Examples with GenomicCoords samTextViewer.GenomicCoords used on opensource projects

Example 71 with GenomicCoords

use of samTextViewer.GenomicCoords in project ASCIIGenome by dariober.

the class TrackIntervalFeature method findNextMatch.

public GenomicCoords findNextMatch(GenomicCoords currentGc, Pattern pattern) throws IOException, InvalidGenomicCoordsException {
    IntervalFeature nextFeature = findNextRegexInGenome(pattern, currentGc.getChrom(), currentGc.getTo());
    if (nextFeature == null) {
        return currentGc;
    }
    GenomicCoords nextGc = new GenomicCoords(Utils.coordinatesToString(nextFeature.getChrom(), nextFeature.getFrom(), nextFeature.getFrom() + currentGc.getGenomicWindowSize() - 1), currentGc.getUserWindowSize(), currentGc.getSamSeqDict(), currentGc.getFastaFile());
    return nextGc;
}

Example 72 with GenomicCoords

use of samTextViewer.GenomicCoords in project ASCIIGenome by dariober.

the class TrackIntervalFeature method startEndOfNextFeature.

protected GenomicCoords startEndOfNextFeature(GenomicCoords currentGc, boolean getPrevious) throws InvalidGenomicCoordsException, IOException {
    IntervalFeature nextFeature;
    if (getPrevious) {
        nextFeature = getPreviousFeature(currentGc.getChrom(), currentGc.getFrom());
    } else {
        nextFeature = getNextFeature(currentGc.getChrom(), currentGc.getTo());
    }
    if (nextFeature == null) {
        return currentGc;
    }
    GenomicCoords nextGc = new GenomicCoords(Utils.coordinatesToString(nextFeature.getChrom(), nextFeature.getFrom(), nextFeature.getTo()), currentGc.getUserWindowSize(), currentGc.getSamSeqDict(), currentGc.getFastaFile());
    return nextGc;
}

Example 73 with GenomicCoords

use of samTextViewer.GenomicCoords in project ASCIIGenome by dariober.

the class TextReadTest method canPrintSquashedRead.

@Test
public void canPrintSquashedRead() throws InvalidGenomicCoordsException, IOException, InvalidColourException {
    GenomicCoords gc = new GenomicCoords("chr7:5566778-5566978", 80, samSeqDict, fastaFile);
    SAMRecord rec = new SAMRecord(null);
    rec.setAlignmentStart(5566780);
    rec.setCigarString("24M");
    rec.setReadBases("AACCGGTTAACCGGTTAACCGGTT".getBytes());
    TextRead textRead = new TextRead(rec, gc, false);
    assertEquals(2, textRead.getTextStart());
    assertEquals(11, textRead.getTextEnd());
    assertEquals(textRead.getTextEnd() - textRead.getTextStart() + 1, ">>>>>>>>>>".length());
    assertEquals(textRead.getPrintableTextRead(false, true, false), ">>>>>>>>>>");
// System.out.println(textRead);
}

Example 74 with GenomicCoords

use of samTextViewer.GenomicCoords in project ASCIIGenome by dariober.

the class TextReadTest method canShowInsertion.

@Test
public void canShowInsertion() throws InvalidGenomicCoordsException, IOException, InvalidColourException {
    GenomicCoords gc = new GenomicCoords("chr7:1-80", 80, null, null);
    SAMRecord rec = new SAMRecord(null);
    rec.setAlignmentStart(1);
    rec.setCigarString("1M3I5M1I3M");
    rec.setReadBases("AnnnACCGGnACT".getBytes());
    TextRead tr = new TextRead(rec, gc, false);
    // 7: code for "invert" colours. Checking for "[7;" is brittle since it assumes 7 is the first code.
    assertEquals(2, StringUtils.countMatches(tr.getPrintableTextRead(false, false, false), "[7;"));
    // Ensure it is the first base being marked. I.e. the "A".
    assertTrue(tr.getPrintableTextRead(false, false, false).replaceAll("A.*", "").contains("[7;"));
    // Hide insertion if resolution is not single base
    GenomicCoords gc2 = new GenomicCoords("chr7:1-80", 79, null, null);
    tr = new TextRead(rec, gc2, false);
    assertTrue(!tr.getPrintableTextRead(false, false, false).contains("[7;"));
    rec.setCigarString("4M");
    rec.setReadBases("ACTG".getBytes());
    tr = new TextRead(rec, gc, false);
    assertTrue(!tr.getPrintableTextRead(false, false, false).contains("7"));
    rec.setCigarString("1M");
    rec.setReadBases("A".getBytes());
    tr = new TextRead(rec, gc, false);
}

