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Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable

This commit is contained in:
Eric Banks 2011-08-17 21:49:25 -04:00
parent 8e83b6646b 2bbf29b07a
commit fa1db3913b
7 changed files with 200 additions and 148 deletions
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14
public/java/src/org/broadinstitute/sting/commandline/ArgumentTypeDescriptor.java
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@ -373,16 +373,16 @@ class RodBindingArgumentTypeDescriptor extends ArgumentTypeDescriptor {
if ( featureDescriptor != null ) { if ( featureDescriptor != null ) {
tribbleType = featureDescriptor.getName(); tribbleType = featureDescriptor.getName();
logger.warn("Dynamically determined type of " + file + " to be " + tribbleType); logger.warn("Dynamically determined type of " + file + " to be " + tribbleType);
} else {
throw new UserException.CommandLineException(
String.format("No tribble type was provided on the command line and the type of the file could not be determined dynamically. " +
"Please add an explicit type tag :TYPE listing the correct type from among the supported types: %s",
manager.userFriendlyListOfAvailableFeatures()));
} }
} }
} }
} }
if ( tribbleType == null ) // error handling
throw new UserException.CommandLineException(
String.format("Could not parse argument %s with value %s",
defaultDefinition.fullName, value));
Constructor ctor = (makeRawTypeIfNecessary(type)).getConstructor(Class.class, String.class, String.class, String.class, Tags.class); Constructor ctor = (makeRawTypeIfNecessary(type)).getConstructor(Class.class, String.class, String.class, String.class, Tags.class);
Class parameterType = getParameterizedTypeClass(type); Class parameterType = getParameterizedTypeClass(type);
RodBinding result = (RodBinding)ctor.newInstance(parameterType, name, value, tribbleType, tags); RodBinding result = (RodBinding)ctor.newInstance(parameterType, name, value, tribbleType, tags);
@ -395,8 +395,8 @@ class RodBindingArgumentTypeDescriptor extends ArgumentTypeDescriptor {
value, source.field.getName())); value, source.field.getName()));
} catch (Exception e) { } catch (Exception e) {
throw new UserException.CommandLineException( throw new UserException.CommandLineException(
String.format("Failed to parse value %s for argument %s.", String.format("Failed to parse value %s for argument %s. Message: %s",
value, source.field.getName())); value, source.field.getName(), e.getMessage()));
} }
} }

2
public/java/src/org/broadinstitute/sting/gatk/refdata/features/refseq/RefSeqCodec.java
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@ -105,6 +105,6 @@ public class RefSeqCodec implements ReferenceDependentFeatureCodec<RefSeqFeature
@Override @Override
public Class getFeatureType() { public Class getFeatureType() {
return RefSeqCodec.class; return RefSeqFeature.class;
} }
} }

