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Merge branch 'stable'

This commit is contained in:
Mark DePristo 2011-09-24 09:26:28 -04:00
parent 92acff46e5 6804ab6d2f
commit 8d9e136bba
6 changed files with 143 additions and 60 deletions
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160
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SnpEff.java
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@ -82,7 +82,8 @@ public class SnpEff extends InfoFieldAnnotation implements ExperimentalAnnotatio
GENE_NAME_KEY ("SNPEFF_GENE_NAME", 3),
GENE_BIOTYPE_KEY ("SNPEFF_GENE_BIOTYPE", 4),
TRANSCRIPT_ID_KEY ("SNPEFF_TRANSCRIPT_ID", 6),
EXON_ID_KEY ("SNPEFF_EXON_ID", 7);
EXON_ID_KEY ("SNPEFF_EXON_ID", 7),
FUNCTIONAL_CLASS_KEY ("SNPEFF_FUNCTIONAL_CLASS", -1);
// Actual text of the key
private final String keyName;
@ -108,48 +109,73 @@ public class SnpEff extends InfoFieldAnnotation implements ExperimentalAnnotatio
// Possible SnpEff biological effects. All effect names found in the SnpEff input file
// are validated against this list.
public enum EffectType {
NONE,
CHROMOSOME,
INTERGENIC,
UPSTREAM,
UTR_5_PRIME,
UTR_5_DELETED,
START_GAINED,
SPLICE_SITE_ACCEPTOR,
SPLICE_SITE_DONOR,
START_LOST,
SYNONYMOUS_START,
NON_SYNONYMOUS_START,
CDS,
GENE,
TRANSCRIPT,
EXON,
EXON_DELETED,
NON_SYNONYMOUS_CODING,
SYNONYMOUS_CODING,
FRAME_SHIFT,
CODON_CHANGE,
CODON_INSERTION,
CODON_CHANGE_PLUS_CODON_INSERTION,
CODON_DELETION,
CODON_CHANGE_PLUS_CODON_DELETION,
STOP_GAINED,
SYNONYMOUS_STOP,
NON_SYNONYMOUS_STOP,
STOP_LOST,
INTRON,
UTR_3_PRIME,
UTR_3_DELETED,
DOWNSTREAM,
INTRON_CONSERVED,
INTERGENIC_CONSERVED,
REGULATION,
CUSTOM,
WITHIN_NON_CODING_GENE
// High-impact effects:
FRAME_SHIFT (EffectFunctionalClass.NONE, false),
STOP_GAINED (EffectFunctionalClass.NONSENSE, false),
START_LOST (EffectFunctionalClass.NONE, false),
SPLICE_SITE_ACCEPTOR (EffectFunctionalClass.NONE, false),
SPLICE_SITE_DONOR (EffectFunctionalClass.NONE, false),
EXON_DELETED (EffectFunctionalClass.NONE, false),
STOP_LOST (EffectFunctionalClass.NONE, false),
// Moderate-impact effects:
NON_SYNONYMOUS_CODING (EffectFunctionalClass.MISSENSE, false),
CODON_CHANGE (EffectFunctionalClass.NONE, false),
CODON_INSERTION (EffectFunctionalClass.NONE, false),
CODON_CHANGE_PLUS_CODON_INSERTION (EffectFunctionalClass.NONE, false),
CODON_DELETION (EffectFunctionalClass.NONE, false),
CODON_CHANGE_PLUS_CODON_DELETION (EffectFunctionalClass.NONE, false),
UTR_5_DELETED (EffectFunctionalClass.NONE, false),
UTR_3_DELETED (EffectFunctionalClass.NONE, false),
// Low-impact effects:
SYNONYMOUS_CODING (EffectFunctionalClass.SILENT, false),
SYNONYMOUS_START (EffectFunctionalClass.SILENT, false),
NON_SYNONYMOUS_START (EffectFunctionalClass.SILENT, false),
SYNONYMOUS_STOP (EffectFunctionalClass.SILENT, false),
NON_SYNONYMOUS_STOP (EffectFunctionalClass.SILENT, false),
START_GAINED (EffectFunctionalClass.NONE, false),
// Modifiers:
NONE (EffectFunctionalClass.NONE, true),
CHROMOSOME (EffectFunctionalClass.NONE, true),
INTERGENIC (EffectFunctionalClass.NONE, true),
UPSTREAM (EffectFunctionalClass.NONE, true),
UTR_5_PRIME (EffectFunctionalClass.NONE, true),
CDS (EffectFunctionalClass.NONE, true),
GENE (EffectFunctionalClass.NONE, true),
TRANSCRIPT (EffectFunctionalClass.NONE, true),
EXON (EffectFunctionalClass.NONE, true),
INTRON (EffectFunctionalClass.NONE, true),
UTR_3_PRIME (EffectFunctionalClass.NONE, true),
DOWNSTREAM (EffectFunctionalClass.NONE, true),
INTRON_CONSERVED (EffectFunctionalClass.NONE, true),
INTERGENIC_CONSERVED (EffectFunctionalClass.NONE, true),
REGULATION (EffectFunctionalClass.NONE, true),
CUSTOM (EffectFunctionalClass.NONE, true),
WITHIN_NON_CODING_GENE (EffectFunctionalClass.NONE, true);
private final EffectFunctionalClass functionalClass;
private final boolean isModifier;
EffectType ( EffectFunctionalClass functionalClass, boolean isModifier ) {
this.functionalClass = functionalClass;
this.isModifier = isModifier;
}
public EffectFunctionalClass getFunctionalClass() {
return functionalClass;
}
public boolean isModifier() {
return isModifier;
}
}
// SnpEff labels each effect as either LOW, MODERATE, or HIGH impact.
// SnpEff labels each effect as either LOW, MODERATE, or HIGH impact. We take the additional step of
// classifying some of the LOW impact effects as MODIFIERs.
public enum EffectImpact {
MODIFIER (0),
LOW (1),
MODERATE (2),
HIGH (3);
@ -163,6 +189,10 @@ public class SnpEff extends InfoFieldAnnotation implements ExperimentalAnnotatio
public boolean isHigherImpactThan ( EffectImpact other ) {
