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Merge pull request #212 from broadinstitute/md_misc_improvements 

Several important bugfixes / improvements to general GATK infrastructure
This commit is contained in:
Mark DePristo 2013-05-03 08:20:55 -07:00
parent aefddaa219 f42bb86bdd
commit 8bac61f9fb
15 changed files with 85 additions and 39 deletions
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14
protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/DeBruijnAssembler.java
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@ -410,9 +410,6 @@ public class DeBruijnAssembler extends LocalAssemblyEngine {
// extend partial haplotypes which are anchored in the reference to include the full active region
h = extendPartialHaplotype(h, activeRegionStart, refWithPadding);
final Cigar leftAlignedCigar = leftAlignCigarSequentially(AlignmentUtils.consolidateCigar(h.getCigar()), refWithPadding, h.getBases(), activeRegionStart, 0);
if( leftAlignedCigar.getReferenceLength() != refHaplotype.getCigar().getReferenceLength() ) { // left alignment failure
continue;
}
if( !returnHaplotypes.contains(h) ) {
h.setAlignmentStartHapwrtRef(activeRegionStart);
h.setCigar(leftAlignedCigar);
@ -548,9 +545,8 @@ public class DeBruijnAssembler extends LocalAssemblyEngine {
final CigarElement ce = cigar.getCigarElement(i);
if (ce.getOperator() == CigarOperator.D || ce.getOperator() == CigarOperator.I) {
cigarToAlign.add(ce);
for( final CigarElement toAdd : AlignmentUtils.leftAlignIndel(cigarToAlign, refSeq, readSeq, refIndex, readIndex, false).getCigarElements() ) {
cigarToReturn.add(toAdd);
}
final Cigar leftAligned = AlignmentUtils.leftAlignSingleIndel(cigarToAlign, refSeq, readSeq, refIndex, readIndex, false);
for ( final CigarElement toAdd : leftAligned.getCigarElements() ) { cigarToReturn.add(toAdd); }
refIndex += cigarToAlign.getReferenceLength();
readIndex += cigarToAlign.getReadLength();
cigarToAlign = new Cigar();
@ -563,7 +559,11 @@ public class DeBruijnAssembler extends LocalAssemblyEngine {
cigarToReturn.add(toAdd);
}
}
return cigarToReturn;
final Cigar result = AlignmentUtils.consolidateCigar(cigarToReturn);
if( result.getReferenceLength() != cigar.getReferenceLength() )
throw new IllegalStateException("leftAlignCigarSequentially failed to produce a valid CIGAR. Reference lengths differ. Initial cigar " + cigar + " left aligned into " + result);
return result;
}
/**

2
protected/java/test/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReadsIntegrationTest.java
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@ -259,7 +259,7 @@ public class ReduceReadsIntegrationTest extends WalkerTest {
public void testDivideByZero() {
String base = String.format("-T ReduceReads %s -npt -R %s -I %s", DIVIDEBYZERO_L, REF, DIVIDEBYZERO_BAM) + " -o %s ";
// we expect to lose coverage due to the downsampling so don't run the systematic tests
executeTestWithoutAdditionalRRTests("testDivideByZero", new WalkerTestSpec(base, Arrays.asList("bam"), Arrays.asList("1663f35802f82333c5e15653e437ce2d")));
executeTestWithoutAdditionalRRTests("testDivideByZero", new WalkerTestSpec(base, Arrays.asList("bam"), Arrays.asList("c459a6153a17c2cbf8441e1918fda9c8")));
}
/**

2
protected/java/test/org/broadinstitute/sting/gatk/walkers/diagnostics/ErrorRatePerCycleIntegrationTest.java
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@ -57,7 +57,7 @@ public class ErrorRatePerCycleIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec(
"-T ErrorRatePerCycle -R " + b37KGReference + " -I " + b37GoodBAM + " -L 20:10,000,000-10,100,000 -o %s",
1,
Arrays.asList("dccdf3cb3193d01a1a767097e4a5c35e"));
Arrays.asList("6191340f0b56ee81fb248c8f5c913a8e"));
executeTest("ErrorRatePerCycle:", spec);
}
}

