Merge pull request #729 from broadinstitute/eb_improve_dangling_head_merging_PT74221002
Improve the accuracy of dangling head merging in the HC assembler.
This commit is contained in:
Eric Banks
commit
78a61dc3e8
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@ -364,16 +364,22 @@ public class HaplotypeCaller extends ActiveRegionWalker<List<VariantContext>, In
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@Argument(fullName="numPruningSamples", shortName="numPruningSamples", doc="The number of samples that must pass the minPuning factor in order for the path to be kept", required = false)
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protected int numPruningSamples = 1;
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/**
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* This mode is currently experimental and should only be used in the RNA-seq calling pipeline.
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*/
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@Advanced
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@Argument(fullName="recoverDanglingHeads", shortName="recoverDanglingHeads", doc="Should we enable dangling head recovery in the read threading assembler?", required = false)
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protected boolean recoverDanglingHeads = false;
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@Deprecated
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@Argument(fullName="recoverDanglingHeads", shortName="recoverDanglingHeads", doc="This argument is no longer needed as it is now the default behavior", required = false)
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protected boolean DEPRECATED_RecoverDanglingHeads = false;
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@Hidden
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@Argument(fullName="doNotRecoverDanglingTails", shortName="doNotRecoverDanglingTails", doc="Should we disable dangling tail recovery in the read threading assembler?", required = false)
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protected boolean doNotRecoverDanglingTails = false;
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@Argument(fullName="doNotRecoverDanglingBranches", shortName="doNotRecoverDanglingBranches", doc="Should we disable dangling head and tail recovery in the read threading assembler?", required = false)
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protected boolean doNotRecoverDanglingBranches = false;
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/**
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* When constructing the assembly graph we are often left with "dangling" branches. The assembly engine attempts to rescue these branches
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* by merging them back into the main graph. This argument describes the minimum length of a dangling branch needed for the engine to
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* try to rescue it. A smaller number here will lead to higher sensitivity to real variation but also to a higher number of false positives.
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*/
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@Advanced
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@Argument(fullName="minDanglingBranchLength", shortName="minDanglingBranchLength", doc="Minimum length of a dangling branch to attempt recovery in the read threading assembler", required = false)
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protected int minDanglingBranchLength = 4;
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@Advanced
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@Argument(fullName="consensus", shortName="consensus", doc="In 1000G consensus mode. Inject all provided alleles to the assembly graph but don't forcibly genotype all of them.", required = false)
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@ -678,7 +684,7 @@ public class HaplotypeCaller extends ActiveRegionWalker<List<VariantContext>, In
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}
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}
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// create a UAC but with the exactCallsLog = null, so we only output the log for the HC caller itself, if requested
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final UnifiedArgumentCollection simpleUAC = SCAC.cloneTo(UnifiedArgumentCollection.class);
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simpleUAC.outputMode = OutputMode.EMIT_VARIANTS_ONLY;
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@ -750,8 +756,8 @@ public class HaplotypeCaller extends ActiveRegionWalker<List<VariantContext>, In
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assemblyEngine.setDebug(SCAC.DEBUG);
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assemblyEngine.setDebugGraphTransformations(debugGraphTransformations);
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assemblyEngine.setAllowCyclesInKmerGraphToGeneratePaths(allowCyclesInKmerGraphToGeneratePaths);
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assemblyEngine.setRecoverDanglingTails(!doNotRecoverDanglingTails);
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assemblyEngine.setRecoverDanglingHeads(recoverDanglingHeads);
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assemblyEngine.setRecoverDanglingBranches(!doNotRecoverDanglingBranches);
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assemblyEngine.setMinDanglingBranchLength(minDanglingBranchLength);
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assemblyEngine.setMinBaseQualityToUseInAssembly(MIN_BASE_QUALTY_SCORE);
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MIN_TAIL_QUALITY = (byte)(MIN_BASE_QUALTY_SCORE - 1);
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@ -86,8 +86,8 @@ public abstract class LocalAssemblyEngine {
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protected boolean debug = false;
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protected boolean allowCyclesInKmerGraphToGeneratePaths = false;
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protected boolean debugGraphTransformations = false;
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protected boolean recoverDanglingTails = true;
