Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
This commit is contained in:
Mauricio Carneiro
commit
baa1c60b80
|
|
@ -31,8 +31,8 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
|
|||
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
|
||||
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
|
||||
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatibleWalker;
|
||||
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ExperimentalAnnotation;
|
||||
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
|
||||
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.RodRequiringAnnotation;
|
||||
import org.broadinstitute.sting.utils.Utils;
|
||||
import org.broadinstitute.sting.utils.codecs.vcf.*;
|
||||
import org.broadinstitute.sting.utils.exceptions.UserException;
|
||||
|
|
@ -50,7 +50,7 @@ import java.util.*;
|
|||
*
|
||||
* @author David Roazen
|
||||
*/
|
||||
public class SnpEff extends InfoFieldAnnotation implements ExperimentalAnnotation {
|
||||
public class SnpEff extends InfoFieldAnnotation implements RodRequiringAnnotation {
|
||||
|
||||
private static Logger logger = Logger.getLogger(SnpEff.class);
|
||||
|
||||
|
|
|
|||
|
|
@ -132,6 +132,13 @@ public class VariantAnnotator extends RodWalker<Integer, Integer> implements Ann
|
|||
@Argument(fullName="annotation", shortName="A", doc="One or more specific annotations to apply to variant calls", required=false)
|
||||
protected List<String> annotationsToUse = new ArrayList<String>();
|
||||
|
||||
/**
|
||||
* Note that this argument has higher priority than the -A or -G arguments,
|
||||
* so annotations will be excluded even if they are explicitly included with the other options.
|
||||
*/
|
||||
@Argument(fullName="excludeAnnotation", shortName="XA", doc="One or more specific annotations to exclude", required=false)
|
||||
protected List<String> annotationsToExclude = new ArrayList<String>();
|
||||
|
||||
/**
|
||||
* See the -list argument to view available groups.
|
||||
*/
|
||||
|
|
@ -148,6 +155,9 @@ public class VariantAnnotator extends RodWalker<Integer, Integer> implements Ann
|
|||
@Argument(fullName="expression", shortName="E", doc="One or more specific expressions to apply to variant calls; see documentation for more details", required=false)
|
||||
protected List<String> expressionsToUse = new ArrayList<String>();
|
||||
|
||||
/**
|
||||
* Note that the -XL argument can be used along with this one to exclude annotations.
|
||||
*/
|
||||
@Argument(fullName="useAllAnnotations", shortName="all", doc="Use all possible annotations (not for the faint of heart)", required=false)
|
||||
protected Boolean USE_ALL_ANNOTATIONS = false;
|
||||
|
||||
|
|
@ -209,9 +219,9 @@ public class VariantAnnotator extends RodWalker<Integer, Integer> implements Ann
|
|||
}
|
||||
|
||||
if ( USE_ALL_ANNOTATIONS )
|
||||
engine = new VariantAnnotatorEngine(this, getToolkit());
|
||||
engine = new VariantAnnotatorEngine(annotationsToExclude, this, getToolkit());
|
||||
else
|
||||
engine = new VariantAnnotatorEngine(annotationGroupsToUse, annotationsToUse, this, getToolkit());
|
||||
engine = new VariantAnnotatorEngine(annotationGroupsToUse, annotationsToUse, annotationsToExclude, this, getToolkit());
|
||||
engine.initializeExpressions(expressionsToUse);
|
||||
|
||||
// setup the header fields
|
||||
|
|
|
|||
|
|
@ -73,19 +73,20 @@ public class VariantAnnotatorEngine {
|
|||
}
|
||||
|
||||
// use this constructor if you want all possible annotations
|
||||
public VariantAnnotatorEngine(AnnotatorCompatibleWalker walker, GenomeAnalysisEngine toolkit) {
|
||||
public VariantAnnotatorEngine(List<String> annotationsToExclude, AnnotatorCompatibleWalker walker, GenomeAnalysisEngine toolkit) {
|
||||