6
protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperGeneralPloidySuite2IntegrationTest.java
View File

@ -58,16 +58,16 @@ public class UnifiedGenotyperGeneralPloidySuite2IntegrationTest extends WalkerTe
@Test(enabled = true)
public void testINDEL_maxAltAlleles2_ploidy3_Pools_noRef() {
executor.PC_LSV_Test_NoRef(" -maxAltAlleles 2 -ploidy 3","LSV_INDEL_DISC_NOREF_p3","INDEL","5eabc12fc7b4f9749e6d1be0f5b45d14");
executor.PC_LSV_Test_NoRef(" -maxAltAlleles 2 -ploidy 3","LSV_INDEL_DISC_NOREF_p3","INDEL","9f960977b1b8d90ac75ba4306336553c");
}
@Test(enabled = true)
public void testMT_SNP_DISCOVERY_sp4() {
executor.PC_MT_Test(CEUTRIO_BAM, " -maxAltAlleles 1 -ploidy 8", "MT_SNP_DISCOVERY_sp4","71b7b9eac1e4a9b2b7e8c3689d1f29ec");
executor.PC_MT_Test(CEUTRIO_BAM, " -maxAltAlleles 1 -ploidy 8", "MT_SNP_DISCOVERY_sp4","eb8b008a463f9fa9ad0155bf2f5b78b3");
}
@Test(enabled = true)
public void testMT_SNP_GGA_sp10() {
executor.PC_MT_Test(CEUTRIO_BAM, String.format(" -maxAltAlleles 1 -ploidy 20 -gt_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -alleles %s",NA12891_CALLS), "MT_SNP_GGA_sp10", "fc36e925e269b035d4b27edb661be06b");
executor.PC_MT_Test(CEUTRIO_BAM, String.format(" -maxAltAlleles 1 -ploidy 20 -gt_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -alleles %s",NA12891_CALLS), "MT_SNP_GGA_sp10", "fb988e9b93bc73b5e532584c83cac833");
}
}

10
protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIndelCallingIntegrationTest.java
View File

@ -73,7 +73,7 @@ public class UnifiedGenotyperIndelCallingIntegrationTest extends WalkerTest {
" -o %s" +
" -L 1:10,000,000-10,500,000",
1,
Arrays.asList("ea4c4e020f59f48901d5820c8e4f6001"));
Arrays.asList("19f77f557150905ef3fa4713f611a1b9"));
executeTest(String.format("test indel caller in SLX"), spec);
}
@ -101,7 +101,7 @@ public class UnifiedGenotyperIndelCallingIntegrationTest extends WalkerTest {
" -o %s" +
" -L 1:10,000,000-10,500,000",
1,
Arrays.asList("8d9b8f8a1479322961c840e461b6dba8"));
Arrays.asList("bb3dbad9666ebf38d338f0c9c211a42e"));
executeTest(String.format("test indel calling, multiple technologies"), spec);
}
@ -111,7 +111,7 @@ public class UnifiedGenotyperIndelCallingIntegrationTest extends WalkerTest {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
baseCommandIndels + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + privateTestDir + "indelAllelesForUG.vcf -I " + validationDataLocation +
"pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,100,000", 1,
Arrays.asList("79f7fc64da8f25eda1f1ee139ecdd657"));
Arrays.asList("8052390ca2b6a57c3ddf379a51225d64"));
executeTest("test MultiSample Pilot2 indels with alleles passed in", spec);
}
@ -121,7 +121,7 @@ public class UnifiedGenotyperIndelCallingIntegrationTest extends WalkerTest {
baseCommandIndels + " --output_mode EMIT_ALL_SITES --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles "
+ privateTestDir + "indelAllelesForUG.vcf -I " + validationDataLocation +
"pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,100,000", 1,
Arrays.asList("15508fcf61380a91b6611307f182447b"));
Arrays.asList("b6b9dba97fbabaeeb458a41051983e7b"));
executeTest("test MultiSample Pilot2 indels with alleles passed in and emitting all sites", spec);
}
@ -136,7 +136,7 @@ public class UnifiedGenotyperIndelCallingIntegrationTest extends WalkerTest {
WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec(
baseCommandIndels + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + result.get(0).getAbsolutePath() + " -I " + validationDataLocation +
"low_coverage_CEU.chr1.10k-11k.bam -o %s -L " + result.get(0).getAbsolutePath(), 1,
Arrays.asList("3d4d66cc253eac55f16e5b0a36f17d8d"));
Arrays.asList("38730c7030271f5d0ca0b59365d57814"));
executeTest("test MultiSample Pilot1 CEU indels using GENOTYPE_GIVEN_ALLELES", spec2);
}