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protected boolean recoverDanglingHeads = true;
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protected boolean recoverDanglingBranches = true;
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protected int minDanglingBranchLength = 0;
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protected byte minBaseQualityToUseInAssembly = DEFAULT_MIN_BASE_QUALITY_TO_USE;
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protected int pruneFactor = 2;
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@ -439,19 +439,11 @@ public abstract class LocalAssemblyEngine {
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this.debugGraphTransformations = debugGraphTransformations;
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}
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public boolean isRecoverDanglingTails() {
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return recoverDanglingTails;
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public boolean isRecoverDanglingBranches() { return recoverDanglingBranches; }
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public void setRecoverDanglingBranches(final boolean recoverDanglingBranches) {
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this.recoverDanglingBranches = recoverDanglingBranches;
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}
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public void setRecoverDanglingTails(boolean recoverDanglingTails) {
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this.recoverDanglingTails = recoverDanglingTails;
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}
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public boolean isRecoverDanglingHeads() {
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return recoverDanglingHeads;
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}
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public void setRecoverDanglingHeads(boolean recoverDanglingHeads) {
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this.recoverDanglingHeads = recoverDanglingHeads;
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}
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public void setMinDanglingBranchLength(final int minDanglingBranchLength) { this.minDanglingBranchLength = minDanglingBranchLength; }
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}
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@ -60,8 +60,7 @@ import java.util.*;
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public abstract class DanglingChainMergingGraph extends BaseGraph<MultiDeBruijnVertex, MultiSampleEdge> {
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private static final int MAX_CIGAR_COMPLEXITY = 3;
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private static final int MIN_DANGLING_TAIL_LENGTH = 5; // SNP + 3 stabilizing nodes + the LCA
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private static final int MAXIMUM_MISMATCHES_IN_DANGLING_HEAD_MERGE = 1;
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private int maxMismatchesInDanglingHead = -1;
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protected boolean alreadyBuilt;
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@ -73,6 +72,10 @@ public abstract class DanglingChainMergingGraph extends BaseGraph<MultiDeBruijnV
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super(kmerSize, edgeFactory);
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}
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protected void setMaxMismatchesInDanglingHead(final int maxMismatchesInDanglingHead) {
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this.maxMismatchesInDanglingHead = maxMismatchesInDanglingHead;
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}
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/**
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* Edge factory that encapsulates the numPruningSamples assembly parameter
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*/
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@ -119,8 +122,9 @@ public abstract class DanglingChainMergingGraph extends BaseGraph<MultiDeBruijnV
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* Try to recover dangling tails
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*
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* @param pruneFactor the prune factor to use in ignoring chain pieces
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* @param minDanglingBranchLength the minimum length of a dangling branch for us to try to merge it
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*/
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public void recoverDanglingTails(final int pruneFactor) {
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public void recoverDanglingTails(final int pruneFactor, final int minDanglingBranchLength) {
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if ( ! alreadyBuilt ) throw new IllegalStateException("recoverDanglingTails requires the graph be already built");
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int attempted = 0;
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@ -128,7 +132,7 @@ public abstract class DanglingChainMergingGraph extends BaseGraph<MultiDeBruijnV
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for ( final MultiDeBruijnVertex v : vertexSet() ) {
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if ( outDegreeOf(v) == 0 && ! isRefSink(v) ) {
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attempted++;
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nRecovered += recoverDanglingTail(v, pruneFactor);
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nRecovered += recoverDanglingTail(v, pruneFactor, minDanglingBranchLength);
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}
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}
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@ -139,8 +143,9 @@ public abstract class DanglingChainMergingGraph extends BaseGraph<MultiDeBruijnV
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* Try to recover dangling heads
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*
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* @param pruneFactor the prune factor to use in ignoring chain pieces
