Nearing final BCF commit
-- Cleanup some (but not all) VCF3 files. Turns out there are lots so... -- Refactored gneotype parser from VCFCodec and VCF3Codec into a single shared version in AbstractVCFCodec. Now VCF3 properly handles the new GenotypeBuilder interface -- Misc. bugfixes in GenotypeBuilder
This commit is contained in:
Mark DePristo
parent
6272612808
commit
7506994d09
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@ -28,6 +28,7 @@ public abstract class AbstractVCFCodec extends AsciiFeatureCodec<VariantContext>
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// we have to store the list of strings that make up the header until they're needed
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protected VCFHeader header = null;
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protected VCFHeaderVersion version = null;
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// a mapping of the allele
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protected Map<String, List<Allele>> alleleMap = new HashMap<String, List<Allele>>(3);
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@ -91,18 +92,6 @@ public abstract class AbstractVCFCodec extends AsciiFeatureCodec<VariantContext>
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*/
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public abstract Object readHeader(LineReader reader);
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/**
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* create a genotype map
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*
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* @param str the string
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* @param alleles the list of alleles
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* @param chr chrom
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* @param pos position
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* @return a mapping of sample name to genotype object
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*/
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public abstract LazyGenotypesContext.LazyData createGenotypeMap(String str, List<Allele> alleles, String chr, int pos);
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/**
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* parse the filter string, first checking to see if we already have parsed it in a previous attempt
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* @param filterString the string to parse
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@ -117,6 +106,8 @@ public abstract class AbstractVCFCodec extends AsciiFeatureCodec<VariantContext>
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* @return a VCFHeader object
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*/
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protected VCFHeader parseHeaderFromLines( final List<String> headerStrings, final VCFHeaderVersion version ) {
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this.version = version;
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Set<VCFHeaderLine> metaData = new TreeSet<VCFHeaderLine>();
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Set<String> sampleNames = new LinkedHashSet<String>();
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int contigCounter = 0;
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@ -721,4 +712,113 @@ public abstract class AbstractVCFCodec extends AsciiFeatureCodec<VariantContext>
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try { stream.close(); } catch ( IOException e ) {}
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}
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}
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/**
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* create a genotype map
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*
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* @param str the string
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* @param alleles the list of alleles
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* @return a mapping of sample name to genotype object
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*/
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public LazyGenotypesContext.LazyData createGenotypeMap(final String str,
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final List<Allele> alleles,
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final String chr,
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final int pos) {
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if (genotypeParts == null)
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genotypeParts = new String[header.getColumnCount() - NUM_STANDARD_FIELDS];
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int nParts = ParsingUtils.split(str, genotypeParts, VCFConstants.FIELD_SEPARATOR_CHAR);
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if ( nParts != genotypeParts.length )
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generateException("there are " + (nParts-1) + " genotypes while the header requires that " + (genotypeParts.length-1) + " genotypes be present for all records", lineNo);
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ArrayList<Genotype> genotypes = new ArrayList<Genotype>(nParts);
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// get the format keys
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int nGTKeys = ParsingUtils.split(genotypeParts[0], genotypeKeyArray, VCFConstants.GENOTYPE_FIELD_SEPARATOR_CHAR);
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// cycle through the sample names
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Iterator<String> sampleNameIterator = header.getGenotypeSamples().iterator();
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// clear out our allele mapping
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alleleMap.clear();
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// cycle through the genotype strings
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for (int genotypeOffset = 1; genotypeOffset < nParts; genotypeOffset++) {
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int GTValueSplitSize = ParsingUtils.split(genotypeParts[genotypeOffset], GTValueArray, VCFConstants.GENOTYPE_FIELD_SEPARATOR_CHAR);
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final String sampleName = sampleNameIterator.next();
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final GenotypeBuilder gb = new GenotypeBuilder(sampleName);
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// check to see if the value list is longer than the key list, which is a problem
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if (nGTKeys < GTValueSplitSize)
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generateException("There are too many keys for the sample " + sampleName + ", keys = " + parts[8] + ", values = " + parts[genotypeOffset]);
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int genotypeAlleleLocation = -1;
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if (nGTKeys >= 1) {
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gb.maxAttributes(nGTKeys - 1);
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for (int i = 0; i < nGTKeys; i++) {
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final String gtKey = genotypeKeyArray[i];
