Add HaplotypeCaller argument so integration tests can specify the hardware dependent PairHMM sub-implementation
This commit is contained in:
Ron Levine
parent
ba5a32107f
commit
386aeda022
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@ -106,9 +106,9 @@ public class HaplotypeScore extends InfoFieldAnnotation implements StandardAnnot
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if ( !(walker instanceof UnifiedGenotyper) ) {
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if ( !walkerIdentityCheckWarningLogged ) {
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if ( walker != null )
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logger.warn("Must be called from UnifiedGenotyper, not " + walker.getClass().getName());
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logger.warn("Annotation will not be calculated, must be called from UnifiedGenotyper, not " + walker.getClass().getName());
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else
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logger.warn("Must be called from UnifiedGenotyper");
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logger.warn("Annotation will not be calculated, must be called from UnifiedGenotyper");
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walkerIdentityCheckWarningLogged = true;
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}
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return null;
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@ -557,6 +557,11 @@ public class HaplotypeCaller extends ActiveRegionWalker<List<VariantContext>, In
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@Argument(fullName = "pair_hmm_implementation", shortName = "pairHMM", doc = "The PairHMM implementation to use for genotype likelihood calculations", required = false)
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public PairHMM.HMM_IMPLEMENTATION pairHMM = PairHMM.HMM_IMPLEMENTATION.VECTOR_LOGLESS_CACHING;
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@Hidden
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@Advanced
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@Argument(fullName = "pair_hmm_sub_implementation", shortName = "pairHMMSub", doc = "The PairHMM machine dependent sub-implementation to use for genotype likelihood calculations. Usage is intended for test suite use only, normal usage you should rely on the architecture auto-detection", required = false)
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public PairHMM.HMM_SUB_IMPLEMENTATION pairHMMSub = PairHMM.HMM_SUB_IMPLEMENTATION.ENABLE_ALL;
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@Hidden
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@Argument(fullName="keepRG", shortName="keepRG", doc="Only use read from this read group when making calls (but use all reads to build the assembly)", required = false)
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protected String keepRG = null;
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@ -887,7 +892,7 @@ public class HaplotypeCaller extends ActiveRegionWalker<List<VariantContext>, In
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private ReadLikelihoodCalculationEngine createLikelihoodCalculationEngine() {
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switch (likelihoodEngineImplementation) {
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case PairHMM:
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return new PairHMMLikelihoodCalculationEngine( (byte)gcpHMM, pairHMM, log10GlobalReadMismappingRate, noFpga, pcrErrorModel );
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return new PairHMMLikelihoodCalculationEngine( (byte)gcpHMM, pairHMM, pairHMMSub, log10GlobalReadMismappingRate, noFpga, pcrErrorModel );
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case GraphBased:
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return new GraphBasedLikelihoodCalculationEngine( (byte)gcpHMM,log10GlobalReadMismappingRate, heterogeneousKmerSizeResolution,SCAC.DEBUG,debugGraphTransformations);
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case Random:
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@ -83,6 +83,7 @@ public class PairHMMLikelihoodCalculationEngine implements ReadLikelihoodCalcula
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private final double log10globalReadMismappingRate;
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private final PairHMM.HMM_IMPLEMENTATION hmmType;
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private final PairHMM.HMM_SUB_IMPLEMENTATION hmmSubType;
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private final boolean noFpga;
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private final ThreadLocal<PairHMM> pairHMMThreadLocal = new ThreadLocal<PairHMM>() {
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@ -99,15 +100,15 @@ public class PairHMMLikelihoodCalculationEngine implements ReadLikelihoodCalcula
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case VECTOR_LOGLESS_CACHING:
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try
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{
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return new VectorLoglessPairHMM();
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return new VectorLoglessPairHMM(hmmSubType);
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}
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catch(UnsatisfiedLinkError ule)
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{
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logger.debug("Failed to load native library for VectorLoglessPairHMM - using Java implementation of LOGLESS_CACHING");
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logger.warn("Failed to load native library for VectorLoglessPairHMM - using Java implementation of LOGLESS_CACHING");
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return new LoglessPairHMM();
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}
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case DEBUG_VECTOR_LOGLESS_CACHING:
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return new DebugJNILoglessPairHMM(PairHMM.HMM_IMPLEMENTATION.VECTOR_LOGLESS_CACHING);
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return new DebugJNILoglessPairHMM(PairHMM.HMM_IMPLEMENTATION.VECTOR_LOGLESS_CACHING, hmmSubType);
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case ARRAY_LOGLESS:
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if (noFpga || !CnyPairHMM.isAvailable())
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return new ArrayLoglessPairHMM();
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@ -148,6 +149,7 @@ public class PairHMMLikelihoodCalculationEngine implements ReadLikelihoodCalcula
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*
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* @param constantGCP the gap continuation penalty to use with the PairHMM
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* @param hmmType the type of the HMM to use
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* @param hmmSubType the type of the machine dependent sub-implementation of HMM to use
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* @param log10globalReadMismappingRate the global mismapping probability, in log10(prob) units. A value of
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* -3 means that the chance that a read doesn't actually belong at this
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* location in the genome is 1 in 1000. The effect of this parameter is
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@ -157,9 +159,12 @@ public class PairHMMLikelihoodCalculationEngine implements ReadLikelihoodCalcula
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* reference haplotype gets a score of -100 from the pairhmm it will be
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* assigned a likelihood of -13.
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* @param noFpga disable FPGA acceleration
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* @param pcrErrorModel model to correct for PCR indel artifacts
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*/
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public PairHMMLikelihoodCalculationEngine( final byte constantGCP, final PairHMM.HMM_IMPLEMENTATION hmmType, final double log10globalReadMismappingRate, final boolean noFpga, final PCR_ERROR_MODEL pcrErrorModel ) {
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public PairHMMLikelihoodCalculationEngine( final byte constantGCP, final PairHMM.HMM_IMPLEMENTATION hmmType, final PairHMM.HMM_SUB_IMPLEMENTATION hmmSubType,
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final double log10globalReadMismappingRate, final boolean noFpga, final PCR_ERROR_MODEL pcrErrorModel ) {
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this.hmmType = hmmType;
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this.hmmSubType = hmmSubType;
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this.constantGCP = constantGCP;
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this.log10globalReadMismappingRate = log10globalReadMismappingRate;
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this.noFpga = noFpga;
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@ -92,14 +92,14 @@ public class DebugJNILoglessPairHMM extends LoglessPairHMM {
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protected HashMap<String, BufferedWriter> filenameToWriter = new HashMap<String, BufferedWriter>();
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private JNILoglessPairHMM jniPairHMM = null;
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public DebugJNILoglessPairHMM(final PairHMM.HMM_IMPLEMENTATION hmmType) {
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public DebugJNILoglessPairHMM(final PairHMM.HMM_IMPLEMENTATION hmmType, PairHMM.HMM_SUB_IMPLEMENTATION pairHMMSub) {
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super();
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switch(hmmType) {
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case VECTOR_LOGLESS_CACHING:
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jniPairHMM = new VectorLoglessPairHMM();
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jniPairHMM = new VectorLoglessPairHMM(pairHMMSub);
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break;
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default:
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throw new UserException.BadArgumentValue("pairHMM","Specified JNIPairHMM implementation is unrecognized or incompatible with the HaplotypeCaller. Acceptable options are VECTOR_LOGLESS_CACHING");
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throw new UserException.BadArgumentValue("pairHMM","Specified JNIPairHMM implementation is unrecognized or incompatible with the HaplotypeCaller. Acceptable options are VECTOR_LOGLESS_CACHING");
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}
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}
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@ -51,6 +51,7 @@
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package org.broadinstitute.gatk.utils.pairhmm;
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import org.broadinstitute.gatk.utils.exceptions.UserException;
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import org.broadinstitute.gatk.utils.genotyper.ReadLikelihoods;
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import org.broadinstitute.gatk.utils.haplotype.Haplotype;
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import org.broadinstitute.gatk.utils.sam.GATKSAMRecord;
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@ -69,12 +70,6 @@ import java.util.Map;
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*/
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public class VectorLoglessPairHMM extends JNILoglessPairHMM {
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//For machine capabilities
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public static final long sse41Mask = 1;
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public static final long sse42Mask = 2;
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public static final long avxMask = 4;
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public static final long enableAll = 0xFFFFFFFFFFFFFFFFl;
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//Used to copy references to byteArrays to JNI from reads
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protected class JNIReadDataHolderClass {
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public byte[] readBases = null;
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@ -97,25 +92,32 @@ public class VectorLoglessPairHMM extends JNILoglessPairHMM {
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* Bit 2 represents AVX availability
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*/
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public native long jniGetMachineType();
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/**
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* Function to initialize the fields of JNIReadDataHolderClass and JNIHaplotypeDataHolderClass from JVM.