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* @param minDanglingBranchLength the minimum length of a dangling branch for us to try to merge it
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*/
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public void recoverDanglingHeads(final int pruneFactor) {
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public void recoverDanglingHeads(final int pruneFactor, final int minDanglingBranchLength) {
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if ( ! alreadyBuilt ) throw new IllegalStateException("recoverDanglingHeads requires the graph be already built");
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// we need to build a list of dangling heads because that process can modify the graph (and otherwise generate
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@ -157,7 +162,7 @@ public abstract class DanglingChainMergingGraph extends BaseGraph<MultiDeBruijnV
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// now we can try to recover the dangling heads
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for ( final MultiDeBruijnVertex v : danglingHeads ) {
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attempted++;
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nRecovered += recoverDanglingHead(v, pruneFactor);
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nRecovered += recoverDanglingHead(v, pruneFactor, minDanglingBranchLength);
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}
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logger.debug("Recovered " + nRecovered + " of " + attempted + " dangling heads");
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@ -168,13 +173,14 @@ public abstract class DanglingChainMergingGraph extends BaseGraph<MultiDeBruijnV
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*
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* @param vertex the vertex to recover
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* @param pruneFactor the prune factor to use in ignoring chain pieces
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* @param minDanglingBranchLength the minimum length of a dangling branch for us to try to merge it
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* @return 1 if we successfully recovered the vertex and 0 otherwise
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*/
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protected int recoverDanglingTail(final MultiDeBruijnVertex vertex, final int pruneFactor) {
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protected int recoverDanglingTail(final MultiDeBruijnVertex vertex, final int pruneFactor, final int minDanglingBranchLength) {
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if ( outDegreeOf(vertex) != 0 ) throw new IllegalStateException("Attempting to recover a dangling tail for " + vertex + " but it has out-degree > 0");
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// generate the CIGAR string from Smith-Waterman between the dangling tail and reference paths
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final DanglingChainMergeHelper danglingTailMergeResult = generateCigarAgainstDownwardsReferencePath(vertex, pruneFactor);
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final DanglingChainMergeHelper danglingTailMergeResult = generateCigarAgainstDownwardsReferencePath(vertex, pruneFactor, minDanglingBranchLength);
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// if the CIGAR is too complex (or couldn't be computed) then we do not allow the merge into the reference path
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if ( danglingTailMergeResult == null || ! cigarIsOkayToMerge(danglingTailMergeResult.cigar, false, true) )
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@ -189,13 +195,14 @@ public abstract class DanglingChainMergingGraph extends BaseGraph<MultiDeBruijnV
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*
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* @param vertex the vertex to recover
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* @param pruneFactor the prune factor to use in ignoring chain pieces
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* @param minDanglingBranchLength the minimum length of a dangling branch for us to try to merge it
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* @return 1 if we successfully recovered a vertex and 0 otherwise
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*/
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protected int recoverDanglingHead(final MultiDeBruijnVertex vertex, final int pruneFactor) {
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protected int recoverDanglingHead(final MultiDeBruijnVertex vertex, final int pruneFactor, final int minDanglingBranchLength) {
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if ( inDegreeOf(vertex) != 0 ) throw new IllegalStateException("Attempting to recover a dangling head for " + vertex + " but it has in-degree > 0");
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// generate the CIGAR string from Smith-Waterman between the dangling tail and reference paths
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final DanglingChainMergeHelper danglingHeadMergeResult = generateCigarAgainstUpwardsReferencePath(vertex, pruneFactor);
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final DanglingChainMergeHelper danglingHeadMergeResult = generateCigarAgainstUpwardsReferencePath(vertex, pruneFactor, minDanglingBranchLength);
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// if the CIGAR is too complex (or couldn't be computed) then we do not allow the merge into the reference path
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if ( danglingHeadMergeResult == null || ! cigarIsOkayToMerge(danglingHeadMergeResult.cigar, true, false) )
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@ -230,7 +237,7 @@ public abstract class DanglingChainMergingGraph extends BaseGraph<MultiDeBruijnV
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if ( requireLastElementM && elements.get(numElements - 1).getOperator() != CigarOperator.M )
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return false;
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// TODO -- do we want to check whether the Ms mismatch too much also?