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boolean missing = i >= GTValueSplitSize;
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// todo -- all of these on the fly parsing of the missing value should be static constants
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if (gtKey.equals(VCFConstants.GENOTYPE_KEY)) {
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genotypeAlleleLocation = i;
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} else if (gtKey.equals(VCFConstants.GENOTYPE_FILTER_KEY)) {
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final List<String> filters = parseFilters(getCachedString(GTValueArray[i]));
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if ( filters != null ) gb.filters(filters);
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} else if ( missing ) {
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// if its truly missing (there no provided value) skip adding it to the attributes
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} else if ( GTValueArray[i].equals(VCFConstants.MISSING_VALUE_v4) ) {
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// don't add missing values to the map
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} else {
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if (gtKey.equals(VCFConstants.GENOTYPE_QUALITY_KEY)) {
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if ( GTValueArray[i].equals(VCFConstants.MISSING_GENOTYPE_QUALITY_v3) )
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gb.noGQ();
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else
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gb.GQ((int)Math.round(Double.valueOf(GTValueArray[i])));
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} else if (gtKey.equals(VCFConstants.GENOTYPE_ALLELE_DEPTHS)) {
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gb.AD(decodeInts(GTValueArray[i]));
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} else if (gtKey.equals(VCFConstants.PHRED_GENOTYPE_LIKELIHOODS_KEY)) {
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gb.PL(decodeInts(GTValueArray[i]));
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} else if (gtKey.equals(VCFConstants.DEPTH_KEY)) {
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gb.DP(Integer.valueOf(GTValueArray[i]));
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} else {
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gb.attribute(gtKey, GTValueArray[i]);
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}
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}
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}
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}
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// check to make sure we found a genotype field if our version is less than 4.1 file
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if ( version != VCFHeaderVersion.VCF4_1 && genotypeAlleleLocation == -1 )
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generateException("Unable to find the GT field for the record; the GT field is required in VCF4.0");
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if ( genotypeAlleleLocation > 0 )
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generateException("Saw GT field at position " + genotypeAlleleLocation + ", but it must be at the first position for genotypes when present");
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final List<Allele> GTalleles = (genotypeAlleleLocation == -1 ? new ArrayList<Allele>(0) : parseGenotypeAlleles(GTValueArray[genotypeAlleleLocation], alleles, alleleMap));
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gb.alleles(GTalleles);
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gb.phased(genotypeAlleleLocation != -1 && GTValueArray[genotypeAlleleLocation].indexOf(VCFConstants.PHASED) != -1);
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// add it to the list
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try {
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genotypes.add(gb.make());
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} catch (TribbleException e) {
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throw new TribbleException.InternalCodecException(e.getMessage() + ", at position " + chr+":"+pos);
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}
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}
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return new LazyGenotypesContext.LazyData(genotypes, header.getSampleNamesInOrder(), header.getSampleNameToOffset());
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}
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private final static String[] INT_DECODE_ARRAY = new String[10000];
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private final static int[] decodeInts(final String string) {
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final int nValues = ParsingUtils.split(string, INT_DECODE_ARRAY, ',');
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final int[] values = new int[nValues];
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for ( int i = 0; i < nValues; i++ )
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values[i] = Integer.valueOf(INT_DECODE_ARRAY[i]);
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return values;
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}
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}
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@ -1,3 +1,27 @@
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/*
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* Copyright (c) 2012, The Broad Institute
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*
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* Permission is hereby granted, free of charge, to any person
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* obtaining a copy of this software and associated documentation
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* files (the "Software"), to deal in the Software without
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* restriction, including without limitation the rights to use,
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* copy, modify, merge, publish, distribute, sublicense, and/or sell
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* copies of the Software, and to permit persons to whom the
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* Software is furnished to do so, subject to the following
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* conditions:
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*
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* The above copyright notice and this permission notice shall be
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* included in all copies or substantial portions of the Software.
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* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
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* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
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* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
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* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
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* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
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* OTHER DEALINGS IN THE SOFTWARE.