26
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SnpEff.java
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@ -161,19 +161,19 @@ public class SnpEff extends InfoFieldAnnotation implements ExperimentalAnnotatio
public List<VCFInfoHeaderLine> getDescriptions() { public List<VCFInfoHeaderLine> getDescriptions() {
return Arrays.asList( return Arrays.asList(
new VCFInfoHeaderLine(GENE_ID_KEY, 1, VCFHeaderLineType.String, "Gene ID"), new VCFInfoHeaderLine(GENE_ID_KEY, 1, VCFHeaderLineType.String, "Gene ID for the highest-impact effect resulting from the current variant"),
new VCFInfoHeaderLine(GENE_NAME_KEY, 1, VCFHeaderLineType.String, "Gene name"), new VCFInfoHeaderLine(GENE_NAME_KEY, 1, VCFHeaderLineType.String, "Gene name for the highest-impact effect resulting from the current variant"),
new VCFInfoHeaderLine(TRANSCRIPT_ID_KEY, 1, VCFHeaderLineType.String, "Transcript ID"), new VCFInfoHeaderLine(TRANSCRIPT_ID_KEY, 1, VCFHeaderLineType.String, "Transcript ID for the highest-impact effect resulting from the current variant"),
new VCFInfoHeaderLine(EXON_ID_KEY, 1, VCFHeaderLineType.String, "Exon ID"), new VCFInfoHeaderLine(EXON_ID_KEY, 1, VCFHeaderLineType.String, "Exon ID for the highest-impact effect resulting from the current variant"),
new VCFInfoHeaderLine(EXON_RANK_KEY, 1, VCFHeaderLineType.Integer, "Exon rank"), new VCFInfoHeaderLine(EXON_RANK_KEY, 1, VCFHeaderLineType.Integer, "Exon rank for the highest-impact effect resulting from the current variant"),
new VCFInfoHeaderLine(WITHIN_NON_CODING_GENE_KEY, 0, VCFHeaderLineType.Flag, "If present, gene is non-coding"), new VCFInfoHeaderLine(WITHIN_NON_CODING_GENE_KEY, 0, VCFHeaderLineType.Flag, "If this flag is present, the highest-impact effect resulting from the current variant is within a non-coding gene"),
new VCFInfoHeaderLine(EFFECT_KEY, 1, VCFHeaderLineType.String, "One of the most high-impact effects across all transcripts at this site"), new VCFInfoHeaderLine(EFFECT_KEY, 1, VCFHeaderLineType.String, "The highest-impact effect resulting from the current variant (or one of the highest-impact effects, if there is a tie)"),
new VCFInfoHeaderLine(EFFECT_IMPACT_KEY, 1, VCFHeaderLineType.String, "Impact of the effect " + Arrays.toString(SnpEffConstants.EffectImpact.values())), new VCFInfoHeaderLine(EFFECT_IMPACT_KEY, 1, VCFHeaderLineType.String, "Impact of the highest-impact effect resulting from the current variant " + Arrays.toString(SnpEffConstants.EffectImpact.values())),
new VCFInfoHeaderLine(EFFECT_EXTRA_INFORMATION_KEY, 1, VCFHeaderLineType.String, "Additional information about the effect"), new VCFInfoHeaderLine(EFFECT_EXTRA_INFORMATION_KEY, 1, VCFHeaderLineType.String, "Additional information about the highest-impact effect resulting from the current variant"),
new VCFInfoHeaderLine(OLD_NEW_AA_KEY, 1, VCFHeaderLineType.String, "Old/New amino acid"), new VCFInfoHeaderLine(OLD_NEW_AA_KEY, 1, VCFHeaderLineType.String, "Old/New amino acid for the highest-impact effect resulting from the current variant"),
new VCFInfoHeaderLine(OLD_NEW_CODON_KEY, 1, VCFHeaderLineType.String, "Old/New codon"), new VCFInfoHeaderLine(OLD_NEW_CODON_KEY, 1, VCFHeaderLineType.String, "Old/New codon for the highest-impact effect resulting from the current variant"),
new VCFInfoHeaderLine(CODON_NUM_KEY, 1, VCFHeaderLineType.Integer, "Codon number"), new VCFInfoHeaderLine(CODON_NUM_KEY, 1, VCFHeaderLineType.Integer, "Codon number for the highest-impact effect resulting from the current variant"),
new VCFInfoHeaderLine(CDS_SIZE_KEY, 1, VCFHeaderLineType.Integer, "CDS size") new VCFInfoHeaderLine(CDS_SIZE_KEY, 1, VCFHeaderLineType.Integer, "CDS size for the highest-impact effect resulting from the current variant")
); );
} }
} }

37
public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCFWalker.java
View File