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* C++ codegets FieldIDs for these classes once and re-uses these IDs for the remainder of the program. Field IDs do not
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* change per JVM session
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* @param readDataHolderClass class type of JNIReadDataHolderClass
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*
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* @param readDataHolderClass class type of JNIReadDataHolderClass
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* @param haplotypeDataHolderClass class type of JNIHaplotypeDataHolderClass
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* @param mask mask is a 64 bit integer identical to the one received from jniGetMachineType(). Users can disable usage of some hardware features by zeroing some bits in the mask
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* */
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* @param mask a 64 bit integer identical to the one received from jniGetMachineType(). Users can disable usage of some hardware features by zeroing bits in the mask
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*/
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private native void jniInitializeClassFieldsAndMachineMask(Class<?> readDataHolderClass, Class<?> haplotypeDataHolderClass, long mask);
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private static Boolean isVectorLoglessPairHMMLibraryLoaded = false;
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//The constructor is called only once inside PairHMMLikelihoodCalculationEngine
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public VectorLoglessPairHMM() {
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public VectorLoglessPairHMM(PairHMM.HMM_SUB_IMPLEMENTATION pairHMMSub) throws UserException.HardwareFeatureException {
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super();
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synchronized(isVectorLoglessPairHMMLibraryLoaded) {
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synchronized (isVectorLoglessPairHMMLibraryLoaded) {
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// Get the mask for the requested hardware sub-implementation
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// If a specifically requested hardware feature can not be supported, throw an exception
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long mask = pairHMMSub.getMask();
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throwIfHardwareFeatureNotSupported(mask, pairHMMSub);
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//Load the library and initialize the FieldIDs
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if(!isVectorLoglessPairHMMLibraryLoaded) {
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if (!isVectorLoglessPairHMMLibraryLoaded) {
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try
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{
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//Try loading from Java's library path first
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@ -123,51 +125,53 @@ public class VectorLoglessPairHMM extends JNILoglessPairHMM {
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//implementation without modifying the Java code
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System.loadLibrary("VectorLoglessPairHMM");
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logger.info("libVectorLoglessPairHMM found in JVM library path");
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}
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catch(UnsatisfiedLinkError ule)
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{
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} catch (UnsatisfiedLinkError ule) {
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//Could not load from Java's library path - try unpacking from jar
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try
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{
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logger.debug("libVectorLoglessPairHMM not found in JVM library path - trying to unpack from GATK jar file");
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loadLibraryFromJar("/org/broadinstitute/gatk/utils/pairhmm/libVectorLoglessPairHMM.so");
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logger.info("libVectorLoglessPairHMM unpacked successfully from GATK jar file");
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}
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catch(IOException ioe)
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{
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} catch (IOException ioe) {
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//Throw the UnsatisfiedLinkError to make it clear to the user what failed
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throw ule;
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}
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}
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logger.info("Using vectorized implementation of PairHMM");
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isVectorLoglessPairHMMLibraryLoaded = true;
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jniInitializeClassFieldsAndMachineMask(JNIReadDataHolderClass.class, JNIHaplotypeDataHolderClass.class, enableAll); //need to do this only once
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//need to do this only once
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jniInitializeClassFieldsAndMachineMask(JNIReadDataHolderClass.class, JNIHaplotypeDataHolderClass.class, mask);
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}
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}
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}
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private native void jniInitializeHaplotypes(final int numHaplotypes, JNIHaplotypeDataHolderClass[] haplotypeDataArray);
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private native void jniInitializeHaplotypes(final int numHaplotypes, JNIHaplotypeDataHolderClass[] haplotypeDataArray);
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//Hold the mapping between haplotype and index in the list of Haplotypes passed to initialize
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//Use this mapping in computeLikelihoods to find the likelihood value corresponding to a given Haplotype
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private HashMap<Haplotype,Integer> haplotypeToHaplotypeListIdxMap = new HashMap<>();
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private HashMap<Haplotype, Integer> haplotypeToHaplotypeListIdxMap = new HashMap<>();
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private JNIHaplotypeDataHolderClass[] mHaplotypeDataArray;
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@Override
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public HashMap<Haplotype, Integer> getHaplotypeToHaplotypeListIdxMap() { return haplotypeToHaplotypeListIdxMap; }
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public HashMap<Haplotype, Integer> getHaplotypeToHaplotypeListIdxMap() {
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return haplotypeToHaplotypeListIdxMap;
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}
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//Used to transfer data to JNI
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//Since the haplotypes are the same for all calls to computeLikelihoods within a region, transfer the haplotypes only once to the JNI per region
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/**
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* {@inheritDoc}
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*/
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@Override
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public void initialize( final List<Haplotype> haplotypes, final Map<String, List<GATKSAMRecord>> perSampleReadList,
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final int readMaxLength, final int haplotypeMaxLength ) {
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public void initialize(final List<Haplotype> haplotypes, final Map<String, List<GATKSAMRecord>> perSampleReadList,
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final int readMaxLength, final int haplotypeMaxLength) {
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int numHaplotypes = haplotypes.size();
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mHaplotypeDataArray = new JNIHaplotypeDataHolderClass[numHaplotypes];
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int idx = 0;
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haplotypeToHaplotypeListIdxMap.clear();
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for(final Haplotype currHaplotype : haplotypes)
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{
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for (final Haplotype currHaplotype : haplotypes) {
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mHaplotypeDataArray[idx] = new JNIHaplotypeDataHolderClass();
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mHaplotypeDataArray[idx].haplotypeBases = currHaplotype.getBases();
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haplotypeToHaplotypeListIdxMap.put(currHaplotype, idx);
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@ -175,6 +179,7 @@ public class VectorLoglessPairHMM extends JNILoglessPairHMM {
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}
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jniInitializeHaplotypes(numHaplotypes, mHaplotypeDataArray);
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}
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/**
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* Tell JNI to release arrays - really important if native code is directly accessing Java memory, if not
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* accessing Java memory directly, still important to release memory from C++
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@ -194,22 +199,22 @@ public class VectorLoglessPairHMM extends JNILoglessPairHMM {
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* Real compute kernel
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*/
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private native void jniComputeLikelihoods(int numReads, int numHaplotypes, JNIReadDataHolderClass[] readDataArray,
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JNIHaplotypeDataHolderClass[] haplotypeDataArray, double[] likelihoodArray, int maxNumThreadsToUse);
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JNIHaplotypeDataHolderClass[] haplotypeDataArray, double[] likelihoodArray, int maxNumThreadsToUse);
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/**
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* {@inheritDoc}
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*/
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@Override
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public void computeLikelihoods( final ReadLikelihoods.Matrix<Haplotype> likelihoods, final List<GATKSAMRecord> processedReads, final Map<GATKSAMRecord,byte[]> gcp ) {
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public void computeLikelihoods(final ReadLikelihoods.Matrix<Haplotype> likelihoods, final List<GATKSAMRecord> processedReads, final Map<GATKSAMRecord, byte[]> gcp) {
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if (processedReads.isEmpty())
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return;
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if(doProfiling)
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if (doProfiling)
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startTime = System.nanoTime();
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int readListSize = processedReads.size();
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int numHaplotypes = likelihoods.alleleCount();
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JNIReadDataHolderClass[] readDataArray = new JNIReadDataHolderClass[readListSize];
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int idx = 0;
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for(GATKSAMRecord read : processedReads)
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{
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for (GATKSAMRecord read : processedReads) {
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readDataArray[idx] = new JNIReadDataHolderClass();
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readDataArray[idx].readBases = read.getReadBases();
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readDataArray[idx].readQuals = read.getBaseQualities();
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@ -219,8 +224,8 @@ public class VectorLoglessPairHMM extends JNILoglessPairHMM {
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++idx;
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}
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mLikelihoodArray = new double[readListSize*numHaplotypes]; //to store results
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if(doProfiling)
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mLikelihoodArray = new double[readListSize * numHaplotypes]; //to store results
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if (doProfiling)
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threadLocalSetupTimeDiff = (System.nanoTime() - startTime);
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//for(reads)
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// for(haplotypes)
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@ -228,21 +233,19 @@ public class VectorLoglessPairHMM extends JNILoglessPairHMM {
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jniComputeLikelihoods(readListSize, numHaplotypes, readDataArray, mHaplotypeDataArray, mLikelihoodArray, 12);
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int readIdx = 0;
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for(int r = 0; r < readListSize; r++)
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{
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for (int r = 0; r < readListSize; r++) {
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int hapIdx = 0;
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for (final Haplotype haplotype : likelihoods.alleles()) {
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//Since the order of haplotypes in the List<Haplotype> and alleleHaplotypeMap is different,
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//get idx of current haplotype in the list and use this idx to get the right likelihoodValue
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final int idxInsideHaplotypeList = haplotypeToHaplotypeListIdxMap.get(haplotype);
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likelihoods.set(hapIdx,r,mLikelihoodArray[readIdx + idxInsideHaplotypeList]);
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likelihoods.set(hapIdx, r, mLikelihoodArray[readIdx + idxInsideHaplotypeList]);
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++hapIdx;
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}
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readIdx += numHaplotypes;
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}
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if(doProfiling)
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{
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if (doProfiling) {
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threadLocalPairHMMComputeTimeDiff = (System.nanoTime() - startTime);
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//synchronized(doProfiling)
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{
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@ -251,29 +254,30 @@ public class VectorLoglessPairHMM extends JNILoglessPairHMM {
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}
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}
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}
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/**
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* Print final profiling information from native code
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*/
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public native void jniClose();
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@Override
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public void close()
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{
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if(doProfiling)
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System.out.println("Time spent in setup for JNI call : "+(pairHMMSetupTime*1e-9));
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public void close() {
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if (doProfiling)
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System.out.println("Time spent in setup for JNI call : " + (pairHMMSetupTime * 1e-9));
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super.close();
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jniClose();
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}
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//Copied from http://frommyplayground.com/how-to-load-native-jni-library-from-jar
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/**
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* Loads library from current JAR archive
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*
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* <p/>
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* The file from JAR is copied into system temporary directory and then loaded. The temporary file is deleted after exiting.
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* Method uses String as filename because the pathname is "abstract", not system-dependent.
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*
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*
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* @param path The filename inside JAR as absolute path (beginning with '/'), e.g. /package/File.ext
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* @throws IOException If temporary file creation or read/write operation fails
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* @throws IOException If temporary file creation or read/write operation fails
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* @throws IllegalArgumentException If source file (param path) does not exist
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* @throws IllegalArgumentException If the path is not absolute or if the filename is shorter than three characters (restriction of {@see File#createTempFile(java.lang.String, java.lang.String)}).
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*/
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@ -293,7 +297,7 @@ public class VectorLoglessPairHMM extends JNILoglessPairHMM {
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if (filename != null) {
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parts = filename.split("\\.", 2);
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prefix = parts[0];
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suffix = (parts.length > 1) ? "."+parts[parts.length - 1] : null; // Thanks, davs! :-)
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suffix = (parts.length > 1) ? "." + parts[parts.length - 1] : null; // Thanks, davs! :-)
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}
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// Check if the filename is okay
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@ -335,4 +339,36 @@ public class VectorLoglessPairHMM extends JNILoglessPairHMM {
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// Finally, load the library
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System.load(temp.getAbsolutePath());
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}
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/**
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* If the machine does not support the requested hardware feature, throw an exception
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* <p/>
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* If requesting a specific hardware feature, check if the machine supports this feature.