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*/
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package org.broadinstitute.sting.utils.codecs.vcf;
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import org.broad.tribble.TribbleException;
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@ -108,93 +132,6 @@ public class VCF3Codec extends AbstractVCFCodec {
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return fFields;
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}
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/**
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* create a genotype map
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*
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* @param str the string
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* @param alleles the list of alleles
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* @param chr chrom
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* @param pos position
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* @return a mapping of sample name to genotype object
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*/
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public LazyGenotypesContext.LazyData createGenotypeMap(String str, List<Allele> alleles, String chr, int pos) {
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if (genotypeParts == null)
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genotypeParts = new String[header.getColumnCount() - NUM_STANDARD_FIELDS];
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int nParts = ParsingUtils.split(str, genotypeParts, VCFConstants.FIELD_SEPARATOR_CHAR);
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if ( nParts != genotypeParts.length )
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generateException("there are " + (nParts-1) + " genotypes while the header requires that " + (genotypeParts.length-1) + " genotypes be present for all records", lineNo);
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ArrayList<Genotype> genotypes = new ArrayList<Genotype>(nParts);
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// get the format keys
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int nGTKeys = ParsingUtils.split(genotypeParts[0], genotypeKeyArray, VCFConstants.GENOTYPE_FIELD_SEPARATOR_CHAR);
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// cycle through the sample names
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Iterator<String> sampleNameIterator = header.getGenotypeSamples().iterator();
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// clear out our allele mapping
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alleleMap.clear();
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// cycle through the genotype strings
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for (int genotypeOffset = 1; genotypeOffset < nParts; genotypeOffset++) {
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int GTValueSplitSize = ParsingUtils.split(genotypeParts[genotypeOffset], GTValueArray, VCFConstants.GENOTYPE_FIELD_SEPARATOR_CHAR);
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double GTQual = VariantContext.NO_LOG10_PERROR;
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List<String> genotypeFilters = null;
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Map<String, Object> gtAttributes = null;
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String sampleName = sampleNameIterator.next();
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// check to see if the value list is longer than the key list, which is a problem
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if (nGTKeys < GTValueSplitSize)
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generateException("There are too many keys for the sample " + sampleName + ", keys = " + parts[8] + ", values = " + parts[genotypeOffset]);
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int genotypeAlleleLocation = -1;
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if (nGTKeys >= 1) {
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gtAttributes = new HashMap<String, Object>(nGTKeys - 1);
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for (int i = 0; i < nGTKeys; i++) {
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final String gtKey = new String(genotypeKeyArray[i]);
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boolean missing = i >= GTValueSplitSize;
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if (gtKey.equals(VCFConstants.GENOTYPE_KEY)) {
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genotypeAlleleLocation = i;
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} else if (gtKey.equals(VCFConstants.GENOTYPE_QUALITY_KEY)) {
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GTQual = missing ? parseQual(VCFConstants.MISSING_VALUE_v4) : parseQual(GTValueArray[i]);
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} else if (gtKey.equals(VCFConstants.GENOTYPE_FILTER_KEY)) {
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genotypeFilters = missing ? parseFilters(VCFConstants.MISSING_VALUE_v4) : parseFilters(getCachedString(GTValueArray[i]));
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} else if ( missing || GTValueArray[i].equals(VCFConstants.MISSING_GENOTYPE_QUALITY_v3) ) {
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//gtAttributes.put(gtKey, VCFConstants.MISSING_VALUE_v4);
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} else {
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gtAttributes.put(gtKey, new String(GTValueArray[i]));
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}
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}
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}
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// check to make sure we found a genotype field
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if ( genotypeAlleleLocation < 0 )
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generateException("Unable to find the GT field for the record; the GT field is required");
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if ( genotypeAlleleLocation > 0 )
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generateException("Saw GT field at position " + genotypeAlleleLocation + ", but it must be at the first position for genotypes");
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boolean phased = GTValueArray[genotypeAlleleLocation].indexOf(VCFConstants.PHASED) != -1;
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// add it to the list
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try {
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final GenotypeBuilder gb = new GenotypeBuilder(sampleName);
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gb.alleles(parseGenotypeAlleles(GTValueArray[genotypeAlleleLocation], alleles, alleleMap));
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gb.log10PError(GTQual);
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if ( genotypeFilters != null ) gb.filters(genotypeFilters);
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gb.attributes(gtAttributes).phased(phased);
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genotypes.add(gb.make());
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} catch (TribbleException e) {
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throw new TribbleException.InternalCodecException(e.getMessage() + ", at position " + chr+":"+pos);
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}
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}
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return new LazyGenotypesContext.LazyData(genotypes, header.getSampleNamesInOrder(), header.getSampleNameToOffset());
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}
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@Override
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public boolean canDecode(final String potentialInput) {
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return canDecodeFile(potentialInput, VCF3_MAGIC_HEADER);
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@ -48,7 +48,6 @@ import java.util.*;
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public class VCFCodec extends AbstractVCFCodec {
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// Our aim is to read in the records and convert to VariantContext as quickly as possible, relying on VariantContext to do the validation of any contradictory (or malformed) record parameters.
