Examples with SAMFileHeader htsjdk.samtools.SAMFileHeader used on opensource projects

Example 46 with SAMFileHeader

use of htsjdk.samtools.SAMFileHeader in project gatk by broadinstitute.

the class SATagBuilderUnitTests method testSetReadsAsSupplementalNo.

@Test
public static void testSetReadsAsSupplementalNo() {
    final SAMFileHeader header = ArtificialReadUtils.createArtificialSamHeader();
    GATKRead primarySup = ArtificialReadUtils.createArtificialRead(header, "read1", 1, 10000, new byte[] {}, new byte[] {}, "4M");
    primarySup.setMappingQuality(100);
    primarySup.setAttribute("NM", 20);
    primarySup.setIsReverseStrand(true);
    GATKRead secondarySup = ArtificialReadUtils.createArtificialRead(header, "read1", 2, 10001, new byte[] {}, new byte[] {}, "4S");
    secondarySup.setMappingQuality(200);
    List<GATKRead> sups = new ArrayList<>();
    sups.add(secondarySup);
    SATagBuilder.setReadsAsSupplemental(primarySup, sups);
    Assert.assertEquals(primarySup.getAttributeAsString("SA"), "3,10001,+,4S,200,*;");
    Assert.assertEquals(primarySup.isSupplementaryAlignment(), false);
    Assert.assertEquals(secondarySup.getAttributeAsString("SA"), "2,10000,-,4M,100,20;");
    Assert.assertEquals(secondarySup.isSupplementaryAlignment(), true);
    GATKRead tertiarySup = ArtificialReadUtils.createArtificialRead(header, "read1", 3, 10003, new byte[] {}, new byte[] {}, "4D");
    tertiarySup.setMappingQuality(200);
    primarySup.clearAttribute("SA");
    secondarySup.clearAttribute("SA");
    sups.add(tertiarySup);
    SATagBuilder.setReadsAsSupplemental(primarySup, sups);
    Assert.assertEquals(sups.size(), 2);
    Assert.assertEquals(sups.get(0).getAttributeAsString("SA"), "2,10000,-,4M,100,20;4,10003,+,4D,200,*;");
    Assert.assertTrue(sups.get(1).getAttributeAsString("SA").startsWith("2,10000,-,4M,100,20;"));
    Assert.assertTrue(primarySup.getAttributeAsString("SA").contains("4,10003,+,4D,200,*;"));
    Assert.assertTrue(primarySup.getAttributeAsString("SA").contains("3,10001,+,4S,200,*;"));
    GATKRead unmappedSup = ArtificialReadUtils.createArtificialUnmappedRead(header, new byte[] {}, new byte[] {});
    primarySup.clearAttribute("SA");
    sups.clear();
    sups.add(unmappedSup);
    SATagBuilder.setReadsAsSupplemental(primarySup, sups);
    Assert.assertEquals(primarySup.getAttributeAsString("SA"), "*,0,+,*,0,*;");
    Assert.assertEquals(sups.get(0).getAttributeAsString("SA"), "2,10000,-,4M,100,20;");
}

Example 47 with SAMFileHeader

use of htsjdk.samtools.SAMFileHeader in project gatk by broadinstitute.

the class SATagBuilderUnitTests method testRemoveTagFunctionality.

@Test
public static void testRemoveTagFunctionality() {
    final SAMFileHeader header = ArtificialReadUtils.createArtificialSamHeader();
    GATKRead testRead = ArtificialReadUtils.createArtificialRead(header, "read1", 1, 10002, new byte[] {}, new byte[] {}, "4M");
    final String attributeVal = "2,10000,+,4M,100,20;4,10003,+,4D,200,0;2,10000,-,4M,100,20;";
    testRead.setAttribute("SA", attributeVal);
    SATagBuilder builder = new SATagBuilder(testRead);
    // Testing that unrelated reads are not removed from the list
    GATKRead unRelatedRead = ArtificialReadUtils.createArtificialRead(header, "read3", 3, 1000, new byte[] {}, new byte[] {}, "4D");
    builder.removeTag(unRelatedRead).setSATag();
    Assert.assertEquals(testRead.getAttributeAsString("SA"), attributeVal);
    // Testing that ALL instances of a particular tag get removed
    GATKRead relatedRead = ArtificialReadUtils.createArtificialRead(header, "read1", 1, 10000, new byte[] {}, new byte[] {}, "4M");
    builder.removeTag(relatedRead).setSATag();
    Assert.assertEquals(testRead.getAttributeAsString("SA"), "4,10003,+,4D,200,0;");
}

Example 48 with SAMFileHeader

use of htsjdk.samtools.SAMFileHeader in project gatk by broadinstitute.

the class NGSPlatformUnitTest method testReadWithoutRG.

@Test
public void testReadWithoutRG() {
    final SAMFileHeader header = ArtificialReadUtils.createArtificialSamHeader(seq.getSequenceDictionary());
    final GATKRead read = ArtificialReadUtils.createArtificialRead(header, "myRead", 0, 1, 10);
    Assert.assertEquals(NGSPlatform.fromRead(read, header), NGSPlatform.UNKNOWN);
}

Example 49 with SAMFileHeader

use of htsjdk.samtools.SAMFileHeader in project gatk by broadinstitute.

the class NGSPlatformUnitTest method testPLFromReadWithRGButNoPL.

@Test()
public void testPLFromReadWithRGButNoPL() {
    final SAMFileHeader header = ArtificialReadUtils.createArtificialSamHeader(seq.getSequenceDictionary());
    final String rgID = "ID";
    final SAMReadGroupRecord rg = new SAMReadGroupRecord(rgID);
    header.addReadGroup(rg);
    final GATKRead read = ArtificialReadUtils.createArtificialRead(header, "myRead", 0, 1, 10);
    read.setAttribute("RG", rgID);
    Assert.assertEquals(NGSPlatform.fromRead(read, header), NGSPlatform.UNKNOWN);
}

Example 50 with SAMFileHeader

use of htsjdk.samtools.SAMFileHeader in project gatk by broadinstitute.

the class IntervalUtilsUnitTest method testIntervalFileToListNegativeOneLength.

// TODO - remove once a corrected version of the exome interval list is released.
@Test(dataProvider = "negativeOneLengthIntervalTestData")
public void testIntervalFileToListNegativeOneLength(GenomeLocParser genomeLocParser, String contig, int intervalStart, int intervalEnd) throws Exception {
    final SAMFileHeader picardFileHeader = new SAMFileHeader();
    picardFileHeader.addSequence(genomeLocParser.getContigInfo("1"));
    final IntervalList picardIntervals = new IntervalList(picardFileHeader);
    // Need one good interval or else a UserException.MalformedFile( is thrown if no intervals
    picardIntervals.add(new Interval(contig, 1, 2, true, "dummyname0"));
    picardIntervals.add(new Interval(contig, intervalStart, intervalEnd, true, "dummyname1"));
    final File picardIntervalFile = createTempFile("testIntervalFileToListNegativeOneLength", ".intervals");
    picardIntervals.write(picardIntervalFile);
    IntervalUtils.intervalFileToList(genomeLocParser, picardIntervalFile.getAbsolutePath());
}