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* If it does not, throw an exception.
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*
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* @param mask a 64 bit integer identical to the one received from jniGetMachineType(). Users can disable usage of some hardware features by zeroing some bits in the mask.
|
||||
* @param pairHMMSub the PairHMM machine dependent sub-implementation to use for genotype likelihood calculations
|
||||
* @throws UserException.HardwareFeatureException if the hardware feature is not supported
|
||||
*/
|
||||
private void throwIfHardwareFeatureNotSupported(long mask, PairHMM.HMM_SUB_IMPLEMENTATION pairHMMSub) throws UserException.HardwareFeatureException
|
||||
{
|
||||
if ( pairHMMSub.getIsSpecificHardwareRequest() ) {
|
||||
if ( !isHardwareFeatureSupported(mask) )
|
||||
throw new UserException.HardwareFeatureException("Machine does not support pairHMM hardware dependent sub-type = " + pairHMMSub);
|
||||
}
|
||||
}
|
||||
|
||||
/**
|
||||
* Check if the machine supports the requested hardware feature
|
||||
* <p/>
|
||||
* Mask the bits for the hardware feature and check if they are set by the machine
|
||||
* If the bits are set, the machine supports this feature
|
||||
*
|
||||
* @param mask a 64 bit integer identical to the one received from jniGetMachineType(). Users can disable usage of some hardware features by zeroing some bits in the mask.
|
||||
* @return true of machine supports the requested hardware feature, false otherwise
|
||||
*/
|
||||
private boolean isHardwareFeatureSupported(long mask)
|
||||
{
|
||||
return (mask & jniGetMachineType()) != 0x0;
|
||||
}
|
||||
}
|
||||
|
|
|
|||
|
|
@ -126,7 +126,7 @@ public class HCLikelihoodCalculationEnginesBenchmark extends SimpleBenchmark {
|
|||
public void timeLoglessPairHMM(final int reps) {
|
||||
for (int i = 0; i < reps; i++) {
|
||||
final PairHMMLikelihoodCalculationEngine engine = new PairHMMLikelihoodCalculationEngine((byte) 10,
|
||||
PairHMM.HMM_IMPLEMENTATION.LOGLESS_CACHING, -3, true, PairHMMLikelihoodCalculationEngine.PCR_ERROR_MODEL.NONE);
|
||||
PairHMM.HMM_IMPLEMENTATION.LOGLESS_CACHING, PairHMM.HMM_SUB_IMPLEMENTATION.ENABLE_ALL,-3, true, PairHMMLikelihoodCalculationEngine.PCR_ERROR_MODEL.NONE);
|
||||
engine.computeReadLikelihoods(dataSet.assemblyResultSet(), SampleListUtils.singletonList("anonymous"), Collections.singletonMap("anonymous", dataSet.readList()));
|
||||
}
|
||||
}
|
||||
|
|
|
|||
|
|
@ -61,8 +61,10 @@ import static org.broadinstitute.gatk.tools.walkers.haplotypecaller.HaplotypeCal
|
|||
|
||||
public class HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest extends WalkerTest {
|
||||
|
||||
final static String HMM_SUB_IMPLEMENTATION = "UNVECTORIZED";
|
||||
|
||||
private void HCTestComplexVariants(String bam, String args, String md5) {
|
||||
final String base = String.format("-T HaplotypeCaller --contamination_fraction_to_filter 0.05 --disableDithering --pcr_indel_model NONE -R %s -I %s", REF, bam) + " -L 20:10028767-10028967 -L 20:10431524-10431924 -L 20:10723661-10724061 -L 20:10903555-10903955 --no_cmdline_in_header -o %s -minPruning 4";
|
||||
final String base = String.format("-T HaplotypeCaller --contamination_fraction_to_filter 0.05 --disableDithering --pcr_indel_model NONE -pairHMMSub %s -R %s -I %s", HMM_SUB_IMPLEMENTATION, REF, bam) + " -L 20:10028767-10028967 -L 20:10431524-10431924 -L 20:10723661-10724061 -L 20:10903555-10903955 --no_cmdline_in_header -o %s -minPruning 4";
|
||||
final WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(base + " " + args, Arrays.asList(md5));
|
||||
executeTest("testHaplotypeCallerComplexVariants: args=" + args, spec);
|
||||
}
|
||||
|
|
@ -73,7 +75,7 @@ public class HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest extends Wa
|
|||
}
|
||||
|
||||
private void HCTestSymbolicVariants(String bam, String args, String md5) {
|
||||
final String base = String.format("-T HaplotypeCaller --disableDithering --pcr_indel_model NONE -R %s -I %s", REF, bam) + " -L 20:5947969-5948369 -L 20:61091236-61091636 --no_cmdline_in_header -o %s -minPruning 1";
|
||||
final String base = String.format("-T HaplotypeCaller --disableDithering --pcr_indel_model NONE -pairHMMSub %s -R %s -I %s", HMM_SUB_IMPLEMENTATION, REF, bam) + " -L 20:5947969-5948369 -L 20:61091236-61091636 --no_cmdline_in_header -o %s -minPruning 1";
|
||||
final WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(base + " " + args, Arrays.asList(md5));
|
||||
executeTest("testHaplotypeCallerSymbolicVariants: args=" + args, spec);
|
||||
}
|
||||
|
|
@ -85,7 +87,7 @@ public class HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest extends Wa
|
|||
}
|
||||
|
||||
private void HCTestComplexGGA(String bam, String args, String md5) {
|
||||
final String base = String.format("-T HaplotypeCaller --disableDithering --pcr_indel_model NONE -R %s -I %s", REF, bam) + " --no_cmdline_in_header -o %s -minPruning 3 -gt_mode GENOTYPE_GIVEN_ALLELES -alleles " + validationDataLocation + "combined.phase1.chr20.raw.indels.sites.vcf";
|
||||
final String base = String.format("-T HaplotypeCaller --disableDithering --pcr_indel_model NONE -pairHMMSub %s -R %s -I %s", HMM_SUB_IMPLEMENTATION, REF, bam) + " --no_cmdline_in_header -o %s -minPruning 3 -gt_mode GENOTYPE_GIVEN_ALLELES -alleles " + validationDataLocation + "combined.phase1.chr20.raw.indels.sites.vcf";
|
||||
final WalkerTestSpec spec = new WalkerTestSpec(base + " " + args, Arrays.asList(md5));
|
||||
executeTest("testHaplotypeCallerComplexGGA: args=" + args, spec);
|
||||
}
|
||||
|
|
@ -103,7 +105,7 @@ public class HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest extends Wa
|
|||
}
|
||||
|
||||
private void HCTestComplexConsensusMode(String bam, String args, String md5) {
|
||||
final String base = String.format("-T HaplotypeCaller --disableDithering --pcr_indel_model NONE -R %s -I %s", REF, bam) + " --no_cmdline_in_header -o %s -consensus -alleles " + validationDataLocation + "combined.phase1.chr20.raw.indels.sites.vcf -alleles " + validationDataLocation + "phase1.projectConsensus.chr20.raw.snps.vcf";
|
||||
final String base = String.format("-T HaplotypeCaller --disableDithering --pcr_indel_model NONE -pairHMMSub %s -R %s -I %s", HMM_SUB_IMPLEMENTATION, REF, bam) + " --no_cmdline_in_header -o %s -consensus -alleles " + validationDataLocation + "combined.phase1.chr20.raw.indels.sites.vcf -alleles " + validationDataLocation + "phase1.projectConsensus.chr20.raw.snps.vcf";
|
||||
final WalkerTestSpec spec = new WalkerTestSpec(base + " " + args, Arrays.asList(md5));
|
||||
executeTest("testHaplotypeCallerComplexConsensusMode: args=" + args, spec);
|
||||
}
|
||||
|
|
|
|||
|
|
@ -63,6 +63,8 @@ import java.util.List;
|
|||
|
||||
public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest {
|
||||
|
||||
final static String HMM_SUB_IMPLEMENTATION = "UNVECTORIZED";
|
||||
|
||||
@DataProvider(name = "MyDataProviderHaploid")
|
||||
public Object[][] makeMyDataProviderHaploid() {
|
||||
List<Object[]> tests = new ArrayList<>();
|
||||
|
|
@ -128,8 +130,8 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest {
|
|||
*/
|
||||
@Test(dataProvider = "MyDataProvider")
|
||||
public void testHCWithGVCF(String bam, ReferenceConfidenceMode mode, String intervals, String md5) {
|
||||
final String commandLine = String.format("-T HaplotypeCaller --disableDithering --pcr_indel_model NONE -R %s -I %s %s -ERC %s --no_cmdline_in_header -variant_index_type %s -variant_index_parameter %d",
|
||||
b37KGReference, bam, intervals, mode, HaplotypeCaller.OPTIMAL_GVCF_INDEX_TYPE, HaplotypeCaller.OPTIMAL_GVCF_INDEX_PARAMETER);
|
||||
final String commandLine = String.format("-T HaplotypeCaller --disableDithering --pcr_indel_model NONE -pairHMMSub %s -R %s -I %s %s -ERC %s --no_cmdline_in_header -variant_index_type %s -variant_index_parameter %d",