this.walker = walker;
|
||||
this.toolkit = toolkit;
|
||||
requestedInfoAnnotations = AnnotationInterfaceManager.createAllInfoFieldAnnotations();
|
||||
requestedGenotypeAnnotations = AnnotationInterfaceManager.createAllGenotypeAnnotations();
|
||||
excludeAnnotations(annotationsToExclude);
|
||||
initializeDBs();
|
||||
}
|
||||
|
||||
// use this constructor if you want to select specific annotations (and/or interfaces)
|
||||
public VariantAnnotatorEngine(List<String> annotationGroupsToUse, List<String> annotationsToUse, AnnotatorCompatibleWalker walker, GenomeAnalysisEngine toolkit) {
|
||||
public VariantAnnotatorEngine(List<String> annotationGroupsToUse, List<String> annotationsToUse, List<String> annotationsToExclude, AnnotatorCompatibleWalker walker, GenomeAnalysisEngine toolkit) {
|
||||
this.walker = walker;
|
||||
this.toolkit = toolkit;
|
||||
initializeAnnotations(annotationGroupsToUse, annotationsToUse);
|
||||
initializeAnnotations(annotationGroupsToUse, annotationsToUse, annotationsToExclude);
|
||||
initializeDBs();
|
||||
}
|
||||
|
||||
|
|
@ -96,10 +97,30 @@ public class VariantAnnotatorEngine {
|
|||
requestedExpressions.add(new VAExpression(expression, walker.getResourceRodBindings()));
|
||||
}
|
||||
|
||||
private void initializeAnnotations(List<String> annotationGroupsToUse, List<String> annotationsToUse) {
|
||||
private void initializeAnnotations(List<String> annotationGroupsToUse, List<String> annotationsToUse, List<String> annotationsToExclude) {
|
||||
AnnotationInterfaceManager.validateAnnotations(annotationGroupsToUse, annotationsToUse);
|
||||
requestedInfoAnnotations = AnnotationInterfaceManager.createInfoFieldAnnotations(annotationGroupsToUse, annotationsToUse);
|
||||
requestedGenotypeAnnotations = AnnotationInterfaceManager.createGenotypeAnnotations(annotationGroupsToUse, annotationsToUse);
|
||||
excludeAnnotations(annotationsToExclude);
|
||||
}
|
||||
|
||||
private void excludeAnnotations(List<String> annotationsToExclude) {
|
||||
if ( annotationsToExclude.size() == 0 )
|
||||
return;
|
||||
|
||||
List<InfoFieldAnnotation> tempRequestedInfoAnnotations = new ArrayList<InfoFieldAnnotation>(requestedInfoAnnotations.size());
|
||||
for ( InfoFieldAnnotation annotation : requestedInfoAnnotations ) {
|
||||
if ( !annotationsToExclude.contains(annotation.getClass().getSimpleName()) )
|
||||
tempRequestedInfoAnnotations.add(annotation);
|
||||
}
|
||||
requestedInfoAnnotations = tempRequestedInfoAnnotations;
|
||||
|
||||
List<GenotypeAnnotation> tempRequestedGenotypeAnnotations = new ArrayList<GenotypeAnnotation>(requestedGenotypeAnnotations.size());
|
||||
for ( GenotypeAnnotation annotation : requestedGenotypeAnnotations ) {
|
||||
if ( !annotationsToExclude.contains(annotation.getClass().getSimpleName()) )
|
||||
tempRequestedGenotypeAnnotations.add(annotation);
|
||||
}
|
||||
requestedGenotypeAnnotations = tempRequestedGenotypeAnnotations;
|
||||
}
|
||||
|
||||
private void initializeDBs() {
|
||||
|
|
|
|||
|
|
@ -0,0 +1,3 @@
|
|||
package org.broadinstitute.sting.gatk.walkers.annotator.interfaces;
|
||||
|
||||
public interface RodRequiringAnnotation extends AnnotationType {}
|
||||
|
|
@ -149,6 +149,13 @@ public class UnifiedGenotyper extends LocusWalker<VariantCallContext, UnifiedGen
|
|||
@Argument(fullName="annotation", shortName="A", doc="One or more specific annotations to apply to variant calls", required=false)
|
||||
protected List<String> annotationsToUse = new ArrayList<String>();
|
||||
|
||||
/**
|
||||
* Which annotations to exclude from output in the VCF file. Note that this argument has higher priority than the -A or -G arguments,
|
||||
* so annotations will be excluded even if they are explicitly included with the other options.