2
protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperNormalCallingIntegrationTest.java
View File

@ -64,7 +64,7 @@ public class UnifiedGenotyperNormalCallingIntegrationTest extends WalkerTest{
public void testMultiSamplePilot1() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
baseCommand + " -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -o %s -L 1:10,022,000-10,025,000", 1,
Arrays.asList("a6c224235c21b4af816b1512eb0624df"));
Arrays.asList("5e8f1fa88dc93320cc0e75e9fe6e153b"));
executeTest("test MultiSample Pilot1", spec);
}

18
protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/DeBruijnAssemblerUnitTest.java
View File

@ -52,10 +52,7 @@ package org.broadinstitute.sting.gatk.walkers.haplotypecaller;
* Date: 3/27/12
*/
import net.sf.samtools.Cigar;
import net.sf.samtools.CigarElement;
import net.sf.samtools.CigarOperator;
import net.sf.samtools.SAMFileHeader;
import net.sf.samtools.*;
import org.broadinstitute.sting.BaseTest;
import org.broadinstitute.sting.gatk.walkers.haplotypecaller.graphs.DeBruijnGraph;
import org.broadinstitute.sting.utils.haplotype.Haplotype;
@ -125,6 +122,17 @@ public class DeBruijnAssemblerUnitTest extends BaseTest {
}
}
@Test(enabled = true)
public void testLeftAlignCigarSequentiallyAdjacentID() {
final String ref = "GTCTCTCTCTCTCTCTCTATATATATATATATATTT";
final String hap = "GTCTCTCTCTCTCTCTCTCTCTATATATATATATTT";
final Cigar originalCigar = TextCigarCodec.getSingleton().decode("18M4I12M4D2M");
final Cigar result = new DeBruijnAssembler().leftAlignCigarSequentially(originalCigar, ref.getBytes(), hap.getBytes(), 0, 0);
logger.warn("Result is " + result);
Assert.assertEquals(originalCigar.getReferenceLength(), result.getReferenceLength(), "Reference lengths are different");
}
private static class MockBuilder extends DeBruijnGraphBuilder {
public final List<Kmer> addedPairs = new LinkedList<Kmer>();
@ -165,7 +173,7 @@ public class DeBruijnAssemblerUnitTest extends BaseTest {
return tests.toArray(new Object[][]{});
}
@Test(dataProvider = "AddReadKmersToGraph")
@Test(dataProvider = "AddReadKmersToGraph", enabled = ! DEBUG)
public void testAddReadKmersToGraph(final String bases, final int kmerSize, final List<Integer> badQualsSites) {
final int readLen = bases.length();
final DeBruijnAssembler assembler = new DeBruijnAssembler();

4
protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest.java
View File

@ -88,12 +88,12 @@ public class HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest extends Wa
@Test
public void testHaplotypeCallerMultiSampleGGAComplex() {
HCTestComplexGGA(NA12878_CHR20_BAM, "-L 20:119673-119823 -L 20:121408-121538",
"7d2cc5c4ece386beedf6b07dfbe5bf26");
"5954a46971b7546d30151b068cded42a");
}
@Test
public void testHaplotypeCallerMultiSampleGGAMultiAllelic() {
HCTestComplexGGA(NA12878_CHR20_BAM, "-L 20:133041-133161 -L 20:300207-300337",
"a17856f709b546eaed486841d78248d2");
"b3684c670f68f5a3a348a7fd2b25f10a");
}
}