|
||||
HMM_SUB_IMPLEMENTATION, b37KGReference, bam, intervals, mode, HaplotypeCaller.OPTIMAL_GVCF_INDEX_TYPE, HaplotypeCaller.OPTIMAL_GVCF_INDEX_PARAMETER);
|
||||
final String name = "testHCWithGVCF bam=" + bam + " intervals= " + intervals + " gvcf= " + mode;
|
||||
final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList(md5));
|
||||
executeTest(name, spec);
|
||||
|
|
@ -140,8 +142,8 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest {
|
|||
*/
|
||||
@Test(dataProvider = "MyDataProviderHaploid", enabled=true)
|
||||
public void testHCWithGVCFHaploid(final String bam, final ReferenceConfidenceMode mode, final String intervals, final String md5) {
|
||||
final String commandLine = String.format("-T HaplotypeCaller -ploidy 1 --disableDithering --pcr_indel_model NONE -R %s -I %s %s -ERC %s --no_cmdline_in_header -variant_index_type %s -variant_index_parameter %d",
|
||||
b37KGReference, bam, intervals, mode, HaplotypeCaller.OPTIMAL_GVCF_INDEX_TYPE, HaplotypeCaller.OPTIMAL_GVCF_INDEX_PARAMETER);
|
||||
final String commandLine = String.format("-T HaplotypeCaller -ploidy 1 --disableDithering --pcr_indel_model NONE -pairHMMSub %s -R %s -I %s %s -ERC %s --no_cmdline_in_header -variant_index_type %s -variant_index_parameter %d",
|
||||
HMM_SUB_IMPLEMENTATION, b37KGReference, bam, intervals, mode, HaplotypeCaller.OPTIMAL_GVCF_INDEX_TYPE, HaplotypeCaller.OPTIMAL_GVCF_INDEX_PARAMETER);
|
||||
final String name = "testHCWithGVCFHaploid bam=" + bam + " intervals= " + intervals + " gvcf= " + mode;
|
||||
final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList(md5));
|
||||
executeTest(name, spec);
|
||||
|
|
@ -152,8 +154,8 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest {
|
|||
*/
|
||||
@Test(dataProvider = "MyDataProviderTetraploid", enabled=true)
|
||||
public void testHCWithGVCFTetraploid(final String bam, final ReferenceConfidenceMode mode, final String intervals, final String md5) {
|
||||
final String commandLine = String.format("-T HaplotypeCaller -ploidy 4 --disableDithering --pcr_indel_model NONE -R %s -I %s %s -ERC %s --no_cmdline_in_header -variant_index_type %s -variant_index_parameter %d",
|
||||
b37KGReference, bam, intervals, mode, HaplotypeCaller.OPTIMAL_GVCF_INDEX_TYPE, HaplotypeCaller.OPTIMAL_GVCF_INDEX_PARAMETER);
|
||||
final String commandLine = String.format("-T HaplotypeCaller -ploidy 4 --disableDithering --pcr_indel_model NONE -pairHMMSub %s -R %s -I %s %s -ERC %s --no_cmdline_in_header -variant_index_type %s -variant_index_parameter %d",
|
||||
HMM_SUB_IMPLEMENTATION, b37KGReference, bam, intervals, mode, HaplotypeCaller.OPTIMAL_GVCF_INDEX_TYPE, HaplotypeCaller.OPTIMAL_GVCF_INDEX_PARAMETER);
|
||||
final String name = "testHCWithGVCFTetraploid bam=" + bam + " intervals= " + intervals + " gvcf= " + mode;
|
||||
final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList(md5));
|
||||
executeTest(name, spec);
|
||||
|
|
@ -161,8 +163,8 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest {
|
|||
|
||||
@Test
|
||||
public void testERCRegionWithNoCalledHaplotypes() {
|
||||
final String commandLine = String.format("-T HaplotypeCaller --pcr_indel_model NONE -R %s -I %s -L %s -ERC GVCF -variant_index_type %s -variant_index_parameter %d",
|
||||
b37KGReference, privateTestDir + "noCallRefModel.bam", "20:17000001-18000001", HaplotypeCaller.OPTIMAL_GVCF_INDEX_TYPE, HaplotypeCaller.OPTIMAL_GVCF_INDEX_PARAMETER);
|
||||
final String commandLine = String.format("-T HaplotypeCaller --pcr_indel_model NONE -pairHMMSub %s -R %s -I %s -L %s -ERC GVCF -variant_index_type %s -variant_index_parameter %d",
|
||||
HMM_SUB_IMPLEMENTATION, b37KGReference, privateTestDir + "noCallRefModel.bam", "20:17000001-18000001", HaplotypeCaller.OPTIMAL_GVCF_INDEX_TYPE, HaplotypeCaller.OPTIMAL_GVCF_INDEX_PARAMETER);
|
||||
final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList(""));
|
||||
spec.disableShadowBCF();
|
||||
executeTest("testERCRegionWithNoCalledHaplotypes", spec);
|
||||
|
|
@ -170,8 +172,8 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest {
|
|||
|
||||
@Test()
|
||||
public void testMissingGVCFIndexException() {
|
||||
final String commandLine = String.format("-T HaplotypeCaller --pcr_indel_model NONE -R %s -I %s -L %s -ERC GVCF",
|
||||
b37KGReference, privateTestDir + "noCallRefModel.bam", "20:17000001-18000001");
|
||||
final String commandLine = String.format("-T HaplotypeCaller --pcr_indel_model NONE -pairHMMSub %s -R %s -I %s -L %s -ERC GVCF",
|
||||
HMM_SUB_IMPLEMENTATION, b37KGReference, privateTestDir + "noCallRefModel.bam", "20:17000001-18000001");
|
||||
final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", 1, UserException.GVCFIndexException.class);
|
||||
spec.disableShadowBCF();
|
||||
executeTest("testMissingGVCFIndexingStrategyException", spec);
|
||||
|
|
@ -179,8 +181,8 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest {
|
|||
|
||||
@Test()
|
||||
public void testWrongParameterGVCFIndexException() {
|
||||
final String commandLine = String.format("-T HaplotypeCaller --pcr_indel_model NONE -R %s -I %s -L %s -ERC GVCF -variant_index_type %s -variant_index_parameter %d",
|
||||
b37KGReference, privateTestDir + "noCallRefModel.bam", "20:17000001-18000001", HaplotypeCaller.OPTIMAL_GVCF_INDEX_TYPE, HaplotypeCaller.OPTIMAL_GVCF_INDEX_PARAMETER + 1);
|
||||
final String commandLine = String.format("-T HaplotypeCaller --pcr_indel_model NONE -pairHMMSub %s -R %s -I %s -L %s -ERC GVCF -variant_index_type %s -variant_index_parameter %d",
|
||||
HMM_SUB_IMPLEMENTATION, b37KGReference, privateTestDir + "noCallRefModel.bam", "20:17000001-18000001", HaplotypeCaller.OPTIMAL_GVCF_INDEX_TYPE, HaplotypeCaller.OPTIMAL_GVCF_INDEX_PARAMETER + 1);
|
||||
final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", 1, UserException.GVCFIndexException.class);
|
||||
spec.disableShadowBCF();
|
||||
executeTest("testMissingGVCFIndexingStrategyException", spec);
|
||||
|
|
@ -193,8 +195,8 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest {
|
|||
if (HaplotypeCaller.OPTIMAL_GVCF_INDEX_TYPE == GATKVCFIndexType.DYNAMIC_SEEK)
|
||||
type = GATKVCFIndexType.DYNAMIC_SIZE;
|
||||
|
||||
final String commandLine = String.format("-T HaplotypeCaller --pcr_indel_model NONE -R %s -I %s -L %s -ERC GVCF -variant_index_type %s -variant_index_parameter %d",
|
||||
b37KGReference, privateTestDir + "noCallRefModel.bam", "20:17000001-18000001", type, HaplotypeCaller.OPTIMAL_GVCF_INDEX_PARAMETER);
|
||||
final String commandLine = String.format("-T HaplotypeCaller --pcr_indel_model NONE -pairHMMSub %s -R %s -I %s -L %s -ERC GVCF -variant_index_type %s -variant_index_parameter %d",
|
||||
HMM_SUB_IMPLEMENTATION, b37KGReference, privateTestDir + "noCallRefModel.bam", "20:17000001-18000001", type, HaplotypeCaller.OPTIMAL_GVCF_INDEX_PARAMETER);
|
||||
final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", 1, UserException.GVCFIndexException.class);
|
||||
spec.disableShadowBCF();
|
||||
executeTest("testMissingGVCFIndexingStrategyException", spec);
|
||||
|
|
@ -205,8 +207,8 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest {
|
|||
|
||||
@Test()
|
||||
public void testWrongGVCFNonVariantRecordOrderBugFix() {
|
||||
final String commandLine = String.format("-T HaplotypeCaller --pcr_indel_model NONE -R %s -I %s -L %s -ERC GVCF --no_cmdline_in_header -variant_index_type %s -variant_index_parameter %d",
|
||||
b37KGReference, WRONG_GVCF_RECORD_ORDER_BUGFIX_BAM, WRONG_GVCF_RECORD_ORDER_BUGFIX_INTERVALS, HaplotypeCaller.OPTIMAL_GVCF_INDEX_TYPE, HaplotypeCaller.OPTIMAL_GVCF_INDEX_PARAMETER);
|
||||
final String commandLine = String.format("-T HaplotypeCaller --pcr_indel_model NONE -pairHMMSub %s -R %s -I %s -L %s -ERC GVCF --no_cmdline_in_header -variant_index_type %s -variant_index_parameter %d",
|
||||