|
||||
*/
|
||||
@Argument(fullName="excludeAnnotation", shortName="XA", doc="One or more specific annotations to exclude", required=false)
|
||||
protected List<String> annotationsToExclude = new ArrayList<String>();
|
||||
|
||||
/**
|
||||
* Which groups of annotations to add to the output VCF file. See the VariantAnnotator -list argument to view available groups.
|
||||
*/
|
||||
|
|
@ -210,11 +217,17 @@ public class UnifiedGenotyper extends LocusWalker<VariantCallContext, UnifiedGen
|
|||
if ( verboseWriter != null )
|
||||
verboseWriter.println("AFINFO\tLOC\tREF\tALT\tMAF\tF\tAFprior\tAFposterior\tNormalizedPosterior");
|
||||
|
||||
annotationEngine = new VariantAnnotatorEngine(Arrays.asList(annotationClassesToUse), annotationsToUse, this, getToolkit());
|
||||
annotationEngine = new VariantAnnotatorEngine(Arrays.asList(annotationClassesToUse), annotationsToUse, annotationsToExclude, this, getToolkit());
|
||||
UG_engine = new UnifiedGenotyperEngine(getToolkit(), UAC, logger, verboseWriter, annotationEngine, samples);
|
||||
|
||||
// initialize the header
|
||||
writer.writeHeader(new VCFHeader(getHeaderInfo(), samples)) ;
|
||||
Set<VCFHeaderLine> headerInfo = getHeaderInfo();
|
||||
|
||||
// invoke initialize() method on each of the annotation classes, allowing them to add their own header lines
|
||||
// and perform any necessary initialization/validation steps
|
||||
annotationEngine.invokeAnnotationInitializationMethods(headerInfo);
|
||||
|
||||
writer.writeHeader(new VCFHeader(headerInfo, samples));
|
||||
}
|
||||
|
||||
private Set<VCFHeaderLine> getHeaderInfo() {
|
||||
|
|
|
|||
|
|
@ -164,6 +164,7 @@ public class CycleCovariate implements StandardCovariate {
|
|||
private static List<String> LS454_NAMES = Arrays.asList("454");
|
||||
private static List<String> COMPLETE_GENOMICS_NAMES = Arrays.asList("COMPLETE");
|
||||
private static List<String> PACBIO_NAMES = Arrays.asList("PACBIO");
|
||||
private static List<String> ION_TORRENT_NAMES = Arrays.asList("IONTORRENT");
|
||||
|
||||
private static boolean isPlatform(SAMRecord read, List<String> names) {
|
||||
String pl = read.getReadGroup().getPlatform().toUpperCase();
|
||||
|
|
@ -224,10 +225,10 @@ public class CycleCovariate implements StandardCovariate {
|
|||
}
|
||||
|
||||
//-----------------------------
|
||||
// 454
|
||||
// 454 and Ion Torrent
|
||||
//-----------------------------
|
||||
|
||||
else if ( isPlatform(read, LS454_NAMES) ) { // Some bams have "LS454" and others have just "454"
|
||||
else if ( isPlatform(read, LS454_NAMES) || isPlatform(read, ION_TORRENT_NAMES)) { // Some bams have "LS454" and others have just "454"
|
||||
|
||||
final int readLength = read.getReadLength();
|
||||
final byte[] bases = read.getReadBases();
|
||||
|
|
|
|||
|
|
@ -39,7 +39,6 @@ import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
|
|||
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine;
|
||||
import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils;
|
||||
import org.broadinstitute.sting.utils.codecs.vcf.VCFWriter;
|
||||
import org.broadinstitute.sting.utils.exceptions.UserException;
|
||||
import org.broadinstitute.sting.utils.variantcontext.MutableVariantContext;
|
||||
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
|
||||
import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
|
||||
|
|
@ -266,8 +265,13 @@ public class GenotypeAndValidateWalker extends RodWalker<GenotypeAndValidateWalk
