public static GATKSAMRecord createRandomRead(int length) { return createRandomRead(length, true); }
@Test (enabled = true) public void testGetMaxReadLength() { for( final int minLength : Arrays.asList( 5, 30, 50 ) ) { for( final int maxLength : Arrays.asList( 50, 75, 100 ) ) { final List<GATKSAMRecord> reads = new ArrayList<>(); for( int readLength = minLength; readLength <= maxLength; readLength++ ) { reads.add( ReadUtils.createRandomRead( readLength ) ); } Assert.assertEquals(ReadUtils.getMaxReadLength(reads), maxLength, "max length does not match"); } } final List<GATKSAMRecord> reads = new LinkedList<>(); Assert.assertEquals(ReadUtils.getMaxReadLength(reads), 0, "Empty list should have max length of zero"); }
public GATKSAMRecord createReadAndAddToBin(String cigarString, int alignmentStart) { final GATKSAMRecord read = ReadUtils.createRandomRead(readLength); read.setCigarString(cigarString); read.setAlignmentStart(alignmentStart); readBin.add(read); return read; } }
@Test(enabled = true, expectedExceptions={UserException.class}) public void testMoreThanMaxCycleFails() { int readLength = RAC.MAXIMUM_CYCLE_VALUE + 1; GATKSAMRecord read = ReadUtils.createRandomRead(readLength); read.setReadPairedFlag(true); read.setReadGroup(new GATKSAMReadGroupRecord("MY.ID")); read.getReadGroup().setPlatform("illumina"); ReadCovariates readCovariates = new ReadCovariates(read.getReadLength(), 1); covariate.recordValues(read, readCovariates); }
@Test(enabled = true) public void testMaxCyclePasses() { int readLength = RAC.MAXIMUM_CYCLE_VALUE; GATKSAMRecord read = ReadUtils.createRandomRead(readLength); read.setReadPairedFlag(true); read.setReadGroup(new GATKSAMReadGroupRecord("MY.ID")); read.getReadGroup().setPlatform("illumina"); ReadCovariates readCovariates = new ReadCovariates(read.getReadLength(), 1); covariate.recordValues(read, readCovariates); } }
private static void runTest(final GATKSAMReadGroupRecord rg, final String expected, final ReadGroupCovariate covariate) { GATKSAMRecord read = ReadUtils.createRandomRead(10); read.setReadGroup(rg); ReadCovariates readCovariates = new ReadCovariates(read.getReadLength(), 1); covariate.recordValues(read, readCovariates); verifyCovariateArray(readCovariates.getMismatchesKeySet(), expected, covariate); }
@Test(enabled = true) public void testSimpleContexts() { GATKSAMRecord read = ReadUtils.createRandomRead(1000); GATKSAMRecord clippedRead = ReadClipper.clipLowQualEnds(read, RAC.LOW_QUAL_TAIL, ClippingRepresentation.WRITE_NS); ReadCovariates readCovariates = new ReadCovariates(read.getReadLength(), 1); covariate.recordValues(read, readCovariates); verifyCovariateArray(readCovariates.getMismatchesKeySet(), RAC.MISMATCHES_CONTEXT_SIZE, clippedRead, covariate); verifyCovariateArray(readCovariates.getInsertionsKeySet(), RAC.INDELS_CONTEXT_SIZE, clippedRead, covariate); verifyCovariateArray(readCovariates.getDeletionsKeySet(), RAC.INDELS_CONTEXT_SIZE, clippedRead, covariate); }
final GATKSAMRecord read = ReadUtils.createRandomRead(length, false); read.setReadGroup(rg); final byte [] readQuals = new byte[length];
for (final String rgs : readGroups) { final int length = 10 + rnd.nextInt(100); // random read length, at least 10 bp long final GATKSAMRecord read = ReadUtils.createRandomRead(length, false); final GATKSAMReadGroupRecord rg = new GATKSAMReadGroupRecord(rgs); rg.setPlatform("illumina");
@Test(enabled = true) public void testSimpleCycles() { short readLength = 10; GATKSAMRecord read = ReadUtils.createRandomRead(readLength); read.setReadPairedFlag(true); read.setReadGroup(new GATKSAMReadGroupRecord("MY.ID")); read.getReadGroup().setPlatform("illumina"); ReadCovariates readCovariates = new ReadCovariates(read.getReadLength(), 1); covariate.recordValues(read, readCovariates); verifyCovariateArray(readCovariates.getMismatchesKeySet(), 1, (short) 1); read.setReadNegativeStrandFlag(true); covariate.recordValues(read, readCovariates); verifyCovariateArray(readCovariates.getMismatchesKeySet(), readLength, -1); read.setSecondOfPairFlag(true); covariate.recordValues(read, readCovariates); verifyCovariateArray(readCovariates.getMismatchesKeySet(), -readLength, 1); read.setReadNegativeStrandFlag(false); covariate.recordValues(read, readCovariates); verifyCovariateArray(readCovariates.getMismatchesKeySet(), -1, -1); }