@ -48,6 +48,31 @@ import static java.lang.Math.log10;
/** /**
* Takes files produced by Beagle imputation engine and creates a vcf with modified annotations. * Takes files produced by Beagle imputation engine and creates a vcf with modified annotations.
*
* <p>This walker is intended to be run after Beagle has successfully executed. The full calling sequence for using Beagle along with the GATK is: </p>
*
* <p>1. Run ProduceBeagleInputWalker. </p>
* <p>2. Run Beagle</p>
* <p>3. Uncompress output files</p>
* <p>4. Run BeagleOutputToVCFWalker.</p>
*
*
* Note that this walker requires all input files produced by Beagle.
*
*
* <h2>Example</h2>
* <pre>
* java -Xmx4000m -jar dist/GenomeAnalysisTK.jar \
* -R reffile.fasta -T BeagleOutputToVCF \
* -V input_vcf.vcf \
* -beagleR2:BEAGLE /myrun.beagle_output.r2 \
* -beaglePhased:BEAGLE /myrun.beagle_output.phased \
* -beagleProbs:BEAGLE /myrun.beagle_output.gprobs \
* -o output_vcf.vcf
* </pre>
<p> Note that Beagle produces some of these files compressed as .gz, so gunzip must be run on them before walker is run in order to decompress them </p>
*/ */
public class BeagleOutputToVCFWalker extends RodWalker<Integer, Integer> { public class BeagleOutputToVCFWalker extends RodWalker<Integer, Integer> {
@ -57,22 +82,18 @@ public class BeagleOutputToVCFWalker extends RodWalker<Integer, Integer> {
@Input(fullName="comp", shortName = "comp", doc="Comparison VCF file", required=false) @Input(fullName="comp", shortName = "comp", doc="Comparison VCF file", required=false)
public RodBinding<VariantContext> comp; public RodBinding<VariantContext> comp;
@Input(fullName="beagleR2", shortName = "beagleR2", doc="VCF file", required=true) @Input(fullName="beagleR2", shortName = "beagleR2", doc="Beagle-produced .r2 file containing R^2 values for all markers", required=true)
public RodBinding<BeagleFeature> beagleR2; public RodBinding<BeagleFeature> beagleR2;
@Input(fullName="beagleProbs", shortName = "beagleProbs", doc="VCF file", required=true) @Input(fullName="beagleProbs", shortName = "beagleProbs", doc="Beagle-produced .probs file containing posterior genotype probabilities", required=true)
public RodBinding<BeagleFeature> beagleProbs; public RodBinding<BeagleFeature> beagleProbs;
@Input(fullName="beaglePhased", shortName = "beaglePhased", doc="VCF file", required=true) @Input(fullName="beaglePhased", shortName = "beaglePhased", doc="Beagle-produced .phased file containing phased genotypes", required=true)
public RodBinding<BeagleFeature> beaglePhased; public RodBinding<BeagleFeature> beaglePhased;
@Output(doc="File to which variants should be written",required=true) @Output(doc="VCF File to which variants should be written",required=true)
protected VCFWriter vcfWriter = null; protected VCFWriter vcfWriter = null;
@Argument(fullName="output_file", shortName="output", doc="Please use --out instead" ,required=false)
@Deprecated
protected String oldOutputArg;
@Argument(fullName="dont_mark_monomorphic_sites_as_filtered", shortName="keep_monomorphic", doc="If provided, we won't filter sites that beagle tags as monomorphic. Useful for imputing a sample's genotypes from a reference panel" ,required=false) @Argument(fullName="dont_mark_monomorphic_sites_as_filtered", shortName="keep_monomorphic", doc="If provided, we won't filter sites that beagle tags as monomorphic. Useful for imputing a sample's genotypes from a reference panel" ,required=false)
public boolean DONT_FILTER_MONOMORPHIC_SITES = false; public boolean DONT_FILTER_MONOMORPHIC_SITES = false;