|
|||
public static class CountedData {
|
||||
private long nAltCalledAlt = 0L;
|
||||
private long nAltCalledRef = 0L;
|
||||
private long nAltNotCalled = 0L;
|
||||
private long nRefCalledAlt = 0L;
|
||||
private long nRefCalledRef = 0L;
|
||||
private long nRefNotCalled = 0L;
|
||||
private long nNoStatusCalledAlt = 0L;
|
||||
private long nNoStatusCalledRef = 0L;
|
||||
private long nNoStatusNotCalled = 0L;
|
||||
private long nNotConfidentCalls = 0L;
|
||||
private long nUncovered = 0L;
|
||||
|
||||
|
|
@ -278,8 +282,13 @@ public class GenotypeAndValidateWalker extends RodWalker<GenotypeAndValidateWalk
|
|||
public void add(CountedData other) {
|
||||
nAltCalledAlt += other.nAltCalledAlt;
|
||||
nAltCalledRef += other.nAltCalledRef;
|
||||
nAltNotCalled += other.nAltNotCalled;
|
||||
nRefCalledAlt += other.nRefCalledAlt;
|
||||
nRefCalledRef += other.nRefCalledRef;
|
||||
nRefNotCalled += other.nRefNotCalled;
|
||||
nNoStatusCalledAlt += other.nNoStatusCalledAlt;
|
||||
nNoStatusCalledRef += other.nNoStatusCalledRef;
|
||||
nNoStatusNotCalled += other.nNoStatusNotCalled;
|
||||
nUncovered += other.nUncovered;
|
||||
nNotConfidentCalls += other.nNotConfidentCalls;
|
||||
}
|
||||
|
|
@ -358,6 +367,13 @@ public class GenotypeAndValidateWalker extends RodWalker<GenotypeAndValidateWalk
|
|||
// Do not operate on variants that are not covered to the optional minimum depth
|
||||
if (!context.hasReads() || (minDepth > 0 && context.getBasePileup().getBases().length < minDepth)) {
|
||||
counter.nUncovered = 1L;
|
||||
if (vcComp.getAttribute("GV").equals("T"))
|
||||
counter.nAltNotCalled = 1L;
|
||||
else if (vcComp.getAttribute("GV").equals("F"))
|
||||
counter.nRefNotCalled = 1L;
|
||||
else
|
||||
counter.nNoStatusNotCalled = 1L;
|
||||
|
||||
return counter;
|
||||
}
|
||||
|
||||
|
|
@ -382,7 +398,7 @@ public class GenotypeAndValidateWalker extends RodWalker<GenotypeAndValidateWalk
|
|||
// If truth is a confident REF call
|
||||
if (call.isVariant()) {
|
||||
if (vcComp.isVariant())
|
||||
counter.nAltCalledAlt = 1L; // todo -- may wanna check if the alts called are the same?
|
||||
counter.nAltCalledAlt = 1L;
|
||||
else {
|
||||
counter.nAltCalledRef = 1L;
|
||||
if ( printInterestingSites )
|
||||
|
|
@ -407,30 +423,41 @@ public class GenotypeAndValidateWalker extends RodWalker<GenotypeAndValidateWalk
|
|||
}
|
||||
}
|
||||
else {
|
||||
if (!vcComp.hasAttribute("GV"))
|
||||
throw new UserException.BadInput("Variant has no GV annotation in the INFO field. " + vcComp.getChr() + ":" + vcComp.getStart());
|
||||
|
||||
|
||||
// if (!vcComp.hasAttribute("GV"))
|
||||
// throw new UserException.BadInput("Variant has no GV annotation in the INFO field. " + vcComp.getChr() + ":" + vcComp.getStart());
|
||||
|
||||
if (call.isCalledAlt(callConf)) {
|
||||
if (vcComp.getAttribute("GV").equals("T"))
|
||||
counter.nAltCalledAlt = 1L;
|
||||
else {
|
||||
else if (vcComp.getAttribute("GV").equals("F")) {
|
||||
counter.nRefCalledAlt = 1L;
|
||||
if ( printInterestingSites )
|
||||
System.out.println("Truth=REF Call=ALT at " + call.getChr() + ":" + call.getStart());
|
||||
}
|
||||
else
|
||||
counter.nNoStatusCalledAlt = 1L;
|
||||
}
|
||||
else if (call.isCalledRef(callConf)) {
|
||||
if (vcComp.getAttribute("GV").equals("T")) {
|
||||
counter.nAltCalledRef = 1L;
|
||||
if ( printInterestingSites )
|
||||
System.out.println("Truth=ALT Call=REF at " + call.getChr() + ":" + call.getStart());