return this.severityRating > other.severityRating;
}
public boolean isSameImpactAs ( EffectImpact other ) {
return this.severityRating == other.severityRating;
}
}
// SnpEff labels most effects as either CODING or NON_CODING, but sometimes omits this information.
@ -172,6 +202,24 @@ public class SnpEff extends InfoFieldAnnotation implements ExperimentalAnnotatio
UNKNOWN
}
// We assign a functional class to each SnpEff effect.
public enum EffectFunctionalClass {
NONE (0),
SILENT (1),
MISSENSE (2),
NONSENSE (3);
private final int priority;
EffectFunctionalClass ( int priority ) {
this.priority = priority;
}
public boolean isHigherPriorityThan ( EffectFunctionalClass other ) {
return this.priority > other.priority;
}
}
public void initialize ( AnnotatorCompatibleWalker walker, GenomeAnalysisEngine toolkit, Set<VCFHeaderLine> headerLines ) {
// Make sure that we actually have a valid SnpEff rod binding (just in case the user specified -A SnpEff
// without providing a SnpEff rod via --snpEffFile):
@ -336,7 +384,8 @@ public class SnpEff extends InfoFieldAnnotation implements ExperimentalAnnotatio
InfoFieldKey.GENE_NAME_KEY.getKeyName(),
InfoFieldKey.GENE_BIOTYPE_KEY.getKeyName(),
InfoFieldKey.TRANSCRIPT_ID_KEY.getKeyName(),
InfoFieldKey.EXON_ID_KEY.getKeyName()
InfoFieldKey.EXON_ID_KEY.getKeyName(),
InfoFieldKey.FUNCTIONAL_CLASS_KEY.getKeyName()
);
}
@ -349,7 +398,8 @@ public class SnpEff extends InfoFieldAnnotation implements ExperimentalAnnotatio
new VCFInfoHeaderLine(InfoFieldKey.GENE_NAME_KEY.getKeyName(), 1, VCFHeaderLineType.String, "Gene name for the highest-impact effect resulting from the current variant"),
new VCFInfoHeaderLine(InfoFieldKey.GENE_BIOTYPE_KEY.getKeyName(), 1, VCFHeaderLineType.String, "Gene biotype for the highest-impact effect resulting from the current variant"),
new VCFInfoHeaderLine(InfoFieldKey.TRANSCRIPT_ID_KEY.getKeyName(), 1, VCFHeaderLineType.String, "Transcript ID for the highest-impact effect resulting from the current variant"),
new VCFInfoHeaderLine(InfoFieldKey.EXON_ID_KEY.getKeyName(), 1, VCFHeaderLineType.String, "Exon ID for the highest-impact effect resulting from the current variant")
new VCFInfoHeaderLine(InfoFieldKey.EXON_ID_KEY.getKeyName(), 1, VCFHeaderLineType.String, "Exon ID for the highest-impact effect resulting from the current variant"),
new VCFInfoHeaderLine(InfoFieldKey.FUNCTIONAL_CLASS_KEY.getKeyName(), 1, VCFHeaderLineType.String, "Functional class of the highest-impact effect resulting from the current variant: " + Arrays.toString(EffectFunctionalClass.values()))
);
}
@ -411,11 +461,16 @@ public class SnpEff extends InfoFieldAnnotation implements ExperimentalAnnotatio
return;
}
try {
impact = EffectImpact.valueOf(effectMetadata[InfoFieldKey.IMPACT_KEY.getFieldIndex()]);
if ( effect != null && effect.isModifier() ) {
impact = EffectImpact.MODIFIER;
}
catch ( IllegalArgumentException e ) {
parseError(String.format("Unrecognized value for effect impact: %s", effectMetadata[InfoFieldKey.IMPACT_KEY.getFieldIndex()]));
else {
try {
impact = EffectImpact.valueOf(effectMetadata[InfoFieldKey.IMPACT_KEY.getFieldIndex()]);
}
catch ( IllegalArgumentException e ) {
parseError(String.format("Unrecognized value for effect impact: %s", effectMetadata[InfoFieldKey.IMPACT_KEY.getFieldIndex()]));
}
}
codonChange = effectMetadata[InfoFieldKey.CODON_CHANGE_KEY.getFieldIndex()];
@ -472,9 +527,17 @@ public class SnpEff extends InfoFieldAnnotation implements ExperimentalAnnotatio
}
// Otherwise, both effects are either in or not in a coding gene, so we compare the impacts
// of the effects themselves:
// of the effects themselves. Effects with the same impact are tie-broken using the
// functional class of the effect:
return impact.isHigherImpactThan(other.impact);
if ( impact.isHigherImpactThan(other.impact) ) {
return true;
}
else if ( impact.isSameImpactAs(other.impact) ) {
return effect.getFunctionalClass().isHigherPriorityThan(other.effect.getFunctionalClass());
}
return false;
}
public Map<String, Object> getAnnotations() {
@ -488,6 +551,7 @@ public class SnpEff extends InfoFieldAnnotation implements ExperimentalAnnotatio
addAnnotation(annotations, InfoFieldKey.GENE_BIOTYPE_KEY.getKeyName(), geneBiotype);
addAnnotation(annotations, InfoFieldKey.TRANSCRIPT_ID_KEY.getKeyName(), transcriptID);
addAnnotation(annotations, InfoFieldKey.EXON_ID_KEY.getKeyName(), exonID);
addAnnotation(annotations, InfoFieldKey.FUNCTIONAL_CLASS_KEY.getKeyName(), effect.getFunctionalClass().toString());
return annotations;
}