HMM_SUB_IMPLEMENTATION, b37KGReference, WRONG_GVCF_RECORD_ORDER_BUGFIX_BAM, WRONG_GVCF_RECORD_ORDER_BUGFIX_INTERVALS, HaplotypeCaller.OPTIMAL_GVCF_INDEX_TYPE, HaplotypeCaller.OPTIMAL_GVCF_INDEX_PARAMETER);
|
||||
final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("e6a4e571abb59b925d59a38d244f0abe"));
|
||||
spec.disableShadowBCF();
|
||||
executeTest("testMissingGVCFIndexingStrategyException", spec);
|
||||
|
|
@ -222,8 +224,8 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest {
|
|||
|
||||
@Test
|
||||
public void testNoCallGVCFMissingPLsBugFix() {
|
||||
final String commandLine = String.format("-T HaplotypeCaller --pcr_indel_model NONE -R %s -I %s -L %s -ERC GVCF --no_cmdline_in_header -variant_index_type %s -variant_index_parameter %d",
|
||||
b37KGReference, NOCALL_GVCF_BUGFIX_BAM, NOCALL_GVCF_BUGFIX_INTERVALS, HaplotypeCaller.OPTIMAL_GVCF_INDEX_TYPE, HaplotypeCaller.OPTIMAL_GVCF_INDEX_PARAMETER);
|
||||
final String commandLine = String.format("-T HaplotypeCaller --pcr_indel_model NONE -pairHMMSub %s -R %s -I %s -L %s -ERC GVCF --no_cmdline_in_header -variant_index_type %s -variant_index_parameter %d",
|
||||
HMM_SUB_IMPLEMENTATION, b37KGReference, NOCALL_GVCF_BUGFIX_BAM, NOCALL_GVCF_BUGFIX_INTERVALS, HaplotypeCaller.OPTIMAL_GVCF_INDEX_TYPE, HaplotypeCaller.OPTIMAL_GVCF_INDEX_PARAMETER);
|
||||
final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("7ef1f30d92178f75e5220b16508b47cd"));
|
||||
spec.disableShadowBCF();
|
||||
executeTest("testNoCallGVCFMissingPLsBugFix", spec);
|
||||
|
|
@ -234,8 +236,8 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest {
|
|||
*/
|
||||
@Test(enabled=true)
|
||||
public void testGeneralPloidyArrayIndexBug1Fix() {
|
||||
final String commandLine = String.format("-T HaplotypeCaller --pcr_indel_model NONE -R %s -I %s -L %s -ERC GVCF --no_cmdline_in_header -variant_index_type %s -variant_index_parameter %d -ploidy 1 -maxAltAlleles 2 -isr INTERSECTION -L 1:23696115-23696189",
|
||||
b37KGReference, GENERAL_PLOIDY_BUGFIX1_BAM, GENERAL_PLOIDY_BUGFIX1_INTERVALS, HaplotypeCaller.OPTIMAL_GVCF_INDEX_TYPE, HaplotypeCaller.OPTIMAL_GVCF_INDEX_PARAMETER);
|
||||
final String commandLine = String.format("-T HaplotypeCaller --pcr_indel_model NONE -pairHMMSub %s -R %s -I %s -L %s -ERC GVCF --no_cmdline_in_header -variant_index_type %s -variant_index_parameter %d -ploidy 1 -maxAltAlleles 2 -isr INTERSECTION -L 1:23696115-23696189",
|
||||
HMM_SUB_IMPLEMENTATION, b37KGReference, GENERAL_PLOIDY_BUGFIX1_BAM, GENERAL_PLOIDY_BUGFIX1_INTERVALS, HaplotypeCaller.OPTIMAL_GVCF_INDEX_TYPE, HaplotypeCaller.OPTIMAL_GVCF_INDEX_PARAMETER);
|
||||
final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList(""));
|
||||
spec.disableShadowBCF();
|
||||
executeTest(" testGeneralPloidyArrayIndexBug1Fix", spec);
|
||||
|
|
@ -246,8 +248,8 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest {
|
|||
*/
|
||||
@Test(enabled=true)
|
||||
public void testGeneralPloidyArrayIndexBug2Fix() {
|
||||
final String commandLine = String.format("-T HaplotypeCaller --pcr_indel_model NONE -R %s -I %s -L %s -ERC GVCF --no_cmdline_in_header -variant_index_type %s -variant_index_parameter %d -ploidy 2 -maxAltAlleles 2 -A DepthPerSampleHC -A StrandBiasBySample -L 1:38052860-38052937",
|
||||
b37KGReference, GENERAL_PLOIDY_BUGFIX2_BAM, GENERAL_PLOIDY_BUGFIX2_INTERVALS, HaplotypeCaller.OPTIMAL_GVCF_INDEX_TYPE, HaplotypeCaller.OPTIMAL_GVCF_INDEX_PARAMETER);
|
||||
final String commandLine = String.format("-T HaplotypeCaller --pcr_indel_model NONE -pairHMMSub %s -R %s -I %s -L %s -ERC GVCF --no_cmdline_in_header -variant_index_type %s -variant_index_parameter %d -ploidy 2 -maxAltAlleles 2 -A DepthPerSampleHC -A StrandBiasBySample -L 1:38052860-38052937",
|
||||
HMM_SUB_IMPLEMENTATION, b37KGReference, GENERAL_PLOIDY_BUGFIX2_BAM, GENERAL_PLOIDY_BUGFIX2_INTERVALS, HaplotypeCaller.OPTIMAL_GVCF_INDEX_TYPE, HaplotypeCaller.OPTIMAL_GVCF_INDEX_PARAMETER);
|
||||
final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList(""));
|
||||
spec.disableShadowBCF();
|
||||
executeTest(" testGeneralPloidyArrayIndexBug2Fix", spec);
|
||||
|
|
|
|||
|
|
@ -61,6 +61,7 @@ import org.broadinstitute.gatk.utils.GenomeLoc;
|
|||
import org.broadinstitute.gatk.utils.GenomeLocParser;
|
||||
import org.broadinstitute.gatk.utils.collections.Pair;
|
||||
import org.broadinstitute.gatk.engine.GATKVCFUtils;
|
||||
import org.broadinstitute.gatk.utils.exceptions.UserException;
|
||||
import org.testng.Assert;
|
||||
import org.testng.annotations.Test;
|
||||
|
||||
|
|
@ -81,9 +82,10 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
|
|||
final static String CEUTRIO_MT_TEST_BAM = privateTestDir + "CEUTrio.HiSeq.b37.MT.1_50.bam";
|
||||
final static String INTERVALS_FILE = validationDataLocation + "NA12878.HiSeq.b37.chr20.10_11mb.test.intervals";
|
||||
final static String GGA_INTERVALS_FILE = privateTestDir + "haplotype-caller-reduced-test-interval.list";
|
||||
final static String HMM_SUB_IMPLEMENTATION = "UNVECTORIZED";
|
||||
|
||||
private void HCTest(String bam, String args, String md5) {
|
||||
final String base = String.format("-T HaplotypeCaller --contamination_fraction_to_filter 0.05 --disableDithering --pcr_indel_model NONE --maxReadsInRegionPerSample 1000 --minReadsPerAlignmentStart 5 --maxProbPropagationDistance 50 --activeProbabilityThreshold 0.002 -R %s -I %s -L %s", REF, bam, INTERVALS_FILE) + " --no_cmdline_in_header -o %s -minPruning 3";
|
||||
final String base = String.format("-T HaplotypeCaller --contamination_fraction_to_filter 0.05 --disableDithering --pcr_indel_model NONE --maxReadsInRegionPerSample 1000 --minReadsPerAlignmentStart 5 --maxProbPropagationDistance 50 --activeProbabilityThreshold 0.002 -pairHMMSub %s -R %s -I %s -L %s", HMM_SUB_IMPLEMENTATION, REF, bam, INTERVALS_FILE) + " --no_cmdline_in_header -o %s -minPruning 3";
|
||||
final WalkerTestSpec spec = new WalkerTestSpec(base + " " + args, Arrays.asList(md5));
|
||||
executeTest("testHaplotypeCaller: args=" + args, spec);
|
||||
}
|
||||
|
|
@ -174,7 +176,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
|
|||
}
|
||||
|
||||
private void HCTestIndelQualityScores(String bam, String args, String md5) {
|
||||
final String base = String.format("-T HaplotypeCaller --disableDithering --pcr_indel_model NONE -R %s -I %s", REF, bam) + " -L 20:10,005,000-10,025,000 --no_cmdline_in_header -o %s -minPruning 2";
|
||||
final String base = String.format("-T HaplotypeCaller --disableDithering --pcr_indel_model NONE -pairHMMSub %s -R %s -I %s", HMM_SUB_IMPLEMENTATION, REF, bam) + " -L 20:10,005,000-10,025,000 --no_cmdline_in_header -o %s -minPruning 2";
|
||||
final WalkerTestSpec spec = new WalkerTestSpec(base + " " + args, Arrays.asList(md5));
|
||||
executeTest("testHaplotypeCallerIndelQualityScores: args=" + args, spec);
|
||||
}
|
||||
|
|
@ -189,7 +191,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
|
|||
final IndexedFastaSequenceFile fasta = new IndexedFastaSequenceFile(new File(b37KGReference));
|
||||
final GenomeLocParser parser = new GenomeLocParser(fasta.getSequenceDictionary());
|
||||
|
||||
final String base = String.format("-T HaplotypeCaller --disableDithering --pcr_indel_model NONE -R %s -I %s", REF, bam) + " -L 20:10,001,603-10,001,642 -L 20:10,001,653-10,001,742 --no_cmdline_in_header -o %s";
|
||||
final String base = String.format("-T HaplotypeCaller --disableDithering --pcr_indel_model NONE -pairHMMSub %s -R %s -I %s", HMM_SUB_IMPLEMENTATION, REF, bam) + " -L 20:10,001,603-10,001,642 -L 20:10,001,653-10,001,742 --no_cmdline_in_header -o %s";
|
||||
final WalkerTestSpec spec = new WalkerTestSpec(base + " " + args, Arrays.asList(md5));
|
||||
for( final File vcf : executeTest("testHaplotypeCallerNearbySmallIntervals: args=" + args, spec).getFirst() ) {
|
||||
if( containsDuplicateRecord(vcf, parser) ) {
|
||||
|
|
@ -227,14 +229,14 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
|
|||
// any of the calls in that region because it is so messy.