2
protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
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@ -96,7 +96,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
@Test
public void testHaplotypeCallerMultiSampleGGA() {
HCTest(CEUTRIO_BAM, "--max_alternate_alleles 3 -gt_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -alleles " + validationDataLocation + "combined.phase1.chr20.raw.indels.sites.vcf",
"e2d32d0dce2c5502a8e877f6bbb65a10");
"65188ec4e3b91796f62bfb5b965ccf1f");
}
@Test

2
public/java/src/org/broadinstitute/sting/utils/Utils.java
View File

@ -294,7 +294,7 @@ public class Utils {
*/
public static String dupString(final String s, int nCopies) {
if ( s == null || s.equals("") ) throw new IllegalArgumentException("Bad s " + s);
if ( nCopies < 1 ) throw new IllegalArgumentException("nCopies must be >= 1 but got " + nCopies);
if ( nCopies < 0 ) throw new IllegalArgumentException("nCopies must be >= 0 but got " + nCopies);
final StringBuilder b = new StringBuilder();
for ( int i = 0; i < nCopies; i++ )

11
public/java/src/org/broadinstitute/sting/utils/sam/AlignmentUtils.java
View File

@ -664,7 +664,7 @@ public final class AlignmentUtils {
if ( numIndels == 0 )
return cigar;
if ( numIndels == 1 )
return leftAlignSingleIndel(cigar, refSeq, readSeq, refIndex, readIndex);
return leftAlignSingleIndel(cigar, refSeq, readSeq, refIndex, readIndex, true);
// if we got here then there is more than 1 indel in the alignment
if ( doNotThrowExceptionForMultipleIndels )
@ -709,10 +709,11 @@ public final class AlignmentUtils {
* @param readSeq read sequence
* @param refIndex 0-based alignment start position on ref
* @param readIndex 0-based alignment start position on read
* @param cleanupCigar if true, we'll cleanup the resulting cigar element, removing 0 length elements and deletions from the first cigar position
* @return a non-null cigar, in which the single indel is guaranteed to be placed at the leftmost possible position across a repeat (if any)
*/
@Ensures("result != null")
public static Cigar leftAlignSingleIndel(Cigar cigar, final byte[] refSeq, final byte[] readSeq, final int refIndex, final int readIndex) {
public static Cigar leftAlignSingleIndel(Cigar cigar, final byte[] refSeq, final byte[] readSeq, final int refIndex, final int readIndex, final boolean cleanupCigar) {
ensureLeftAlignmentHasGoodArguments(cigar, refSeq, readSeq, refIndex, readIndex);
int indexOfIndel = -1;
@ -751,7 +752,7 @@ public final class AlignmentUtils {
cigar = newCigar;
i = -1;
if (reachedEndOfRead)
cigar = cleanUpCigar(cigar);
cigar = cleanupCigar ? cleanUpCigar(cigar) : cigar;
}
if (reachedEndOfRead)
@ -933,7 +934,7 @@ public final class AlignmentUtils {
*/
public static Cigar trimCigarByBases(final Cigar cigar, final int start, final int end) {
if ( start < 0 ) throw new IllegalArgumentException("Start must be >= 0 but got " + start);
if ( end < start ) throw new IllegalArgumentException("End " + end + " is < start start " + start);
if ( end < start ) throw new IllegalArgumentException("End " + end + " is < start = " + start);
if ( end > cigar.getReadLength() ) throw new IllegalArgumentException("End is beyond the cigar's read length " + end + " for cigar " + cigar );
final Cigar result = trimCigar(cigar, start, end, false);
@ -961,7 +962,7 @@ public final class AlignmentUtils {
int pos = 0;
for ( final CigarElement elt : cigar.getCigarElements() ) {
if ( pos > end ) break;
if ( pos > end && (byReference || elt.getOperator() != CigarOperator.D) ) break;
switch ( elt.getOperator() ) {
case D:

15
public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java
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@ -28,6 +28,7 @@ package org.broadinstitute.sting.utils.sam;
import com.google.java.contract.Ensures;
import com.google.java.contract.Requires;
import net.sf.samtools.*;
import org.apache.log4j.Logger;
import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.GenomeLoc;
@ -47,6 +48,7 @@ import java.util.*;
* @version 0.1
*/
public class ReadUtils {
private final static Logger logger = Logger.getLogger(ReadUtils.class);
private static final String OFFSET_OUT_OF_BOUNDS_EXCEPTION = "Offset cannot be greater than read length %d : %d";
private static final String OFFSET_NOT_ZERO_EXCEPTION = "We ran past the end of the read and never found the offset, something went wrong!";
@ -209,7 +211,16 @@ public class ReadUtils {
if (insertSize == 0 || read.getReadUnmappedFlag()) // no adaptors in reads with mates in another chromosome or unmapped pairs
return CANNOT_COMPUTE_ADAPTOR_BOUNDARY;
if ( read.getReadPairedFlag() && read.getReadNegativeStrandFlag() == read.getMateNegativeStrandFlag() ) {
// note that the read.getProperPairFlag() is not reliably set, so many reads may have this tag but still be overlapping
// logger.info(String.format("Read %s start=%d end=%d insert=%d mateStart=%d readNeg=%b mateNeg=%b not properly paired, returning CANNOT_COMPUTE_ADAPTOR_BOUNDARY",
// read.getReadName(), read.getAlignmentStart(), read.getAlignmentEnd(), insertSize, read.getMateAlignmentStart(),
// read.getReadNegativeStrandFlag(), read.getMateNegativeStrandFlag()));
return CANNOT_COMPUTE_ADAPTOR_BOUNDARY;
}
int adaptorBoundary; // the reference coordinate for the adaptor boundary (effectively the first base IN the adaptor, closest to the read)
if (read.getReadNegativeStrandFlag())
adaptorBoundary = read.getMateAlignmentStart() - 1; // case 1 (see header)
@ -218,7 +229,7 @@ public class ReadUtils {
if ( (adaptorBoundary < read.getAlignmentStart() - MAXIMUM_ADAPTOR_LENGTH) || (adaptorBoundary > read.getAlignmentEnd() + MAXIMUM_ADAPTOR_LENGTH) )
adaptorBoundary = CANNOT_COMPUTE_ADAPTOR_BOUNDARY; // we are being conservative by not allowing the adaptor boundary to go beyond what we belive is the maximum size of an adaptor
return adaptorBoundary;
}
public static int CANNOT_COMPUTE_ADAPTOR_BOUNDARY = Integer.MIN_VALUE;

8
public/java/test/org/broadinstitute/sting/gatk/walkers/coverage/CallableLociIntegrationTest.java
View File