|
||||
} else
|
||||
}
|
||||
else if (vcComp.getAttribute("GV").equals("F"))
|
||||
counter.nRefCalledRef = 1L;
|
||||
|
||||
else
|
||||
counter.nNoStatusCalledRef = 1L;
|
||||
}
|
||||
else {
|
||||
counter.nNotConfidentCalls = 1L;
|
||||
if (vcComp.getAttribute("GV").equals("T"))
|
||||
counter.nAltNotCalled = 1L;
|
||||
else if (vcComp.getAttribute("GV").equals("F"))
|
||||
counter.nRefNotCalled = 1L;
|
||||
else
|
||||
counter.nNoStatusNotCalled = 1L;
|
||||
|
||||
if ( printInterestingSites )
|
||||
System.out.println("Truth is not confident at " + call.getChr() + ":" + call.getStart());
|
||||
writeVariant = false;
|
||||
|
|
@ -475,20 +502,21 @@ public class GenotypeAndValidateWalker extends RodWalker<GenotypeAndValidateWalk
|
|||
double sensitivity = 100 * ((double) reduceSum.nAltCalledAlt /( reduceSum.nAltCalledAlt + reduceSum.nAltCalledRef));
|
||||
double specificity = (reduceSum.nRefCalledRef + reduceSum.nRefCalledAlt > 0) ? 100 * ((double) reduceSum.nRefCalledRef /( reduceSum.nRefCalledRef + reduceSum.nRefCalledAlt)) : 100;
|
||||
logger.info(String.format("Resulting Truth Table Output\n\n" +
|
||||
"---------------------------------------------------\n" +
|
||||
"\t\t|\tALT\t|\tREF\t\n" +
|
||||
"---------------------------------------------------\n" +
|
||||
"called alt\t|\t%d\t|\t%d\n" +
|
||||
"called ref\t|\t%d\t|\t%d\n" +
|
||||
"---------------------------------------------------\n" +
|
||||
"------------------------------------------------------------------\n" +
|
||||
"\t\t|\tALT\t|\tREF\t|\tNo Status\n" +
|
||||
"------------------------------------------------------------------\n" +
|
||||
"called alt\t|\t%d\t|\t%d\t|\t%d\n" +
|
||||
"called ref\t|\t%d\t|\t%d\t|\t%d\n" +
|
||||
"not called\t|\t%d\t|\t%d\t|\t%d\n" +
|
||||
"------------------------------------------------------------------\n" +
|
||||
"positive predictive value: %f%%\n" +
|
||||
"negative predictive value: %f%%\n" +
|
||||
"---------------------------------------------------\n" +
|
||||
"------------------------------------------------------------------\n" +
|
||||
"sensitivity: %f%%\n" +
|
||||
"specificity: %f%%\n" +
|
||||
"---------------------------------------------------\n" +
|
||||
"------------------------------------------------------------------\n" +
|
||||
"not confident: %d\n" +
|
||||
"not covered: %d\n" +
|
||||
"---------------------------------------------------\n", reduceSum.nAltCalledAlt, reduceSum.nRefCalledAlt, reduceSum.nAltCalledRef, reduceSum.nRefCalledRef, ppv, npv, sensitivity, specificity, reduceSum.nNotConfidentCalls, reduceSum.nUncovered));
|
||||
"------------------------------------------------------------------\n", reduceSum.nAltCalledAlt, reduceSum.nRefCalledAlt, reduceSum.nNoStatusCalledAlt, reduceSum.nAltCalledRef, reduceSum.nRefCalledRef, reduceSum.nNoStatusCalledRef, reduceSum.nAltNotCalled, reduceSum.nRefNotCalled, reduceSum.nNoStatusNotCalled, ppv, npv, sensitivity, specificity, reduceSum.nNotConfidentCalls, reduceSum.nUncovered));
|
||||
}
|
||||
}
|
||||
|
|
|
|||
|
|
@ -31,7 +31,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
|
|||
@Test
|
||||
public void testHasAnnotsAsking1() {
|
||||
WalkerTestSpec spec = new WalkerTestSpec(
|
||||
baseTestString() + " -G \"Standard\" --variant:VCF3 " + validationDataLocation + "vcfexample2.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
|
||||