|
||||
@Test
|
||||
public void HCTestProblematicReadsModifiedInActiveRegions() {
|
||||
final String base = String.format("-T HaplotypeCaller --disableDithering --pcr_indel_model NONE -R %s -I %s", REF, privateTestDir + "haplotype-problem-4.bam") + " --no_cmdline_in_header -o %s -minPruning 3 -L 4:49139026-49139965";
|
||||
final String base = String.format("-T HaplotypeCaller --disableDithering --pcr_indel_model NONE -pairHMMSub %s -R %s -I %s", HMM_SUB_IMPLEMENTATION, REF, privateTestDir + "haplotype-problem-4.bam") + " --no_cmdline_in_header -o %s -minPruning 3 -L 4:49139026-49139965";
|
||||
final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList("cf6fbb3636c52cd47dd14e0bd415a320"));
|
||||
executeTest("HCTestProblematicReadsModifiedInActiveRegions: ", spec);
|
||||
}
|
||||
|
||||
@Test
|
||||
public void HCTestStructuralIndels() {
|
||||
final String base = String.format("-T HaplotypeCaller --disableDithering --pcr_indel_model NONE -R %s -I %s", REF, privateTestDir + "AFR.structural.indels.bam") + " --no_cmdline_in_header -o %s -minPruning 6 -L 20:8187565-8187800 -L 20:18670537-18670730";
|
||||
final String base = String.format("-T HaplotypeCaller --disableDithering --pcr_indel_model NONE -pairHMMSub %s -R %s -I %s", HMM_SUB_IMPLEMENTATION, REF, privateTestDir + "AFR.structural.indels.bam") + " --no_cmdline_in_header -o %s -minPruning 6 -L 20:8187565-8187800 -L 20:18670537-18670730";
|
||||
final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList("a145c3c0e99b278054a9960923da8aaa"));
|
||||
executeTest("HCTestStructuralIndels: ", spec);
|
||||
}
|
||||
|
|
@ -242,14 +244,14 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
|
|||
@Test
|
||||
public void HCTestDoesNotFailOnBadRefBase() {
|
||||
// don't care about the output - just want to make sure it doesn't fail
|
||||
final String base = String.format("-T HaplotypeCaller --disableDithering -R %s -I %s", REF, privateTestDir + "NA12878.readsOverBadBase.chr3.bam") + " --no_cmdline_in_header -o /dev/null -L 3:60830000-60840000 --minPruning 3 -stand_call_conf 2 -stand_emit_conf 2";
|
||||
final String base = String.format("-T HaplotypeCaller --disableDithering -pairHMMSub %s -R %s -I %s", HMM_SUB_IMPLEMENTATION, REF, privateTestDir + "NA12878.readsOverBadBase.chr3.bam") + " --no_cmdline_in_header -o /dev/null -L 3:60830000-60840000 --minPruning 3 -stand_call_conf 2 -stand_emit_conf 2";
|
||||
final WalkerTestSpec spec = new WalkerTestSpec(base, Collections.<String>emptyList());
|
||||
executeTest("HCTestDoesNotFailOnBadRefBase: ", spec);
|
||||
}
|
||||
|
||||
@Test
|
||||
public void HCTestDanglingTailMergingForDeletions() throws IOException {
|
||||
final String base = String.format("-T HaplotypeCaller --disableDithering --pcr_indel_model NONE -R %s -I %s", REF, NA12878_BAM) + " --no_cmdline_in_header -o %s -L 20:10130740-10130800 --allowNonUniqueKmersInRef";
|
||||
final String base = String.format("-T HaplotypeCaller --disableDithering --pcr_indel_model NONE -pairHMMSub %s -R %s -I %s", HMM_SUB_IMPLEMENTATION, REF, NA12878_BAM) + " --no_cmdline_in_header -o %s -L 20:10130740-10130800 --allowNonUniqueKmersInRef";
|
||||
final WalkerTestSpec spec = new WalkerTestSpec(base, 1, Arrays.asList(""));
|
||||
final File outputVCF = executeTest("HCTestDanglingTailMergingForDeletions", spec).getFirst().get(0);
|
||||
|
||||
|
|
@ -273,7 +275,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
|
|||
|
||||
@Test
|
||||
public void testLeftAlignmentBamOutBugFix() {
|
||||
final String base = String.format("-T HaplotypeCaller -R %s -I %s", REF, LEFT_ALIGNMENT_BAMOUT_TEST_INPUT)
|
||||
final String base = String.format("-T HaplotypeCaller -pairHMMSub %s -R %s -I %s", HMM_SUB_IMPLEMENTATION, REF, LEFT_ALIGNMENT_BAMOUT_TEST_INPUT)
|
||||
+ " --no_cmdline_in_header -bamout %s -o /dev/null -L 1:11740000-11740700 --allowNonUniqueKmersInRef";
|
||||
final WalkerTestSpec spec = new WalkerTestSpec(base, 1, Arrays.asList("c19f0e62f90794661f5927c360d50998"));
|
||||
executeTest("LeftAlignmentBamOutBugFix", spec);
|
||||
|
|
@ -289,7 +291,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
|
|||
@Test
|
||||
public void HCTestDBSNPAnnotationWGS() {
|
||||
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
|
||||
"-T HaplotypeCaller --disableDithering --pcr_indel_model NONE -R " + b37KGReference + " --no_cmdline_in_header -I " + NA12878_PCRFREE + " -o %s -L 20:10,090,000-10,100,000 -D " + b37dbSNP132, 1,
|
||||
"-T HaplotypeCaller --disableDithering --pcr_indel_model NONE -pairHMMSub " + HMM_SUB_IMPLEMENTATION + " -R " + b37KGReference + " --no_cmdline_in_header -I " + NA12878_PCRFREE + " -o %s -L 20:10,090,000-10,100,000 -D " + b37dbSNP132, 1,
|
||||
Arrays.asList("f0618b66e088b2d6fd831bb357de933c"));
|
||||
executeTest("HC calling with dbSNP ID annotation on WGS intervals", spec);
|
||||
}
|
||||
|
|
@ -297,7 +299,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
|
|||
@Test
|
||||
public void HCTestDBSNPAnnotationWEx() {
|
||||
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
|
||||
"-T HaplotypeCaller --disableDithering --pcr_indel_model NONE -R " + b37KGReference + " --no_cmdline_in_header -I " + NA12878_PCRFREE + " -o %s -L 20:10,100,000-11,000,000 -D " + b37dbSNP132
|
||||
"-T HaplotypeCaller --disableDithering --pcr_indel_model NONE -pairHMMSub " + HMM_SUB_IMPLEMENTATION + " -R " + b37KGReference + " --no_cmdline_in_header -I " + NA12878_PCRFREE + " -o %s -L 20:10,100,000-11,000,000 -D " + b37dbSNP132
|
||||
+ " -L " + hg19Intervals + " -isr INTERSECTION", 1,
|
||||
Arrays.asList("b279dfa0864495d0cbe45167c13d5a75"));
|
||||
executeTest("HC calling with dbSNP ID annotation on WEx intervals", spec);
|
||||
|
|
@ -306,7 +308,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
|
|||
@Test
|
||||
public void HCTestDBSNPAnnotationWGSGraphBased() {
|
||||
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
|
||||
"-T HaplotypeCaller -likelihoodEngine GraphBased --disableDithering --pcr_indel_model NONE -R " + b37KGReference + " --no_cmdline_in_header -I " + NA12878_PCRFREE + " -o %s -L 20:10,090,000-10,100,000 -D " + b37dbSNP132, 1,
|
||||
"-T HaplotypeCaller -likelihoodEngine GraphBased --disableDithering --pcr_indel_model NONE -pairHMMSub " + HMM_SUB_IMPLEMENTATION + " -R " + b37KGReference + " --no_cmdline_in_header -I " + NA12878_PCRFREE + " -o %s -L 20:10,090,000-10,100,000 -D " + b37dbSNP132, 1,
|
||||
Arrays.asList("1b15b696671a9da000d5ec0372f939a2"));
|
||||
executeTest("HC calling with dbSNP ID annotation on WGS intervals", spec);
|
||||
}
|
||||
|
|
@ -314,7 +316,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
|
|||
@Test
|
||||
public void HCTestDBSNPAnnotationWExGraphBased() {
|
||||
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
|
||||
"-T HaplotypeCaller -likelihoodEngine GraphBased --disableDithering --pcr_indel_model NONE -R " + b37KGReference + " --no_cmdline_in_header -I " + NA12878_PCRFREE + " -o %s -L 20:10,000,000-11,000,000 -D " + b37dbSNP132
|
||||
"-T HaplotypeCaller -likelihoodEngine GraphBased --disableDithering --pcr_indel_model NONE -pairHMMSub " + HMM_SUB_IMPLEMENTATION + " -R " + b37KGReference + " --no_cmdline_in_header -I " + NA12878_PCRFREE + " -o %s -L 20:10,000,000-11,000,000 -D " + b37dbSNP132
|
||||
+ " -L " + hg19Intervals + " -isr INTERSECTION", 1,
|
||||
Arrays.asList("e46d99fb778e2aff09ccbbc1bda2a1bf"));
|
||||
executeTest("HC calling with dbSNP ID annotation on WEx intervals", spec);
|
||||
|
|
@ -323,7 +325,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
|
|||
@Test
|
||||
public void HCTestGraphBasedPCRFreePositiveLogLkFix() {
|
||||
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
|
||||
"-T HaplotypeCaller -likelihoodEngine GraphBased --disableDithering --pcr_indel_model NONE -R " + hg19Reference + " --no_cmdline_in_header -I " + NA12878_PCRFREE250_ADAPTER_TRIMMED + " -o %s -L 20:10,024,000-10,024,500 "
|
||||
"-T HaplotypeCaller -likelihoodEngine GraphBased --disableDithering --pcr_indel_model NONE -pairHMMSub " + HMM_SUB_IMPLEMENTATION + " -R " + hg19Reference + " --no_cmdline_in_header -I " + NA12878_PCRFREE250_ADAPTER_TRIMMED + " -o %s -L 20:10,024,000-10,024,500 "
|
||||
, 1,
|
||||
Arrays.asList(""));
|
||||
executeTest("HCTestGraphBasedPCRFreePositiveLogLkFix", spec);
|
||||
|
|
@ -338,7 +340,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