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// note that there are checks for too many mismatches in the dangling branch later in the process
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return true;
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}
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@ -313,11 +320,12 @@ public abstract class DanglingChainMergingGraph extends BaseGraph<MultiDeBruijnV
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* @param pruneFactor the prune factor to use in ignoring chain pieces
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* @return a SmithWaterman object which can be null if no proper alignment could be generated
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*/
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protected DanglingChainMergeHelper generateCigarAgainstDownwardsReferencePath(final MultiDeBruijnVertex vertex, final int pruneFactor) {
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protected DanglingChainMergeHelper generateCigarAgainstDownwardsReferencePath(final MultiDeBruijnVertex vertex, final int pruneFactor, final int minDanglingBranchLength) {
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final int minTailPathLength = Math.max(1, minDanglingBranchLength); // while heads can be 0, tails absolutely cannot
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// find the lowest common ancestor path between this vertex and the diverging master path if available
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final List<MultiDeBruijnVertex> altPath = findPathUpwardsToLowestCommonAncestor(vertex, pruneFactor);
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if ( altPath == null || isRefSource(altPath.get(0)) || altPath.size() < MIN_DANGLING_TAIL_LENGTH )
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if ( altPath == null || isRefSource(altPath.get(0)) || altPath.size() < minTailPathLength + 1 ) // add 1 to include the LCA
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return null;
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// now get the reference path from the LCA
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@ -340,11 +348,11 @@ public abstract class DanglingChainMergingGraph extends BaseGraph<MultiDeBruijnV
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* @param pruneFactor the prune factor to use in ignoring chain pieces
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* @return a SmithWaterman object which can be null if no proper alignment could be generated
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*/
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protected DanglingChainMergeHelper generateCigarAgainstUpwardsReferencePath(final MultiDeBruijnVertex vertex, final int pruneFactor) {
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protected DanglingChainMergeHelper generateCigarAgainstUpwardsReferencePath(final MultiDeBruijnVertex vertex, final int pruneFactor, final int minDanglingBranchLength) {
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// find the highest common descendant path between vertex and the reference source if available
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final List<MultiDeBruijnVertex> altPath = findPathDownwardsToHighestCommonDescendantOfReference(vertex, pruneFactor);
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if ( altPath == null || isRefSink(altPath.get(0)) )
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if ( altPath == null || isRefSink(altPath.get(0)) || altPath.size() < minDanglingBranchLength + 1 ) // add 1 to include the LCA
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return null;
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// now get the reference path from the LCA
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@ -477,14 +485,15 @@ public abstract class DanglingChainMergingGraph extends BaseGraph<MultiDeBruijnV
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* @param maxIndex the maximum index to traverse (not inclusive)
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* @return the index of the ideal prefix match or -1 if it cannot find one, must be less than maxIndex
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*/
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protected static int bestPrefixMatch(final byte[] path1, final byte[] path2, final int maxIndex) {
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protected int bestPrefixMatch(final byte[] path1, final byte[] path2, final int maxIndex) {
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final int maxMismatches = getMaxMismatches(maxIndex);
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int mismatches = 0;
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int index = 0;
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int lastGoodIndex = -1;
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while ( index < maxIndex ) {
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if ( path1[index] != path2[index] ) {
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if ( ++mismatches > MAXIMUM_MISMATCHES_IN_DANGLING_HEAD_MERGE )
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return lastGoodIndex;
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if ( ++mismatches > maxMismatches )
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return -1;
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lastGoodIndex = index;
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}
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index++;
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@ -493,6 +502,17 @@ public abstract class DanglingChainMergingGraph extends BaseGraph<MultiDeBruijnV
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return lastGoodIndex;
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}
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/**
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* Determine the maximum number of mismatches permitted on the branch.