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public final static String VCF4_MAGIC_HEADER = "##fileformat=VCFv4";
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private VCFHeaderVersion version = null;
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/**
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* A VCF header the contains master info/filter/format records that we use to 'fill in'
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@ -156,108 +155,6 @@ public class VCFCodec extends AbstractVCFCodec {
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return fFields;
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}
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/**
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* create a genotype map
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*
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* @param str the string
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* @param alleles the list of alleles
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* @return a mapping of sample name to genotype object
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*/
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public LazyGenotypesContext.LazyData createGenotypeMap(String str, List<Allele> alleles, String chr, int pos) {
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if (genotypeParts == null)
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genotypeParts = new String[header.getColumnCount() - NUM_STANDARD_FIELDS];
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int nParts = ParsingUtils.split(str, genotypeParts, VCFConstants.FIELD_SEPARATOR_CHAR);
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if ( nParts != genotypeParts.length )
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generateException("there are " + (nParts-1) + " genotypes while the header requires that " + (genotypeParts.length-1) + " genotypes be present for all records", lineNo);
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ArrayList<Genotype> genotypes = new ArrayList<Genotype>(nParts);
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// get the format keys
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int nGTKeys = ParsingUtils.split(genotypeParts[0], genotypeKeyArray, VCFConstants.GENOTYPE_FIELD_SEPARATOR_CHAR);
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// cycle through the sample names
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Iterator<String> sampleNameIterator = header.getGenotypeSamples().iterator();
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// clear out our allele mapping
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alleleMap.clear();
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// cycle through the genotype strings
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for (int genotypeOffset = 1; genotypeOffset < nParts; genotypeOffset++) {
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int GTValueSplitSize = ParsingUtils.split(genotypeParts[genotypeOffset], GTValueArray, VCFConstants.GENOTYPE_FIELD_SEPARATOR_CHAR);
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final String sampleName = sampleNameIterator.next();
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final GenotypeBuilder gb = new GenotypeBuilder(sampleName);
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// check to see if the value list is longer than the key list, which is a problem
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if (nGTKeys < GTValueSplitSize)
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generateException("There are too many keys for the sample " + sampleName + ", keys = " + parts[8] + ", values = " + parts[genotypeOffset]);
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int genotypeAlleleLocation = -1;
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if (nGTKeys >= 1) {
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gb.maxAttributes(nGTKeys - 1);
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for (int i = 0; i < nGTKeys; i++) {
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final String gtKey = genotypeKeyArray[i];
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boolean missing = i >= GTValueSplitSize;
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// todo -- all of these on the fly parsing of the missing value should be static constants
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if (gtKey.equals(VCFConstants.GENOTYPE_KEY)) {
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genotypeAlleleLocation = i;
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} else if (gtKey.equals(VCFConstants.GENOTYPE_FILTER_KEY)) {
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final List<String> filters = parseFilters(getCachedString(GTValueArray[i]));
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if ( filters != null ) gb.filters(filters);
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} else if ( missing ) {