|
|||
@Test
|
||||
public void HCTestAggressivePcrIndelModelWGS() {
|
||||
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
|
||||
"-T HaplotypeCaller --disableDithering --pcr_indel_model AGGRESSIVE -R " + b37KGReference + " --no_cmdline_in_header -I " + NA12878_BAM + " -o %s -L 20:10,270,000-10,300,000", 1,
|
||||
"-T HaplotypeCaller --disableDithering --pcr_indel_model AGGRESSIVE -pairHMMSub " + HMM_SUB_IMPLEMENTATION + " -R " + b37KGReference + " --no_cmdline_in_header -I " + NA12878_BAM + " -o %s -L 20:10,270,000-10,300,000", 1,
|
||||
Arrays.asList("163a42e1144be1dc905233a8a42b72f6"));
|
||||
executeTest("HC calling with aggressive indel error modeling on WGS intervals", spec);
|
||||
}
|
||||
|
|
@ -346,16 +348,16 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
|
|||
@Test
|
||||
public void HCTestConservativePcrIndelModelWGS() {
|
||||
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
|
||||
"-T HaplotypeCaller --disableDithering --pcr_indel_model CONSERVATIVE -R " + b37KGReference + " --no_cmdline_in_header -I " + NA12878_BAM + " -o %s -L 20:10,270,000-10,300,000", 1,
|
||||
"-T HaplotypeCaller --disableDithering --pcr_indel_model CONSERVATIVE -pairHMMSub " + HMM_SUB_IMPLEMENTATION + " -R " + b37KGReference + " --no_cmdline_in_header -I " + NA12878_BAM + " -o %s -L 20:10,270,000-10,300,000", 1,
|
||||
Arrays.asList("13298981348351e79a2ff5407f206c1d"));
|
||||
executeTest("HC calling with conservative indel error modeling on WGS intervals", spec);
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testNoSuchEdgeBugFix() {
|
||||
final String commandLine = String.format("-T HaplotypeCaller --pcr_indel_model NONE -R %s -I %s -L %s -dontTrimActiveRegions -ERC GVCF " +
|
||||
final String commandLine = String.format("-T HaplotypeCaller --pcr_indel_model NONE -pairHMMSub %s -R %s -I %s -L %s -dontTrimActiveRegions -ERC GVCF " +
|
||||
"-likelihoodEngine GraphBased -variant_index_type %s -variant_index_parameter %d",
|
||||
b37KGReferenceWithDecoy, privateTestDir + "graphbased_no_such_edge_bug.bam", privateTestDir + "graphbased_no_such_edge_bug.intervals.bed",
|
||||
HMM_SUB_IMPLEMENTATION, b37KGReferenceWithDecoy, privateTestDir + "graphbased_no_such_edge_bug.bam", privateTestDir + "graphbased_no_such_edge_bug.intervals.bed",
|
||||
HaplotypeCaller.OPTIMAL_GVCF_INDEX_TYPE, HaplotypeCaller.OPTIMAL_GVCF_INDEX_PARAMETER);
|
||||
final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList(""));
|
||||
spec.disableShadowBCF();
|
||||
|
|
@ -365,8 +367,8 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
|
|||
// This test takes longer than 15 secs ... ~ 25-35 ,
|
||||
@Test
|
||||
public void testLackSensitivityDueToBadHaplotypeSelectionFix() {
|
||||
final String commandLine = String.format("-T HaplotypeCaller -R %s -I %s -L %s --no_cmdline_in_header --maxNumHaplotypesInPopulation 16",
|
||||
b37KGReferenceWithDecoy, privateTestDir + "hc-lack-sensitivity.bam", privateTestDir + "hc-lack-sensitivity.interval_list");
|
||||
final String commandLine = String.format("-T HaplotypeCaller -pairHMMSub %s -R %s -I %s -L %s --no_cmdline_in_header --maxNumHaplotypesInPopulation 16",
|
||||
HMM_SUB_IMPLEMENTATION, b37KGReferenceWithDecoy, privateTestDir + "hc-lack-sensitivity.bam", privateTestDir + "hc-lack-sensitivity.interval_list");
|
||||
final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("9fa83f82ba63729edd8696e82bfeea49"));
|
||||
spec.disableShadowBCF();
|
||||
executeTest("testLackSensitivityDueToBadHaplotypeSelectionFix", spec);
|
||||
|
|
@ -374,8 +376,8 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
|
|||
|
||||
@Test
|
||||
public void testMissingKeyAlternativeHaplotypesBugFix() {
|
||||
final String commandLine = String.format("-T HaplotypeCaller -R %s -I %s -L %s --no_cmdline_in_header ",
|
||||
b37KGReferenceWithDecoy, privateTestDir + "lost-alt-key-hap.bam", privateTestDir + "lost-alt-key-hap.interval_list");
|
||||
final String commandLine = String.format("-T HaplotypeCaller -pairHMMSub %s -R %s -I %s -L %s --no_cmdline_in_header ",
|
||||
HMM_SUB_IMPLEMENTATION, b37KGReferenceWithDecoy, privateTestDir + "lost-alt-key-hap.bam", privateTestDir + "lost-alt-key-hap.interval_list");
|
||||
final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("423b70c151a5d0028e104aa3372b8783"));
|
||||
spec.disableShadowBCF();
|
||||
executeTest("testMissingKeyAlternativeHaplotypesBugFix", spec);
|
||||
|
|
@ -388,9 +390,9 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
|
|||
final String TEST_BAM = privateTestDir + "sw_epsilon_test.bam";
|
||||
final String REFERENCE = b37KGReference;
|
||||
final String DBSNP = b37dbSNP138;
|
||||
final String commandLineWithoutInterval = String.format("-T HaplotypeCaller -I %s -R %s -D %s "
|
||||
final String commandLineWithoutInterval = String.format("-T HaplotypeCaller -pairHMMSub %s -I %s -R %s -D %s "
|
||||
+ "-variant_index_type LINEAR -variant_index_parameter 128000 --no_cmdline_in_header "
|
||||
+ "-stand_call_conf 10.0 -stand_emit_conf 10.0",TEST_BAM,REFERENCE,DBSNP);
|
||||
+ "-stand_call_conf 10.0 -stand_emit_conf 10.0",HMM_SUB_IMPLEMENTATION,TEST_BAM,REFERENCE,DBSNP);
|
||||
|
||||
final String commandLineShortInterval = commandLineWithoutInterval + " -L " + SHORT_INTERVAL;
|
||||
final String commandLineLongInterval = commandLineWithoutInterval + " -L " + LONG_INTERVAL;
|
||||
|
|
@ -406,4 +408,18 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
|
|||
executeTest("testDifferentIndelLocationsDueToSWExactDoubleComparisonsFix::longInterval",longSpec);
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testHaplotypeCallerPairHMMException(){
|
||||
executeTest("HaplotypeCallerPairHMMException",
|
||||
new WalkerTest.WalkerTestSpec(
|
||||
" -T HaplotypeCaller" +
|
||||
" --contamination_fraction_to_filter 0.05 --disableDithering --pcr_indel_model NONE --maxReadsInRegionPerSample 1000 " +
|
||||
" --minReadsPerAlignmentStart 5 --maxProbPropagationDistance 50 --activeProbabilityThreshold 0.002 " +
|
||||
" --no_cmdline_in_header -minPruning 3 -pairHMM VECTOR_LOGLESS_CACHING -pairHMMSub TEST_BEYOND_CAPABILITIES" +
|
||||
" -R " + REF +
|
||||
" -I " + NA12878_BAM +
|
||||
" -L " + INTERVALS_FILE +
|
||||
" -o %s",
|
||||
1, UserException.HardwareFeatureException.class));
|
||||
}
|
||||
}
|
||||
|
|
|
|||
|
|
@ -70,6 +70,8 @@ public class HaplotypeCallerModesIntegrationTest extends WalkerTest {
|
|||
//
|
||||
// --------------------------------------------------------------------------------------------------------------
|
||||
|
||||
final static String HMM_SUB_IMPLEMENTATION = "UNVECTORIZED";
|
||||
|
||||
@Test
|
||||
public void HCTestBamWriterCalledHaplotypes() {
|
||||
HCTestBamWriter(HaplotypeBAMWriter.Type.CALLED_HAPLOTYPES, ""); // current MD5 = 9a2b6157f14b44b872a77f4e75c56023
|
||||
|
|
@ -82,7 +84,7 @@ public class HaplotypeCallerModesIntegrationTest extends WalkerTest {
|
|||
|
||||
public void HCTestBamWriter(final HaplotypeBAMWriter.Type type, final String md5) {
|
||||
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
|
||||
"-T HaplotypeCaller -R " + b37KGReference + " --no_cmdline_in_header -I " + privateTestDir + "PCRFree.2x250.Illumina.20_10_11.bam -o /dev/null " +
|
||||
"-T HaplotypeCaller -pairHMMSub " + HMM_SUB_IMPLEMENTATION + " -R " + b37KGReference + " --no_cmdline_in_header -I " + privateTestDir + "PCRFree.2x250.Illumina.20_10_11.bam -o /dev/null " +
|
||||
"-bamout %s -L 20:10,000,000-10,010,000 -bamWriterType " + type, 1,
|
||||
Arrays.asList(md5));
|
||||
executeTest("HC writing bams with mode " + type, spec);
|
||||
|
|
|
|||
|
|
@ -60,6 +60,9 @@ import java.util.Arrays;
|
|||
import java.util.List;
|
||||
|
||||
public class HaplotypeCallerParallelIntegrationTest extends WalkerTest {
|
||||
|
||||
final static String HMM_SUB_IMPLEMENTATION = "UNVECTORIZED";
|
||||
|
||||
@DataProvider(name = "NCTDataProvider")
|
||||
public Object[][] makeNCTDataProvider() {
|
||||
List<Object[]> tests = new ArrayList<>();
|
||||
|
|
@ -74,7 +77,7 @@ public class HaplotypeCallerParallelIntegrationTest extends WalkerTest {
|
|||
@Test(dataProvider = "NCTDataProvider")
|
||||
public void testHCNCT(final int nct, final String md5) {
|
||||
WalkerTestSpec spec = new WalkerTestSpec(
|
||||
"-T HaplotypeCaller --pcr_indel_model NONE -R " + b37KGReference + " --no_cmdline_in_header -I "