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* Unless it's preset (e.g. by unit tests) it should be the length of the branch divided by the kmer size.
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*
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* @param lengthOfDanglingBranch the length of the branch itself
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* @return positive integer
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*/
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private int getMaxMismatches(final int lengthOfDanglingBranch) {
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return maxMismatchesInDanglingHead > 0 ? maxMismatchesInDanglingHead : Math.max(1, (lengthOfDanglingBranch / kmerSize));
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}
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protected boolean extendDanglingPathAgainstReference(final DanglingChainMergeHelper danglingHeadMergeResult, final int numNodesToExtend) {
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final int indexOfLastDanglingNode = danglingHeadMergeResult.danglingPath.size() - 1;
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@ -69,7 +69,6 @@ public class ReadThreadingAssembler extends LocalAssemblyEngine {
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/** The min and max kmer sizes to try when building the graph. */
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private final List<Integer> kmerSizes;
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private final int maxAllowedPathsForReadThreadingAssembler;
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private final boolean dontIncreaseKmerSizesForCycles;
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private final boolean allowNonUniqueKmersInRef;
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@ -85,7 +84,6 @@ public class ReadThreadingAssembler extends LocalAssemblyEngine {
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public ReadThreadingAssembler(final int maxAllowedPathsForReadThreadingAssembler, final List<Integer> kmerSizes, final boolean dontIncreaseKmerSizesForCycles, final boolean allowNonUniqueKmersInRef, final int numPruningSamples) {
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super(maxAllowedPathsForReadThreadingAssembler);
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this.kmerSizes = kmerSizes;
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this.maxAllowedPathsForReadThreadingAssembler = maxAllowedPathsForReadThreadingAssembler;
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this.dontIncreaseKmerSizesForCycles = dontIncreaseKmerSizesForCycles;
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this.allowNonUniqueKmersInRef = allowNonUniqueKmersInRef;
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this.numPruningSamples = numPruningSamples;
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@ -159,7 +157,7 @@ public class ReadThreadingAssembler extends LocalAssemblyEngine {
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final ReadThreadingGraph rtgraph = new ReadThreadingGraph(kmerSize, debugGraphTransformations, minBaseQualityToUseInAssembly, numPruningSamples);
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rtgraph.setThreadingStartOnlyAtExistingVertex(!recoverDanglingHeads);
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rtgraph.setThreadingStartOnlyAtExistingVertex(!recoverDanglingBranches);
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// add the reference sequence to the graph
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rtgraph.addSequence("ref", refHaplotype.getBases(), true);
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@ -199,8 +197,10 @@ public class ReadThreadingAssembler extends LocalAssemblyEngine {
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// look at all chains in the graph that terminate in a non-ref node (dangling sources and sinks) and see if
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// we can recover them by merging some N bases from the chain back into the reference
