Examples with Read com.google.api.services.genomics.model.Read used on opensource projects

Example 16 with Read

use of com.google.api.services.genomics.model.Read in project gatk by broadinstitute.

the class GATKReadAdaptersUnitTest method mateIsReverseStrandData.

@DataProvider(name = "MateIsReverseStrandData")
public Object[][] mateIsReverseStrandData() {
    SAMRecord samWithReverseStrandMate = basicSAMRecord();
    samWithReverseStrandMate.setMateNegativeStrandFlag(true);
    Read googleReadWithReverseStrandMate = basicGoogleGenomicsRead();
    googleReadWithReverseStrandMate.getNextMatePosition().setReverseStrand(true);
    return new Object[][] { { basicReadBackedBySam(), false }, { basicReadBackedByGoogle(), false }, { new SAMRecordToGATKReadAdapter(samWithReverseStrandMate), true }, { new GoogleGenomicsReadToGATKReadAdapter(googleReadWithReverseStrandMate), true } };
}

Example 17 with Read

use of com.google.api.services.genomics.model.Read in project gatk by broadinstitute.

the class GATKReadAdaptersUnitTest method invalidMateIsReverseStrandData.

@DataProvider(name = "InvalidMateIsReverseStrandData")
public Object[][] invalidMateIsReverseStrandData() {
    SAMRecord unpairedSAM = basicSAMRecord();
    unpairedSAM.setReadPairedFlag(false);
    Read unpairedGoogleRead = basicGoogleGenomicsRead();
    unpairedGoogleRead.setNumberReads(1);
    return new Object[][] { { new SAMRecordToGATKReadAdapter(unpairedSAM) }, { new GoogleGenomicsReadToGATKReadAdapter(unpairedGoogleRead) } };
}

Example 18 with Read

use of com.google.api.services.genomics.model.Read in project gatk by broadinstitute.

the class GATKReadAdaptersUnitTest method getAssignedPositionData.

@DataProvider(name = "GetAssignedPositionData")
public Object[][] getAssignedPositionData() {
    List<Object[]> testCases = new ArrayList<>();
    testCases.add(new Object[] { basicReadBackedBySam(), BASIC_READ_CONTIG, BASIC_READ_START });
    testCases.add(new Object[] { basicReadBackedByGoogle(), BASIC_READ_CONTIG, BASIC_READ_START });
    // SAMRecord, unmapped flag set, but has an assigned position
    final SAMRecord unmappedFlagSam = basicSAMRecord();
    unmappedFlagSam.setReadUnmappedFlag(true);
    testCases.add(new Object[] { new SAMRecordToGATKReadAdapter(unmappedFlagSam), BASIC_READ_CONTIG, BASIC_READ_START });
    // SAMRecord, unmapped flag not set, but no contig
    final SAMRecord unmappedContigSam = basicSAMRecord();
    unmappedContigSam.setReferenceName(SAMRecord.NO_ALIGNMENT_REFERENCE_NAME);
    testCases.add(new Object[] { new SAMRecordToGATKReadAdapter(unmappedContigSam), SAMRecord.NO_ALIGNMENT_REFERENCE_NAME, BASIC_READ_START });
    // SAMRecord, unmapped flag not set, but no start
    final SAMRecord noAlignmentStartSam = basicSAMRecord();
    noAlignmentStartSam.setAlignmentStart(SAMRecord.NO_ALIGNMENT_START);
    testCases.add(new Object[] { new SAMRecordToGATKReadAdapter(noAlignmentStartSam), BASIC_READ_CONTIG, ReadConstants.UNSET_POSITION });
    // Google read, no alignment
    final Read noAlignmentGoogleRead = basicGoogleGenomicsRead();
    noAlignmentGoogleRead.setAlignment(null);
    testCases.add(new Object[] { new GoogleGenomicsReadToGATKReadAdapter(noAlignmentGoogleRead), null, ReadConstants.UNSET_POSITION });
    // Google read, no position
    final Read noPositionGoogleRead = basicGoogleGenomicsRead();
    noPositionGoogleRead.getAlignment().setPosition(null);
    testCases.add(new Object[] { new GoogleGenomicsReadToGATKReadAdapter(noPositionGoogleRead), null, ReadConstants.UNSET_POSITION });
    // Google read, position with no contig
    final Read noContigGoogleRead = basicGoogleGenomicsRead();
    noContigGoogleRead.getAlignment().getPosition().setReferenceName(null);
    testCases.add(new Object[] { new GoogleGenomicsReadToGATKReadAdapter(noContigGoogleRead), null, BASIC_READ_START });
    // Google read, position with * contig
    final Read starContigGoogleRead = basicGoogleGenomicsRead();
    starContigGoogleRead.getAlignment().getPosition().setReferenceName(SAMRecord.NO_ALIGNMENT_REFERENCE_NAME);
    testCases.add(new Object[] { new GoogleGenomicsReadToGATKReadAdapter(starContigGoogleRead), SAMRecord.NO_ALIGNMENT_REFERENCE_NAME, BASIC_READ_START });
    // Google read, position with contig but no start
    final Read noStartGoogleRead = basicGoogleGenomicsRead();
    noStartGoogleRead.getAlignment().getPosition().setPosition(-1l);
    testCases.add(new Object[] { new GoogleGenomicsReadToGATKReadAdapter(noStartGoogleRead), BASIC_READ_CONTIG, ReadConstants.UNSET_POSITION });
    return testCases.toArray(new Object[][] {});
}