|
||||
"-T HaplotypeCaller --pcr_indel_model NONE -pairHMMSub " + HMM_SUB_IMPLEMENTATION + " -R " + b37KGReference + " --no_cmdline_in_header -I "
|
||||
+ privateTestDir + "PCRFree.2x250.Illumina.20_10_11.bam -o %s " +
|
||||
" -L 20:10,000,000-10,100,000 -G none -A none -contamination 0.0 -nct " + nct, 1,
|
||||
Arrays.asList(md5));
|
||||
|
|
|
|||
|
|
@ -138,7 +138,7 @@ public class PairHMMLikelihoodCalculationEngineUnitTest extends BaseTest {
|
|||
public void createPcrErrorModelTest(final String repeat, final int repeatLength) {
|
||||
|
||||
final PairHMMLikelihoodCalculationEngine engine = new PairHMMLikelihoodCalculationEngine((byte)0,
|
||||
PairHMM.HMM_IMPLEMENTATION.ORIGINAL, 0.0, true,
|
||||
PairHMM.HMM_IMPLEMENTATION.ORIGINAL, PairHMM.HMM_SUB_IMPLEMENTATION.ENABLE_ALL, 0.0, true,
|
||||
PairHMMLikelihoodCalculationEngine.PCR_ERROR_MODEL.CONSERVATIVE);
|
||||
|
||||
final String readString = Utils.dupString(repeat, repeatLength);
|
||||
|
|
|
|||
|
|
@ -95,7 +95,8 @@ public class ReadThreadingLikelihoodCalculationEngineUnitTest extends ActiveRegi
|
|||
//final PairHMMLikelihoodCalculationEngine fullPairHMM = new PairHMMLikelihoodCalculationEngine((byte)10, false,
|
||||
// PairHMM.HMM_IMPLEMENTATION.LOGLESS_CACHING, -3);
|
||||
final PairHMMLikelihoodCalculationEngine fullPairHMM = new PairHMMLikelihoodCalculationEngine((byte)10,
|
||||
PairHMM.HMM_IMPLEMENTATION.LOGLESS_CACHING, Double.NEGATIVE_INFINITY,true, PairHMMLikelihoodCalculationEngine.PCR_ERROR_MODEL.NONE);
|
||||
PairHMM.HMM_IMPLEMENTATION.LOGLESS_CACHING, PairHMM.HMM_SUB_IMPLEMENTATION.ENABLE_ALL, Double.NEGATIVE_INFINITY,
|
||||
true, PairHMMLikelihoodCalculationEngine.PCR_ERROR_MODEL.NONE);
|
||||
|
||||
// When using likelihoods it should be around 0.05 since
|
||||
// When using maximum-likelihoods it can be as low as 0.00001
|
||||
|
|
|
|||
|
|
@ -69,7 +69,7 @@ public class Sandbox {
|
|||
* change per JVM session
|
||||
* @param readDataHolderClass class type of JNIReadDataHolderClass
|
||||
* @param haplotypeDataHolderClass class type of JNIHaplotypeDataHolderClass
|
||||
* @param mask mask is a 64 bit integer identical to the one received from jniGetMachineType(). Users can disable usage of some hardware features by zeroing some bits in the mask
|
||||
* @param mask 64 bit integer identical to the one received from jniGetMachineType(). Users can disable usage of some hardware features by zeroing bits in the mask
|
||||
* */
|
||||
private native void jniInitializeClassFieldsAndMachineMask(Class<?> readDataHolderClass, Class<?> haplotypeDataHolderClass, long mask);
|
||||
|
||||
|
|
|
|||
|
|
@ -482,4 +482,13 @@ public class UserException extends ReviewedGATKException {
|
|||
super(s);
|
||||
}
|
||||
}
|
||||
|
||||
/**
|
||||
* A trivial specialization of UserException to mark that a hardware feature is not supported
|
||||
*/
|
||||
public static class HardwareFeatureException extends UserException {
|
||||
public HardwareFeatureException(String message) {
|
||||
super(message);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
|
|
|||
|
|
@ -68,6 +68,33 @@ public abstract class PairHMM {
|
|||
ARRAY_LOGLESS
|
||||
}
|
||||
|
||||
/* Instruction sets for computing VectorLoglessHMM */
|
||||
public enum HMM_SUB_IMPLEMENTATION {
|
||||
/* standard un-vectorized instructions */
|
||||
UNVECTORIZED(0x0L, false),
|
||||
/* Streaming SIMD Extensions (SSE), version 4.1 */
|
||||
SSE41(0x1L, true),
|
||||
/* Streaming SIMD Extensions (SSE), version 4.2 */
|
||||
SSE42(0x2L, true),
|
||||
/* Advanced Vector Extensions (AVX) */
|
||||
AVX(0x4L, true),
|
||||
/* For testing only, set bit beyond hardware capabilities */
|
||||
TEST_BEYOND_CAPABILITIES(0x400L, true),
|
||||
/* Enable all implementations */
|
||||
ENABLE_ALL(0xFFFFFFFFFFFFFFFFl, false);
|
||||
|
||||
/* Masks for machine capabilities */
|
||||
private final long mask;
|
||||
/* Is a specific hardware instruction set requested? */
|
||||
private final boolean isSpecificHardwareRequest;
|
||||
HMM_SUB_IMPLEMENTATION(long mask, boolean isSpecificHardwareRequest) {
|
||||
this.mask = mask;
|
||||
this.isSpecificHardwareRequest = isSpecificHardwareRequest;
|
||||
}
|
||||
long getMask() { return mask; }
|
||||
boolean getIsSpecificHardwareRequest() { return isSpecificHardwareRequest; }
|
||||
}
|
||||
|
||||
protected int maxHaplotypeLength, maxReadLength;
|
||||
protected int paddedMaxReadLength, paddedMaxHaplotypeLength;
|
||||
protected int paddedReadLength, paddedHaplotypeLength;
|
||||
|
|
@ -93,8 +120,9 @@ public abstract class PairHMM {
|
|||
*
|
||||
* @param haplotypeMaxLength the max length of haplotypes we want to use with this PairHMM
|
||||
* @param readMaxLength the max length of reads we want to use with this PairHMM
|
||||
* @throws IllegalArgumentException if readMaxLength or haplotypeMaxLength is less than or equal to zero
|
||||
*/
|
||||
public void initialize( final int readMaxLength, final int haplotypeMaxLength ) {
|
||||
public void initialize( final int readMaxLength, final int haplotypeMaxLength ) throws IllegalArgumentException {
|
||||
if ( readMaxLength <= 0 ) throw new IllegalArgumentException("READ_MAX_LENGTH must be > 0 but got " + readMaxLength);
|
||||
if ( haplotypeMaxLength <= 0 ) throw new IllegalArgumentException("HAPLOTYPE_MAX_LENGTH must be > 0 but got " + haplotypeMaxLength);
|
||||
|
||||
|
|
@ -178,8 +206,6 @@ public abstract class PairHMM {
|
|||
* conditional to {@code alleles[a]}.
|
||||
* @param gcp penalty for gap continuations base array map for processed reads.
|
||||
*
|
||||
* @throws IllegalArgumentException
|
||||
*
|
||||
* @return never {@code null}.
|
||||
*/
|
||||
public void computeLikelihoods(final ReadLikelihoods.Matrix<Haplotype> likelihoods,
|
||||
|
|
@ -248,6 +274,10 @@ public abstract class PairHMM {
|
|||
* @param overallGCP the phred-scaled gap continuation penalties scores of read. Must be the same length as readBases
|
||||
* @param recacheReadValues if false, we don't recalculate any cached results, assuming that readBases and its associated
|
||||
* parameters are the same, and only the haplotype bases are changing underneath us
|
||||
* @throws IllegalStateException if did not call initialize() beforehand
|
||||
* @throws IllegalArgumentException haplotypeBases is null or greater than maxHaplotypeLength
|
||||
* @throws IllegalArgumentException readBases is null or greater than maxReadLength
|
||||
* @throws IllegalArgumentException readBases, readQuals, insertionGOP, deletionGOP and overallGCP are not the same size
|
||||
* @return the log10 probability of read coming from the haplotype under the provided error model
|
||||
*/
|
||||
protected final double computeReadLikelihoodGivenHaplotypeLog10( final byte[] haplotypeBases,
|
||||
|
|
@ -257,7 +287,7 @@ public abstract class PairHMM {
|
|||
final byte[] deletionGOP,
|
||||
final byte[] overallGCP,
|
||||
final boolean recacheReadValues,
|
||||
final byte[] nextHaploytpeBases) {
|
||||
final byte[] nextHaploytpeBases) throws IllegalStateException, IllegalArgumentException {
|
||||
|
||||
if ( ! initialized ) throw new IllegalStateException("Must call initialize before calling computeReadLikelihoodGivenHaplotypeLog10");
|
||||
if ( haplotypeBases == null ) throw new IllegalArgumentException("haplotypeBases cannot be null");
|
||||
|
|
@ -318,9 +348,10 @@ public abstract class PairHMM {
|
|||
*
|
||||
* @param haplotype1 the first haplotype1
|
||||
* @param haplotype2 the second haplotype1
|
||||
* @throws IllegalArgumentException if haplotype1 or haplotype2 are null or zero length
|
||||
* @return the index of the first position in haplotype1 and haplotype2 where the byte isn't the same
|
||||
*/
|
||||
public static int findFirstPositionWhereHaplotypesDiffer(final byte[] haplotype1, final byte[] haplotype2) {
|
||||
public static int findFirstPositionWhereHaplotypesDiffer(final byte[] haplotype1, final byte[] haplotype2) throws IllegalArgumentException {
|
||||
if ( haplotype1 == null || haplotype1.length == 0 ) throw new IllegalArgumentException("Haplotype1 is bad " + Arrays.toString(haplotype1));
|
||||
if ( haplotype2 == null || haplotype2.length == 0 ) throw new IllegalArgumentException("Haplotype2 is bad " + Arrays.toString(haplotype2));
|
||||
|
||||
|
|
|
|||
Loading…
Reference in New Issue