baseTestString() + " -G Standard --variant:VCF3 " + validationDataLocation + "vcfexample2.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
|
||||
Arrays.asList("8e7de435105499cd71ffc099e268a83e"));
|
||||
executeTest("test file has annotations, asking for annotations, #1", spec);
|
||||
}
|
||||
|
|
@ -39,7 +39,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
|
|||
@Test
|
||||
public void testHasAnnotsAsking2() {
|
||||
WalkerTestSpec spec = new WalkerTestSpec(
|
||||
baseTestString() + " -G \"Standard\" --variant:VCF3 " + validationDataLocation + "vcfexample3.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1,
|
||||
baseTestString() + " -G Standard --variant:VCF3 " + validationDataLocation + "vcfexample3.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1,
|
||||
Arrays.asList("64b6804cb1e27826e3a47089349be581"));
|
||||
executeTest("test file has annotations, asking for annotations, #2", spec);
|
||||
}
|
||||
|
|
@ -63,7 +63,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
|
|||
@Test
|
||||
public void testNoAnnotsAsking1() {
|
||||
WalkerTestSpec spec = new WalkerTestSpec(
|
||||
baseTestString() + " -G \"Standard\" --variant:VCF3 " + validationDataLocation + "vcfexample2empty.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
|
||||
baseTestString() + " -G Standard --variant:VCF3 " + validationDataLocation + "vcfexample2empty.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
|
||||
Arrays.asList("fd1ffb669800c2e07df1e2719aa38e49"));
|
||||
executeTest("test file doesn't have annotations, asking for annotations, #1", spec);
|
||||
}
|
||||
|
|
@ -71,15 +71,23 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
|
|||
@Test
|
||||
public void testNoAnnotsAsking2() {
|
||||
WalkerTestSpec spec = new WalkerTestSpec(
|
||||
baseTestString() + " -G \"Standard\" --variant:VCF3 " + validationDataLocation + "vcfexample3empty.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1,
|
||||
baseTestString() + " -G Standard --variant:VCF3 " + validationDataLocation + "vcfexample3empty.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1,
|
||||
Arrays.asList("09f8e840770a9411ff77508e0ed0837f"));
|
||||
executeTest("test file doesn't have annotations, asking for annotations, #2", spec);
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testExcludeAnnotations() {
|
||||
WalkerTestSpec spec = new WalkerTestSpec(
|
||||
baseTestString() + " -G Standard -XA FisherStrand -XA ReadPosRankSumTest --variant:VCF3 " + validationDataLocation + "vcfexample2empty.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
|
||||
Arrays.asList("b49fe03aa4b675db80a9db38a3552c95"));
|
||||
executeTest("test exclude annotations", spec);
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testOverwritingHeader() {
|
||||
WalkerTestSpec spec = new WalkerTestSpec(
|
||||
baseTestString() + " -G \"Standard\" --variant:VCF " + validationDataLocation + "vcfexample4.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,001,292", 1,
|
||||
baseTestString() + " -G Standard --variant:VCF " + validationDataLocation + "vcfexample4.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,001,292", 1,
|
||||
Arrays.asList("78d2c19f8107d865970dbaf3e12edd92"));
|
||||
executeTest("test overwriting header", spec);
|
||||
}
|
||||
|
|
@ -87,7 +95,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
|
|||
@Test
|
||||
public void testNoReads() {
|
||||
WalkerTestSpec spec = new WalkerTestSpec(
|
||||
