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

Example 11 with Read

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

the class GATKReadAdaptersUnitTest method readNumberTestData.

@DataProvider(name = "ReadNumberTestData")
public Object[][] readNumberTestData() {
    SAMRecord secondOfPairSam = basicSAMRecord();
    secondOfPairSam.setSecondOfPairFlag(true);
    secondOfPairSam.setFirstOfPairFlag(false);
    Read secondOfPairGoogleRead = basicGoogleGenomicsRead();
    secondOfPairGoogleRead.setReadNumber(1);
    return new Object[][] { { basicReadBackedBySam(), true, false }, { basicReadBackedByGoogle(), true, false }, { new SAMRecordToGATKReadAdapter(secondOfPairSam), false, true }, { new GoogleGenomicsReadToGATKReadAdapter(secondOfPairGoogleRead), false, true } };
}

Example 12 with Read

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

the class GATKReadAdaptersUnitTest method getAndSetMatePositionData.

@DataProvider(name = "GetAndSetMatePositionData")
public Object[][] getAndSetMatePositionData() {
    final SAMRecord samWithUnmappedMate = basicSAMRecord();
    samWithUnmappedMate.setMateUnmappedFlag(true);
    final Read googleReadWithUnmappedMate = basicGoogleGenomicsRead();
    // NOTE: we're taking advantage here of a quirk of the current adapter implementation to allow us to run
    // all the getSAMString tests.
    //
    // The GoogleGenomicsReadToGATKReadAdapter throws if the caller attempts to call isMateReverseStrand
    // when it has never previously been explicitly set to true or false, but we need to query it in order
    // to get the flags needed for getSAMString. In order to ensure that all of the getSAMString tests here
    // can query this flag, we artificially set a matePosition with no position value but with the reverseStrandFlag
    // set to false. Doing this does not toggle the value returned by the mateIsUnmapped (it will still return true),
    // and ensures that we will subsequently be able to run all the getSAMString tests on these reads once they have
    // had a mate position established.
    //
    // (See the note on setMatePosition in GoogleGenomicsReadToGATKReadAdapter)
    final Position matePos = new Position();
    matePos.setReverseStrand(false);
    googleReadWithUnmappedMate.setNextMatePosition(matePos);
    // verify that the read still has mateIsUnmapped == true
    Assert.assertTrue(new GoogleGenomicsReadToGATKReadAdapter(googleReadWithUnmappedMate).mateIsUnmapped());
    return new Object[][] { { basicReadBackedBySam(), BASIC_READ_MATE_CONTIG, BASIC_READ_MATE_START }, { basicReadBackedByGoogle(), BASIC_READ_MATE_CONTIG, BASIC_READ_MATE_START }, { new SAMRecordToGATKReadAdapter(samWithUnmappedMate), null, ReadConstants.UNSET_POSITION }, { new GoogleGenomicsReadToGATKReadAdapter(googleReadWithUnmappedMate), null, ReadConstants.UNSET_POSITION } };
}

Example 13 with Read

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

the class GATKReadAdaptersUnitTest method getAndSetBasesData.

@DataProvider(name = "GetAndSetBasesData")
public Object[][] getAndSetBasesData() {
    final SAMRecord baselessSam = basicSAMRecord();
    baselessSam.setReadBases(null);
    final SAMRecord noAlignedSequenceSam = basicSAMRecord();
    noAlignedSequenceSam.setReadBases(SAMRecord.NULL_SEQUENCE);
    final Read baselessGoogleRead = basicGoogleGenomicsRead();
    baselessGoogleRead.setAlignedSequence(null);
    final Read emptyStringSequenceGoogleRead = basicGoogleGenomicsRead();
    emptyStringSequenceGoogleRead.setAlignedSequence("");
    final Read noAlignedSequenceGoogleRead = basicGoogleGenomicsRead();
    noAlignedSequenceGoogleRead.setAlignedSequence(SAMRecord.NULL_SEQUENCE_STRING);
    return new Object[][] { { basicReadBackedBySam(), BASIC_READ_BASES, "ACGT" }, { basicReadBackedByGoogle(), BASIC_READ_BASES, "ACGT" }, { new SAMRecordToGATKReadAdapter(baselessSam), new byte[0], "*" }, { new SAMRecordToGATKReadAdapter(noAlignedSequenceSam), new byte[0], "*" }, { new GoogleGenomicsReadToGATKReadAdapter(baselessGoogleRead), new byte[0], "*" }, { new GoogleGenomicsReadToGATKReadAdapter(emptyStringSequenceGoogleRead), new byte[0], "*" }, { new GoogleGenomicsReadToGATKReadAdapter(noAlignedSequenceGoogleRead), new byte[0], "*" } };
}

Example 14 with Read

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

the class GATKReadAdaptersUnitTest method invalidMateIsUnmappedData.

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

Example 15 with Read

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

the class GATKReadAdaptersUnitTest method mateIsUnmappedData.

@DataProvider(name = "MateIsUnmappedData")
public Object[][] mateIsUnmappedData() {
    SAMRecord samWithUnmappedMate = basicSAMRecord();
    samWithUnmappedMate.setMateUnmappedFlag(true);
    SAMRecord samWithUnmappedMate2 = basicSAMRecord();
    samWithUnmappedMate2.setMateReferenceName(SAMRecord.NO_ALIGNMENT_REFERENCE_NAME);
    SAMRecord samWithUnmappedMate3 = basicSAMRecord();
    samWithUnmappedMate3.setMateAlignmentStart(SAMRecord.NO_ALIGNMENT_START);
    Read googleReadWithUnmappedMate = basicGoogleGenomicsRead();
    // We have to explicitly set the mate reverse strand flag in order to ensure that we can call getSAMString
    // on the read once its been wrapped by the adapter; if it hasn't been explicitly set the adapter will
    // throw when we query for the flags.
    Position newPosition = new Position();
    newPosition.setReverseStrand(false);
    googleReadWithUnmappedMate.setNextMatePosition(newPosition);
    Read googleReadWithUnmappedMate2 = basicGoogleGenomicsRead();
    googleReadWithUnmappedMate2.getNextMatePosition().setReferenceName(SAMRecord.NO_ALIGNMENT_REFERENCE_NAME);
    Read googleReadWithUnmappedMate3 = basicGoogleGenomicsRead();
    googleReadWithUnmappedMate3.getNextMatePosition().setPosition(-1l);
    Read googleReadWithUnmappedMate4 = basicGoogleGenomicsRead();
    googleReadWithUnmappedMate4.getNextMatePosition().setReferenceName(null);
    Read googleReadWithUnmappedMate5 = basicGoogleGenomicsRead();
    googleReadWithUnmappedMate5.getNextMatePosition().setPosition(null);
    return new Object[][] { { basicReadBackedBySam(), false }, { basicReadBackedByGoogle(), false }, { new SAMRecordToGATKReadAdapter(samWithUnmappedMate), true }, { new SAMRecordToGATKReadAdapter(samWithUnmappedMate2), true }, { new SAMRecordToGATKReadAdapter(samWithUnmappedMate3), true }, { new GoogleGenomicsReadToGATKReadAdapter(googleReadWithUnmappedMate), true }, { new GoogleGenomicsReadToGATKReadAdapter(googleReadWithUnmappedMate2), true }, { new GoogleGenomicsReadToGATKReadAdapter(googleReadWithUnmappedMate3), true }, { new GoogleGenomicsReadToGATKReadAdapter(googleReadWithUnmappedMate4), true }, { new GoogleGenomicsReadToGATKReadAdapter(googleReadWithUnmappedMate5), true } };
}