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if ( recoverDanglingTails ) rtgraph.recoverDanglingTails(pruneFactor);
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if ( recoverDanglingHeads ) rtgraph.recoverDanglingHeads(pruneFactor);
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if ( recoverDanglingBranches ) {
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rtgraph.recoverDanglingTails(pruneFactor, minDanglingBranchLength);
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rtgraph.recoverDanglingHeads(pruneFactor, minDanglingBranchLength);
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}
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// remove all heading and trailing paths
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if ( removePathsNotConnectedToRef ) rtgraph.removePathsNotConnectedToRef();
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@ -64,7 +64,7 @@ public class HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest extends Wa
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@Test
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public void testHaplotypeCallerMultiSampleComplex1() {
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HCTestComplexVariants(privateTestDir + "AFR.complex.variants.bam", "", "50f00994d0e9ae043c163425a2073675");
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HCTestComplexVariants(privateTestDir + "AFR.complex.variants.bam", "", "29f216779f0db9a08f4907ea82f0c7fb");
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}
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private void HCTestSymbolicVariants(String bam, String args, String md5) {
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@ -88,7 +88,7 @@ public class HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest extends Wa
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@Test
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public void testHaplotypeCallerMultiSampleGGAComplex() {
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HCTestComplexGGA(NA12878_CHR20_BAM, "-L 20:119673-119823 -L 20:121408-121538",
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"e497d592078f999d37af4badef0f3c32");
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"9de64c4405e0dab99c70c2fae54d4841");
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}
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@Test
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@ -106,7 +106,7 @@ public class HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest extends Wa
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@Test
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public void testHaplotypeCallerMultiSampleConsensusModeComplex() {
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HCTestComplexGGA(NA12878_CHR20_BAM, "-L 20:119673-119823 -L 20:121408-121538 -L 20:133041-133161 -L 20:300207-300337",
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"c44bd3a3bf241fc106496510450746fd");
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"272e096b7dc2839d11343f35e5d5442d");
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}
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}
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@ -85,28 +85,28 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
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@Test
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public void testHaplotypeCallerMultiSample() {
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HCTest(CEUTRIO_BAM, "", "fd31a5da51e46b021db055177841c8c2");
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HCTest(CEUTRIO_BAM, "", "7bc718c6a604405e6d33c3073630cc66");
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}
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@Test
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public void testHaplotypeCallerSingleSample() {
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HCTest(NA12878_BAM, "", "4f80b7c7e448d719e308b7d73751bebc");