45
public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInputWalker.java
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@ -48,19 +48,45 @@ import java.io.PrintStream;
import java.util.*; import java.util.*;
/** /**
* Produces an input file to Beagle imputation engine, listing genotype likelihoods for each sample in input variant file * Converts the input VCF into a format accepted by the Beagle imputation/analysis program.
* <p>
*
* <h2>Input</h2>
* <p>
* A VCF with variants to convert to Beagle format
* </p>
*
* <h2>Outputs</h2>
* <p>
* A single text file which can be fed to Beagle
* </p>
* <p>
* Optional: A file with a list of markers
* </p>
*
* <h2>Examples</h2>
* <pre>
* java -Xmx2g -jar dist/GenomeAnalysisTK.jar -L 20 \
* -R reffile.fasta -T ProduceBeagleInput \
* -V path_to_input_vcf/inputvcf.vcf -o path_to_beagle_output/beagle_output
* </pre>
*
*/ */
public class ProduceBeagleInputWalker extends RodWalker<Integer, Integer> { public class ProduceBeagleInputWalker extends RodWalker<Integer, Integer> {
@ArgumentCollection protected StandardVariantContextInputArgumentCollection variantCollection = new StandardVariantContextInputArgumentCollection(); @ArgumentCollection protected StandardVariantContextInputArgumentCollection variantCollection = new StandardVariantContextInputArgumentCollection();
@Input(fullName="validation", shortName = "validation", doc="Input VCF file", required=false) @Hidden
@Input(fullName="validation", shortName = "validation", doc="Validation VCF file", required=false)
public RodBinding<VariantContext> validation; public RodBinding<VariantContext> validation;
@Output(doc="File to which BEAGLE input should be written",required=true) @Output(doc="File to which BEAGLE input should be written",required=true)
protected PrintStream beagleWriter = null; protected PrintStream beagleWriter = null;
@Output(doc="File to which BEAGLE markers should be written", shortName="markers", fullName = "markers", required = false) @Hidden
@Output(doc="File to which BEAGLE markers should be written", shortName="markers", fullName = "markers", required = false)
protected PrintStream markers = null; protected PrintStream markers = null;
int markerCounter = 1; int markerCounter = 1;
@ -73,14 +99,19 @@ public class ProduceBeagleInputWalker extends RodWalker<Integer, Integer> {
@Argument(doc="VQSqual key", shortName = "vqskey", required=false) @Argument(doc="VQSqual key", shortName = "vqskey", required=false)
protected String VQSLOD_KEY = "VQSqual"; protected String VQSLOD_KEY = "VQSqual";
@Argument(fullName = "inserted_nocall_rate", shortName = "nc_rate", doc = "Rate (0-1) at which genotype no-calls will be randomly inserted, for testing", required = false) @Hidden
@Argument(fullName = "inserted_nocall_rate", shortName = "nc_rate", doc = "Rate (0-1) at which genotype no-calls will be randomly inserted, for testing", required = false)
public double insertedNoCallRate = 0; public double insertedNoCallRate = 0;
@Argument(fullName = "validation_genotype_ptrue", shortName = "valp", doc = "Flat probability to assign to validation genotypes. Will override GL field.", required = false) @Hidden
@Argument(fullName = "validation_genotype_ptrue", shortName = "valp", doc = "Flat probability to assign to validation genotypes. Will override GL field.", required = false)
public double validationPrior = -1.0; public double validationPrior = -1.0;
@Argument(fullName = "validation_bootstrap", shortName = "bs", doc = "Proportion of records to be used in bootstrap set", required = false) @Hidden
@Argument(fullName = "validation_bootstrap", shortName = "bs", doc = "Proportion of records to be used in bootstrap set", required = false)
public double bootstrap = 0.0; public double bootstrap = 0.0;
@Argument(fullName = "bootstrap_vcf",shortName = "bvcf", doc = "Output a VCF with the records used for bootstrapping filtered out", required = false) @Hidden
@Argument(fullName = "bootstrap_vcf",shortName = "bvcf", doc = "Output a VCF with the records used for bootstrapping filtered out", required = false)
VCFWriter bootstrapVCFOutput = null; VCFWriter bootstrapVCFOutput = null;
@Argument(fullName = "checkIsMaleOnChrX", shortName = "checkIsMaleOnChrX", doc = "Set to true when Beagle-ing chrX and want to ensure male samples don't have heterozygous calls.", required = false) @Argument(fullName = "checkIsMaleOnChrX", shortName = "checkIsMaleOnChrX", doc = "Set to true when Beagle-ing chrX and want to ensure male samples don't have heterozygous calls.", required = false)
public boolean CHECK_IS_MALE_ON_CHR_X = false; public boolean CHECK_IS_MALE_ON_CHR_X = false;

4
public/java/src/org/broadinstitute/sting/utils/text/ListFileUtils.java
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@ -160,8 +160,8 @@ public class ListFileUtils {
rodBinding.getName(), rodBinding.getTribbleType(), builderForValidation.userFriendlyListOfAvailableFeatures())); rodBinding.getName(), rodBinding.getTribbleType(), builderForValidation.userFriendlyListOfAvailableFeatures()));
if ( ! rodBinding.getType().isAssignableFrom(descriptor.getFeatureClass()) ) if ( ! rodBinding.getType().isAssignableFrom(descriptor.getFeatureClass()) )
throw new UserException.BadArgumentValue(rodBinding.getName(), throw new UserException.BadArgumentValue(rodBinding.getName(),
String.format("Field %s expected type %s, but the type of the input file provided on the command line was %s. Please make sure that you have provided the correct file type and/or that you are not binding your rod to a name matching one of the available types.", String.format("Field %s expected type %s, but the type of the input file provided on the command line was %s producing %s. Please make sure that you have provided the correct file type and/or that you are not binding your rod to a name matching one of the available types.",
rodBinding.getName(), rodBinding.getType(), descriptor.getName())); rodBinding.getName(), rodBinding.getType(), descriptor.getName(), descriptor.getFeatureClass()));
rodBindings.add(triplet); rodBindings.add(triplet);

2
public/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java
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@ -133,7 +133,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
validationDataLocation + "1000G.exomes.vcf --snpEffFile " + validationDataLocation + validationDataLocation + "1000G.exomes.vcf --snpEffFile " + validationDataLocation +
"snpEff_1.9.6_1000G.exomes.vcf_hg37.61.out -L 1:26,000,000-26,500,000", "snpEff_1.9.6_1000G.exomes.vcf_hg37.61.out -L 1:26,000,000-26,500,000",
1, 1,
Arrays.asList("c08648a078368c80530bff004b3157f1") Arrays.asList("03eae1dab19a9358250890594bf53607")
); );
executeTest("Testing SnpEff annotations", spec); executeTest("Testing SnpEff annotations", spec);
} }