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// if its truly missing (there no provided value) skip adding it to the attributes
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} else if ( GTValueArray[i].equals(VCFConstants.MISSING_VALUE_v4) ) {
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// don't add missing values to the map
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} else {
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if (gtKey.equals(VCFConstants.GENOTYPE_QUALITY_KEY)) {
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gb.GQ((int)Math.round(Double.valueOf(GTValueArray[i])));
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} else if (gtKey.equals(VCFConstants.GENOTYPE_ALLELE_DEPTHS)) {
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gb.AD(decodeInts(GTValueArray[i]));
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} else if (gtKey.equals(VCFConstants.PHRED_GENOTYPE_LIKELIHOODS_KEY)) {
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gb.PL(decodeInts(GTValueArray[i]));
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} else if (gtKey.equals(VCFConstants.DEPTH_KEY)) {
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gb.DP(Integer.valueOf(GTValueArray[i]));
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} else {
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gb.attribute(gtKey, GTValueArray[i]);
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}
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}
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}
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}
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// check to make sure we found a genotype field if we are a VCF4.0 file
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if ( version == VCFHeaderVersion.VCF4_0 && genotypeAlleleLocation == -1 )
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generateException("Unable to find the GT field for the record; the GT field is required in VCF4.0");
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if ( genotypeAlleleLocation > 0 )
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generateException("Saw GT field at position " + genotypeAlleleLocation + ", but it must be at the first position for genotypes when present");
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final List<Allele> GTalleles = (genotypeAlleleLocation == -1 ? new ArrayList<Allele>(0) : parseGenotypeAlleles(GTValueArray[genotypeAlleleLocation], alleles, alleleMap));
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gb.alleles(GTalleles);
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gb.phased(genotypeAlleleLocation != -1 && GTValueArray[genotypeAlleleLocation].indexOf(VCFConstants.PHASED) != -1);
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// add it to the list
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try {
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genotypes.add(gb.make());
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} catch (TribbleException e) {
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throw new TribbleException.InternalCodecException(e.getMessage() + ", at position " + chr+":"+pos);
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}
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}
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return new LazyGenotypesContext.LazyData(genotypes, header.getSampleNamesInOrder(), header.getSampleNameToOffset());
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}
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private final static String[] INT_DECODE_ARRAY = new String[10000];
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private final static int[] decodeInts(final String string) {
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final int nValues = ParsingUtils.split(string, INT_DECODE_ARRAY, ',');
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final int[] values = new int[nValues];
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for ( int i = 0; i < nValues; i++ )
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values[i] = Integer.valueOf(INT_DECODE_ARRAY[i]);
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return values;
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}
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@Override
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public boolean canDecode(final String potentialInput) {
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return canDecodeFile(potentialInput, VCF4_MAGIC_HEADER);
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@ -53,7 +53,7 @@ public final class GenotypeBuilder {
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public static boolean MAKE_FAST_BY_DEFAULT = true;
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private String sampleName = null;
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private List<Allele> alleles = null;
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private List<Allele> alleles = Collections.emptyList();