Example 75 with GenomicCoords

use of samTextViewer.GenomicCoords in project ASCIIGenome by dariober.

the class TextReadTest method canPrintDNARead.

// @Test
// public void canShowSoftClips() throws InvalidGenomicCoordsException, IOException, InvalidColourException {
// 
// GenomicCoords gc= new GenomicCoords("chr7:1-80", 80, null, null);
// SAMRecord rec= new SAMRecord(null);
// rec.setAlignmentStart(1);
// rec.setCigarString("1S10M5S3H");
// 
// TextRead textRead= new TextRead(rec, gc, true);
// 
// System.err.println(textRead.getSoftUnclippedAlignmentStart(textRead.getSamRecord()));
// 
// assertEquals(15, textRead.getTextEnd());
// assertEquals(1, textRead.getTextStart());
// // We start with N even if the first operation is S. This is because the
// // alignment starts at 1 so the first soft clip base(s) is lost on the left.
// assertTrue(textRead.getPrintableTextRead(false, true, false).startsWith("N"));
// assertTrue(textRead.getPrintableTextRead(false, true, false).endsWith("S"));
// 
// rec.setCigarString("10S");
// textRead= new TextRead(rec, gc, true);
// assertEquals(10, textRead.getTextEnd());
// assertEquals(1, textRead.getTextStart());
// 
// rec.setCigarString("1S10M");
// rec.setAlignmentStart(2);
// textRead= new TextRead(rec, gc, true);
// assertEquals(1, textRead.getTextStart());
// 
// rec.setAlignmentStart(3);
// textRead= new TextRead(rec, gc, true);
// assertEquals(2, textRead.getTextStart());
// 
// rec.setCigarString("1S2S10M");
// rec.setAlignmentStart(4);
// textRead= new TextRead(rec, gc, true);
// assertEquals(1, textRead.getTextStart());
// }
@Test
public void canPrintDNARead() throws InvalidGenomicCoordsException, IOException, InvalidColourException {
    GenomicCoords gc = new GenomicCoords("chr7:5566778-5566798", 80, samSeqDict, fastaFile);
    SAMRecord rec = new SAMRecord(null);
    rec.setAlignmentStart(5566780);
    rec.setCigarString("24M");
    rec.setReadNegativeStrandFlag(true);
    rec.setReadBases("AACCGGTTAACCGGTTAACCGGTT".getBytes());
    TextRead textRead = new TextRead(rec, gc, false);
    assertEquals(textRead.getTextStart(), 3);
    assertEquals(textRead.getTextEnd(), 21);
    assertEquals("AACCGGTTAACCGGTTAAC".length(), textRead.getTextEnd() - textRead.getTextStart() + 1);
    System.out.println(textRead.getPrintableTextRead(false, true, false));
    assertEquals("a,ccgg,t,acc,gtt,ac", textRead.getPrintableTextRead(false, true, false));
    assertEquals("a,ccgg,t,uccmgtt,ac", textRead.getPrintableTextRead(true, true, false));
    gc = new GenomicCoords("chr7:5566778-5566798", 80, samSeqDict, null);
    textRead = new TextRead(rec, gc, false);
    assertEquals("aaccggttaaccggttaac", textRead.getPrintableTextRead(false, true, false));
    gc = new GenomicCoords("chr7:5566780-5566782", 80, samSeqDict, fastaFile);
    textRead = new TextRead(rec, gc, false);
    System.out.println(textRead.getPrintableTextRead(true, true, false));
    System.out.println(textRead.getPrintableTextRead(true, false, false));
}