19
public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/FunctionalClass.java
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@ -62,14 +62,17 @@ public List<String> getRelevantStates(ReferenceContext ref, RefMetaDataTracker t
annotationId++;
} while (eval.hasAttribute(key));
} else if ( eval.hasAttribute(SnpEff.InfoFieldKey.EFFECT_KEY.getKeyName() ) ) {
SnpEff.EffectType snpEffType = SnpEff.EffectType.valueOf(eval.getAttribute(SnpEff.InfoFieldKey.EFFECT_KEY.getKeyName()).toString());
if ( snpEffType == SnpEff.EffectType.STOP_GAINED )
type = FunctionalType.nonsense;
else if ( snpEffType == SnpEff.EffectType.NON_SYNONYMOUS_CODING )
type = FunctionalType.missense;
else if ( snpEffType == SnpEff.EffectType.SYNONYMOUS_CODING )
type = FunctionalType.silent;
} else if ( eval.hasAttribute(SnpEff.InfoFieldKey.FUNCTIONAL_CLASS_KEY.getKeyName()) ) {
try {
SnpEff.EffectFunctionalClass snpEffFunctionalClass = SnpEff.EffectFunctionalClass.valueOf(eval.getAttribute(SnpEff.InfoFieldKey.FUNCTIONAL_CLASS_KEY.getKeyName()).toString());
if ( snpEffFunctionalClass == SnpEff.EffectFunctionalClass.NONSENSE )
type = FunctionalType.nonsense;
else if ( snpEffFunctionalClass == SnpEff.EffectFunctionalClass.MISSENSE )
type = FunctionalType.missense;
else if ( snpEffFunctionalClass == SnpEff.EffectFunctionalClass.SILENT )
type = FunctionalType.silent;
}
catch ( Exception e ) {} // don't error out if the type isn't supported
}
if ( type != null ) {