Example 19 with Read

use of com.google.api.services.genomics.model.Read in project gatk by broadinstitute.

the class GATKReadAdaptersUnitTest method getAndSetCigarData.

@DataProvider(name = "GetAndSetCigarData")
public Object[][] getAndSetCigarData() {
    SAMRecord noCigarSam = basicSAMRecord();
    noCigarSam.setCigar(null);
    SAMRecord emptyCigarSam = basicSAMRecord();
    emptyCigarSam.setCigar(new Cigar());
    Read noCigarRead = basicGoogleGenomicsRead();
    noCigarRead.getAlignment().setCigar(null);
    Read emptyCigarRead = basicGoogleGenomicsRead();
    emptyCigarRead.getAlignment().setCigar(null);
    return new Object[][] { { basicReadBackedBySam(), TextCigarCodec.decode(BASIC_READ_CIGAR) }, { basicReadBackedByGoogle(), TextCigarCodec.decode(BASIC_READ_CIGAR) }, { new SAMRecordToGATKReadAdapter(noCigarSam), new Cigar() }, { new SAMRecordToGATKReadAdapter(emptyCigarSam), new Cigar() }, { new GoogleGenomicsReadToGATKReadAdapter(noCigarRead), new Cigar() }, { new GoogleGenomicsReadToGATKReadAdapter(emptyCigarRead), new Cigar() } };
}

Example 20 with Read

use of com.google.api.services.genomics.model.Read in project gatk by broadinstitute.

the class GATKReadAdaptersUnitTest method getAndSetMappingQualityData.

@DataProvider(name = "GetAndSetMappingQualityData")
public Object[][] getAndSetMappingQualityData() {
    final SAMRecord samWithMappingQualityZero = basicSAMRecord();
    samWithMappingQualityZero.setMappingQuality(0);
    final Read googleReadWithMappingQualityZero = basicGoogleGenomicsRead();
    googleReadWithMappingQualityZero.getAlignment().setMappingQuality(0);
    final Read googleReadWithNoMappingQuality = basicGoogleGenomicsRead();
    googleReadWithNoMappingQuality.getAlignment().setMappingQuality(null);
    return new Object[][] { { basicReadBackedBySam(), BASIC_READ_MAPPING_QUALITY }, { basicReadBackedByGoogle(), BASIC_READ_MAPPING_QUALITY }, { new SAMRecordToGATKReadAdapter(samWithMappingQualityZero), 0 }, { new GoogleGenomicsReadToGATKReadAdapter(googleReadWithMappingQualityZero), 0 }, { new GoogleGenomicsReadToGATKReadAdapter(googleReadWithNoMappingQuality), ReadConstants.NO_MAPPING_QUALITY } };
}