@ -34,13 +34,13 @@ public class CallableLociIntegrationTest extends WalkerTest {
final static String commonArgs = "-R " + b36KGReference + " -T CallableLoci -I " + validationDataLocation + "/NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s";
final static String reduceReadArgs = "-R " + b37KGReference + " -T CallableLoci -I " + " private/testdata/NA12878.HiSeq.b37.chr20.10_11mb.reduced.bam -o %s";
final static String SUMMARY_MD5 = "ffdbd9cdcb4169ebed5ae4bec797260f";
final static String SUMMARY_MD5 = "a6f5963669f19d9d137ced87d65834b0";
@Test
public void testCallableLociWalkerBed() {
String gatk_args = commonArgs + " -format BED -L 1:10,000,000-11,000,000 -summary %s";
WalkerTestSpec spec = new WalkerTestSpec(gatk_args, 2,
Arrays.asList("42e86c06c167246a28bffdacaca75ffb", SUMMARY_MD5));
Arrays.asList("9b4ffea1dbcfefadeb1c9fa74b0e0e59", SUMMARY_MD5));
executeTest("formatBed", spec);
}
@ -48,7 +48,7 @@ public class CallableLociIntegrationTest extends WalkerTest {
public void testCallableLociWalkerPerBase() {
String gatk_args = commonArgs + " -format STATE_PER_BASE -L 1:10,000,000-11,000,000 -summary %s";
WalkerTestSpec spec = new WalkerTestSpec(gatk_args, 2,
Arrays.asList("d66c525d9c70f62df8156261d3e535ad", SUMMARY_MD5));
Arrays.asList("d6505e489899e80c08a7168777f6e07b", SUMMARY_MD5));
executeTest("format_state_per_base", spec);
}
@ -64,7 +64,7 @@ public class CallableLociIntegrationTest extends WalkerTest {
public void testCallableLociWalker3() {
String gatk_args = commonArgs + " -format BED -L 1:10,000,000-11,000,000 -minDepth 10 -maxDepth 100 --minBaseQuality 10 --minMappingQuality 20 -summary %s";
WalkerTestSpec spec = new WalkerTestSpec(gatk_args, 2,
Arrays.asList("46a53379aaaf9803276a0a34b234f6ab", "da431d393f7c2b2b3e27556b86c1dbc7"));
Arrays.asList("7f79ad8195c4161060463eeb21d2bb11", "7ee269e5f4581a924529a356cc806e55"));
executeTest("formatBed lots of arguments", spec);
}

3
public/java/test/org/broadinstitute/sting/utils/sam/AlignmentUtilsUnitTest.java
View File

@ -792,7 +792,8 @@ public class AlignmentUtilsUnitTest {
tests.add(new Object[]{"2M2D2I", 3, 3, "1I"});
tests.add(new Object[]{"2M2D2I", 2, 2, "2D1I"});
tests.add(new Object[]{"2M2D2I", 1, 2, "1M2D1I"});
tests.add(new Object[]{"2M2D2I", 1, 1, "1M"});
tests.add(new Object[]{"2M2D2I", 0, 1, "2M2D"});
tests.add(new Object[]{"2M2D2I", 1, 1, "1M2D"});
return tests.toArray(new Object[][]{});
}

25
public/java/test/org/broadinstitute/sting/utils/sam/ReadUtilsUnitTest.java
View File

@ -151,6 +151,31 @@ public class ReadUtilsUnitTest extends BaseTest {
read.setReadNegativeStrandFlag(false);
boundary = get.getAdaptor(read);
Assert.assertEquals(boundary, ReadUtils.CANNOT_COMPUTE_ADAPTOR_BOUNDARY);
// Test case 8: read doesn't have proper pair flag set
read = makeRead(fragmentSize, mateStart);
read.setReadPairedFlag(true);
read.setProperPairFlag(false);
Assert.assertEquals(get.getAdaptor(read), ReadUtils.CANNOT_COMPUTE_ADAPTOR_BOUNDARY);
// Test case 9: read and mate have same negative flag setting
for ( final boolean negFlag: Arrays.asList(true, false) ) {
read = makeRead(fragmentSize, mateStart);
read.setAlignmentStart(BEFORE);
read.setReadPairedFlag(true);
read.setProperPairFlag(true);
read.setReadNegativeStrandFlag(negFlag);
read.setMateNegativeStrandFlag(!negFlag);
Assert.assertTrue(get.getAdaptor(read) != ReadUtils.CANNOT_COMPUTE_ADAPTOR_BOUNDARY, "Get adaptor should have succeeded");
read = makeRead(fragmentSize, mateStart);
read.setAlignmentStart(BEFORE);
read.setReadPairedFlag(true);
read.setProperPairFlag(true);
read.setReadNegativeStrandFlag(negFlag);
read.setMateNegativeStrandFlag(negFlag);
Assert.assertEquals(get.getAdaptor(read), ReadUtils.CANNOT_COMPUTE_ADAPTOR_BOUNDARY, "Get adaptor should have failed for reads with bad alignment orientation");
}
}
@Test (enabled = true)