2
public/java/src/org/broadinstitute/sting/utils/clipreads/ClippingRepresentation.java
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@ -21,6 +21,8 @@ public enum ClippingRepresentation {
SOFTCLIP_BASES,
/**
* WARNING: THIS OPTION IS STILL UNDER DEVELOPMENT AND IS NOT SUPPORTED.
*
* Change the read's cigar string to hard clip (H, see sam-spec) away the bases.
* Hard clipping, unlike soft clipping, actually removes bases from the read,
* reducing the resulting file's size but introducing an irrevesible (i.e.,

4
public/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java
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@ -132,9 +132,9 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec(
"-T VariantAnnotator -R " + hg19Reference + " -NO_HEADER -o %s -A SnpEff --variant " +
validationDataLocation + "1kg_exomes_unfiltered.AFR.unfiltered.vcf --snpEffFile " + validationDataLocation +
"snpEff.AFR.unfiltered.vcf -L 1:1-1,500,000",
"snpEff.AFR.unfiltered.vcf -L 1:1-1,500,000 -L 2:232,325,429",
1,
Arrays.asList("ed9d1b37b0bd8b65ff9ce2688e0e102e")
Arrays.asList("122321a85e448f21679f6ca15c5e22ad")
);
executeTest("Testing SnpEff annotations", spec);
}

2
public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java
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@ -30,7 +30,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
"-o %s"
),
1,
Arrays.asList("f5f811ceb973d7fd6c1b2b734f1b2b12")
Arrays.asList("d9dcb352c53106f54fcc981f15d35a90")
);
executeTest("testFunctionClassWithSnpeff", spec);
}

16
public/java/test/org/broadinstitute/sting/jna/drmaa/v1_0/JnaSessionIntegrationTest.java
View File

@ -34,6 +34,7 @@ import java.io.File;
import java.util.*;
public class JnaSessionIntegrationTest extends BaseTest {
private String implementation = null;
private static final SessionFactory factory = new JnaSessionFactory();
@Test
@ -44,10 +45,23 @@ public class JnaSessionIntegrationTest extends BaseTest {
System.out.println(String.format("DRMAA contact(s): %s", session.getContact()));
System.out.println(String.format("DRM system(s): %s", session.getDrmSystem()));
System.out.println(String.format("DRMAA implementation(s): %s", session.getDrmaaImplementation()));
this.implementation = session.getDrmaaImplementation();
}
@Test
@Test(dependsOnMethods = { "testDrmaa" })
public void testSubmitEcho() throws Exception {
if (implementation.contains("LSF")) {
System.err.println(" ***********************************************************");
System.err.println(" *************************************************************");
System.err.println(" **** ****");
System.err.println(" **** Skipping JnaSessionIntegrationTest.testSubmitEcho() ****");
System.err.println(" **** Are you using the dotkit .combined_LSF_SGE? ****");
System.err.println(" **** ****");
System.err.println(" *************************************************************");
System.err.println(" ***********************************************************");
return;
}
File outFile = createNetworkTempFile("JnaSessionIntegrationTest-", ".out");
Session session = factory.getSession();
session.init(null);