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HCTest(NA12878_BAM, "", "07125724eb465a739df9c6ab191216b0");
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}
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@Test
|
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public void testHaplotypeCallerMultiSampleHaploid() {
|
||||
HCTest(CEUTRIO_BAM,
|
||||
"-ploidy 1", "466d423a3bacd0032549bda987fb1574");
|
||||
"-ploidy 1", "c93650f842aa4dfa4ef2b5f1b908a576");
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testHaplotypeCallerSingleSampleHaploid() {
|
||||
HCTest(NA12878_BAM, "-ploidy 1", "f588569b6d14246b7e6678ac80286012");
|
||||
HCTest(NA12878_BAM, "-ploidy 1", "e5c8a8bfb4d9d522e610a2299a9b32ad");
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testHaplotypeCallerSingleSampleTetraploid() {
|
||||
HCTest(NA12878_BAM, "-ploidy 4", "95d4cca48fcbb82d5e41cfe60d68531e");
|
||||
HCTest(NA12878_BAM, "-ploidy 4", "af711f92b33d3f42e87a719745d93a68");
|
||||
}
|
||||
|
||||
@Test
|
||||
|
|
@ -126,41 +126,41 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
|
|||
|
||||
@Test
|
||||
public void testHaplotypeCallerGraphBasedSingleSample() {
|
||||
HCTest(NA12878_BAM, "-likelihoodEngine GraphBased", "4577a7c82300950eff0fae10aa4cc4ae");
|
||||
HCTest(NA12878_BAM, "-likelihoodEngine GraphBased", "79b0f8fa5e42ef23f3d166d84d92fa23");
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testHaplotypeCallerGraphBasedMultiSampleHaploid() {
|
||||
HCTest(CEUTRIO_BAM, "-likelihoodEngine GraphBased -ploidy 1", "2ce7ef54258261c9e869fc69db3312e3");
|
||||
HCTest(CEUTRIO_BAM, "-likelihoodEngine GraphBased -ploidy 1", "0962d7723ef1e5e20fb42e869f12e1da");
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testHaplotypeCallerGraphBasedMultiSample() {
|
||||
HCTest(CEUTRIO_BAM, "-likelihoodEngine GraphBased", "958511863caca47833b1df03a2f1e130");
|
||||
HCTest(CEUTRIO_BAM, "-likelihoodEngine GraphBased", "10119fbb494e966a6f1b54307cfbeb8b");
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testHaplotypeCallerSingleSampleWithDbsnp() {
|
||||
HCTest(NA12878_BAM, "-D " + b37dbSNP132, "8294e5a78f2e1091369ae5d9735533cd");
|
||||
HCTest(NA12878_BAM, "-D " + b37dbSNP132, "fded195a0436242673718e6dc083c172");
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testHaplotypeCallerMultiSampleGGA() {
|
||||
HCTest(CEUTRIO_BAM, "--max_alternate_alleles 3 -gt_mode GENOTYPE_GIVEN_ALLELES -alleles " + validationDataLocation + "combined.phase1.chr20.raw.indels.sites.vcf" +
|
||||
" -isr INTERSECTION -L " + GGA_INTERVALS_FILE,
|
||||
"368f42869cc651c8fd94ec2a572bb545");
|
||||
"5bc8892b68e281a3ceb4f2d141f8c723");
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testHaplotypeCallerMultiSampleGGAHaploid() {
|
||||
HCTest(CEUTRIO_BAM, "--max_alternate_alleles 3 -gt_mode GENOTYPE_GIVEN_ALLELES -ploidy 1 -alleles " + validationDataLocation + "combined.phase1.chr20.raw.indels.sites.vcf",
|
||||
"52494fae89dd37abd0029013557dfa9d");
|
||||
"d1e872b1d9c484e94f826255e5dde548");
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testHaplotypeCallerMultiSampleGGATetraploid() {
|
||||
HCTest(CEUTRIO_BAM, "--max_alternate_alleles 3 -gt_mode GENOTYPE_GIVEN_ALLELES -ploidy 4 -alleles " + validationDataLocation + "combined.phase1.chr20.raw.indels.sites.vcf",
|
||||
"6a70e9d87459f274bc9b20f9b97ea274");
|
||||
"874f5fc9d7eed8894f72b8d2587de4b6");
|
||||
}
|
||||
|
||||
@Test
|
||||
|
|
@ -176,7 +176,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
|
|||
|
||||
@Test
|
||||
public void testHaplotypeCallerSingleSampleIndelQualityScores() {
|
||||
HCTestIndelQualityScores(NA12878_RECALIBRATED_BAM, "", "77f56e9211b13690ad4c30f40469381a");
|
||||
HCTestIndelQualityScores(NA12878_RECALIBRATED_BAM, "", "f2242d1696ef542196d363cf56159851");
|
||||
}
|
||||
|
||||
private void HCTestNearbySmallIntervals(String bam, String args, String md5) {
|
||||
|
|
@ -223,7 +223,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
|
|||
@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 WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList("2be5ac87d698d7f92525a9721e66ed94"));
|
||||