baseTestString() + " -G \"Standard\" --variant:VCF3 " + validationDataLocation + "vcfexample3empty.vcf -BTI variant", 1,
|
||||
baseTestString() + " -G Standard --variant:VCF3 " + validationDataLocation + "vcfexample3empty.vcf -BTI variant", 1,
|
||||
Arrays.asList("16e3a1403fc376320d7c69492cad9345"));
|
||||
executeTest("not passing it any reads", spec);
|
||||
}
|
||||
|
|
@ -103,7 +111,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
|
|||
@Test
|
||||
public void testDBTagWithHapMap() {
|
||||
WalkerTestSpec spec = new WalkerTestSpec(
|
||||
baseTestString() + " --comp:H3 " + validationDataLocation + "fakeHM3.vcf -G \"Standard\" --variant:VCF3 " + validationDataLocation + "vcfexample3empty.vcf -BTI variant", 1,
|
||||
baseTestString() + " --comp:H3 " + validationDataLocation + "fakeHM3.vcf -G Standard --variant:VCF3 " + validationDataLocation + "vcfexample3empty.vcf -BTI variant", 1,
|
||||
Arrays.asList("1bc01c5b3bd0b7aef75230310c3ce688"));
|
||||
executeTest("getting DB tag with HM3", spec);
|
||||
}
|
||||
|
|
@ -111,7 +119,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
|
|||
@Test
|
||||
public void testUsingExpression() {
|
||||
WalkerTestSpec spec = new WalkerTestSpec(
|
||||
baseTestString() + " --resource:foo " + validationDataLocation + "targetAnnotations.vcf -G \"Standard\" --variant:VCF3 " + validationDataLocation + "vcfexample3empty.vcf -E foo.AF -BTI variant", 1,
|
||||
baseTestString() + " --resource:foo " + validationDataLocation + "targetAnnotations.vcf -G Standard --variant:VCF3 " + validationDataLocation + "vcfexample3empty.vcf -E foo.AF -BTI variant", 1,
|
||||
Arrays.asList("e9c0d832dc6b4ed06c955060f830c140"));
|
||||
executeTest("using expression", spec);
|
||||
}
|
||||
|
|
@ -121,7 +129,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
|
|||
final String MD5 = "13269d5a2e16f06fd755cc0fb9271acf";
|
||||
for ( String file : Arrays.asList("CEU.exon.2010_03.sites.vcf", "CEU.exon.2010_03.sites.vcf.gz")) {
|
||||
WalkerTestSpec spec = new WalkerTestSpec(
|
||||
baseTestString() + " -A HomopolymerRun --variant:VCF " + validationDataLocation + "/" + file + " -BTI variant -NO_HEADER", 1,
|
||||
baseTestString() + " -A HomopolymerRun --variant:VCF " + validationDataLocation + file + " -BTI variant -NO_HEADER", 1,
|
||||
Arrays.asList(MD5));
|
||||
executeTest("Testing lookup vcf tabix vs. vcf tribble", spec);
|
||||
}
|
||||
|
|
|
|||
|
|
@ -2,6 +2,7 @@ package org.broadinstitute.sting.gatk.walkers.genotyper;
|
|||
|
||||
import org.broadinstitute.sting.WalkerTest;
|
||||
import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
|
||||
import org.broadinstitute.sting.utils.exceptions.UserException;
|
||||
import org.testng.annotations.Test;
|
||||
|
||||
import java.io.File;
|
||||
|
|
@ -293,4 +294,14 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
|
|||
Arrays.asList("37d908a682ac269f8f19dec939ff5b01"));
|
||||
executeTest("test MultiSample 1000G Phase1 indels with complicated records emitting all sites", spec4);
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testSnpEffAnnotationRequestedWithoutRodBinding() {
|
||||
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
|
||||
baseCommand + " -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -o %s -L 1:10,022,000-10,025,000 " +
|
||||
"-A SnpEff",
|
||||
1,
|
||||
UserException.class);
|
||||
executeTest("testSnpEffAnnotationRequestedWithoutRodBinding", spec);
|
||||
}
|
||||
}
|
||||
|
|
|
|||
Loading…
Reference in New Issue