInRead + 1 + i); insertBase.setBase(insertedBases[i]); features.add(insertBase); } }
@Override public int compare(final ReadFeature o1, final ReadFeature o2) { return o1.getPosition() - o2.getPosition(); } };
private void addSoftClip(final List<ReadFeature> features, final int zeroBasedPositionInRead, final int cigarElementLength, final byte[] bases) { final byte[] insertedBases = Arrays.copyOfRange(bases, zeroBasedPositionInRead, zeroBasedPositionInRead + cigarElementLength); final SoftClip softClip = new SoftClip(zeroBasedPositionInRead + 1, insertedBases); features.add(softClip); }
private void addHardClip(final List<ReadFeature> features, final int zeroBasedPositionInRead, final int cigarElementLength, final byte[] bases) { final byte[] insertedBases = Arrays.copyOfRange(bases, zeroBasedPositionInRead, zeroBasedPositionInRead + cigarElementLength); final HardClip hardClip = new HardClip(zeroBasedPositionInRead + 1, insertedBases.length); features.add(hardClip); }
@Override public int compare(final ReadFeature o1, final ReadFeature o2) { return o1.getPosition() - o2.getPosition(); } };