final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList("cf6fbb3636c52cd47dd14e0bd415a320"));
|
||||
executeTest("HCTestProblematicReadsModifiedInActiveRegions: ", spec);
|
||||
}
|
||||
|
||||
|
|
@ -272,7 +272,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
|
|||
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,
|
||||
Arrays.asList("defb00b7f19a4626a1ace1bbf4fdf81d"));
|
||||
Arrays.asList("86fb942473b3f8df2f8865209e551200"));
|
||||
executeTest("HC calling with dbSNP ID annotation on WGS intervals", spec);
|
||||
}
|
||||
|
||||
|
|
@ -289,7 +289,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
|
|||
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,
|
||||
Arrays.asList("6d221ed702f7f241e1af6f9016754a50"));
|
||||
Arrays.asList("b6dab8a6223afeb9d0fa7c178c84c024"));
|
||||
executeTest("HC calling with dbSNP ID annotation on WGS intervals", spec);
|
||||
}
|
||||
|
||||
|
|
@ -359,7 +359,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
|
|||
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 WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("ca3d7b611b57835724fabd78f202bede"));
|
||||
final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("423b70c151a5d0028e104aa3372b8783"));
|
||||
spec.disableShadowBCF();
|
||||
executeTest("testMissingKeyAlternativeHaplotypesBugFix", spec);
|
||||
}
|
||||
|
|
|
|||
|
|
@ -119,7 +119,7 @@ public class DanglingChainMergingGraphUnitTest extends BaseTest {
|
|||
Assert.assertTrue(altSink != null, "We did not find a non-reference sink");
|
||||
|
||||
// confirm that the SW alignment agrees with our expectations
|
||||
final ReadThreadingGraph.DanglingChainMergeHelper result = rtgraph.generateCigarAgainstDownwardsReferencePath(altSink, 0);
|
||||
final ReadThreadingGraph.DanglingChainMergeHelper result = rtgraph.generateCigarAgainstDownwardsReferencePath(altSink, 0, 4);
|
||||
|
||||
if ( result == null ) {
|
||||
Assert.assertFalse(cigarIsGood);
|
||||
|
|
@ -209,6 +209,7 @@ public class DanglingChainMergingGraphUnitTest extends BaseTest {
|
|||
rtgraph.addSequence("ref", ref.getBytes(), true);
|
||||
final GATKSAMRecord read = ArtificialSAMUtils.createArtificialRead(alt.getBytes(), Utils.dupBytes((byte) 30, alt.length()), alt.length() + "M");
|
||||
rtgraph.addRead(read);
|
||||
rtgraph.setMaxMismatchesInDanglingHead(10);
|
||||
rtgraph.buildGraphIfNecessary();
|
||||
|
||||
// confirm that we have just a single dangling head
|
||||
|
|
@ -223,7 +224,7 @@ public class DanglingChainMergingGraphUnitTest extends BaseTest {
|
|||
Assert.assertTrue(altSource != null, "We did not find a non-reference source");
|
||||
|
||||
// confirm that the SW alignment agrees with our expectations
|
||||
final ReadThreadingGraph.DanglingChainMergeHelper result = rtgraph.generateCigarAgainstUpwardsReferencePath(altSource, 0);
|
||||
final ReadThreadingGraph.DanglingChainMergeHelper result = rtgraph.generateCigarAgainstUpwardsReferencePath(altSource, 0, 1);
|
||||
|
||||
if ( result == null ) {
|
||||
Assert.assertFalse(shouldBeMerged);
|
||||
|
|
|
|||
|
|
@ -85,7 +85,7 @@ public class ReadThreadingAssemblerUnitTest extends BaseTest {
|
|||
|
||||
public SeqGraph assemble() {
|
||||
assembler.removePathsNotConnectedToRef = false; // needed to pass some of the tests
|
||||
assembler.setRecoverDanglingTails(false); // needed to pass some of the tests
|
||||
assembler.setRecoverDanglingBranches(false); // needed to pass some of the tests
|
||||
assembler.setDebugGraphTransformations(true);
|
||||
final SeqGraph graph = assembler.assemble(reads, refHaplotype, Collections.<Haplotype>emptyList()).get(0).getGraph();
|
||||
if ( DEBUG ) graph.printGraph(new File("test.dot"), 0);
|
||||
|
|
@ -171,7 +171,7 @@ public class ReadThreadingAssemblerUnitTest extends BaseTest {
|
|||
Assert.assertNotNull(graph.getReferenceSinkVertex());
|
||||
|
||||
final List<KBestHaplotype> paths = new KBestHaplotypeFinder(graph);
|
||||
Assert.assertEquals(paths.size(), 2);
|
||||
Assert.assertEquals(paths.size(), 1);
|
||||
}
|
||||
|
||||
@Test(enabled = ! DEBUG)
|
||||
|
|
|
|||
Loading…
Reference in New Issue