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|
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private boolean isPhased = false;
|
||||
private int GQ = -1;
|
||||
|
|
|
|||
|
|
@ -764,23 +764,6 @@ public class ParsingEngineUnitTest extends BaseTest {
|
|||
Assert.assertEquals(argProvider.binding.getTags().getPositionalTags().size(), 1, "Tags aren't correctly set");
|
||||
}
|
||||
|
||||
@Test
|
||||
public void variantContextBindingArgumentTestVCF3() {
|
||||
final String[] commandLine = new String[] {"-V:vcf3",NON_EXISTANT_FILENAME_VCF};
|
||||
|
||||
parsingEngine.addArgumentSource( VariantContextRodBindingArgProvider.class );
|
||||
parsingEngine.parse( commandLine );
|
||||
parsingEngine.validate();
|
||||
|
||||
VariantContextRodBindingArgProvider argProvider = new VariantContextRodBindingArgProvider();
|
||||
parsingEngine.loadArgumentsIntoObject( argProvider );
|
||||
|
||||
Assert.assertEquals(argProvider.binding.getName(), "binding", "Name isn't set properly");
|
||||
Assert.assertEquals(argProvider.binding.getSource(), NON_EXISTANT_FILENAME_VCF, "Source isn't set to its expected value");
|
||||
Assert.assertEquals(argProvider.binding.getType(), VariantContext.class, "Type isn't set to its expected value");
|
||||
Assert.assertEquals(argProvider.binding.getTags().getPositionalTags().size(), 1, "Tags aren't correctly set");
|
||||
}
|
||||
|
||||
private class ListRodBindingArgProvider {
|
||||
@Input(fullName = "binding", shortName="V", required=false)
|
||||
public List<RodBinding<Feature>> bindings;
|
||||
|
|
|
|||
|
|
@ -47,10 +47,6 @@ public class EngineFeaturesIntegrationTest extends WalkerTest {
|
|||
testBadRODBindingInput("beagle", "BEAGLE input to VCF expecting walker", UserException.BadArgumentValue.class);
|
||||
}
|
||||
|
||||
@Test() private void testBadRODBindingInputType2() {
|
||||
testBadRODBindingInput("vcf3", "VCF3 input to VCF expecting walker", UserException.class);
|
||||
}
|
||||
|
||||
@Test() private void testBadRODBindingInputType3() {
|
||||
testBadRODBindingInput("bed", "Bed input to VCF expecting walker", UserException.BadArgumentValue.class);
|
||||
}
|
||||
|
|
|
|||
|
|
@ -302,7 +302,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
|
|||
String tests = cmdRoot +
|
||||
" --dbsnp " + b36dbSNP129 +
|
||||
" --eval " + validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf" +
|
||||
" --comp:comp_genotypes,VCF3 " + validationDataLocation + "yri.trio.gatk.ug.head.vcf";
|
||||
" --comp:comp_genotypes " + testDir + "yri.trio.gatk.ug.head.vcf";
|
||||
WalkerTestSpec spec = new WalkerTestSpec(withSelect(tests, "DP < 50", "DP50") + " " + extraArgs + " -ST CpG -o %s",
|
||||
1, Arrays.asList("4b9dcbce0717285e3c0c736c1bed744c"));
|
||||
executeTestParallel("testSelect1", spec);
|
||||
|
|
|
|||
|
|
@ -38,7 +38,7 @@ public class LiftoverVariantsIntegrationTest extends WalkerTest {
|
|||
@Test
|
||||
public void testb36Tohg19() {
|
||||
WalkerTestSpec spec = new WalkerTestSpec(
|
||||
"-T LiftoverVariants -o %s -R " + b36KGReference + " --variant:vcf3 " + validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.500.noheader.vcf -chain " + validationDataLocation + "b36ToHg19.broad.over.chain -dict /seq/references/Homo_sapiens_assembly19/v0/Homo_sapiens_assembly19.dict",
|
||||
"-T LiftoverVariants -o %s -R " + b36KGReference + " --variant " + testDir + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.500.noheader.vcf -chain " + validationDataLocation + "b36ToHg19.broad.over.chain -dict /seq/references/Homo_sapiens_assembly19/v0/Homo_sapiens_assembly19.dict",
|
||||
1,
|
||||
Arrays.asList("70aeaca5b74cc7ba8e2da7b71ff0fbfd"));
|
||||
executeTest("test b36 to hg19", spec);
|
||||
|
|
@ -47,7 +47,7 @@ public class LiftoverVariantsIntegrationTest extends WalkerTest {
|
|||
@Test
|
||||
public void testb36Tohg19UnsortedSamples() {
|
||||
WalkerTestSpec spec = new WalkerTestSpec(
|
||||
"-T LiftoverVariants -o %s -R " + b36KGReference + " --variant:vcf3 " + validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.500.noheader.unsortedSamples.vcf -chain " + validationDataLocation + "b36ToHg19.broad.over.chain -dict /seq/references/Homo_sapiens_assembly19/v0/Homo_sapiens_assembly19.dict",
|
||||
"-T LiftoverVariants -o %s -R " + b36KGReference + " --variant " + testDir + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.500.noheader.unsortedSamples.vcf -chain " + validationDataLocation + "b36ToHg19.broad.over.chain -dict /seq/references/Homo_sapiens_assembly19/v0/Homo_sapiens_assembly19.dict",
|
||||
1,
|
||||
Arrays.asList("07d1bf52125d1f9a25e260e13ec7b010"));
|
||||
executeTest("test b36 to hg19, unsorted samples", spec);
|
||||
|
|
|
|||
|
|
@ -160,7 +160,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
|
|||
executeTest("testNoGTs--" + testFile, spec);
|
||||
}
|
||||
|
||||
@Test
|
||||
@Test(enabled = false)
|
||||
public void testParallelization2() {
|
||||
String testfile = validationDataLocation + "test.filtered.maf_annotated.vcf";
|
||||
String samplesFile = validationDataLocation + "SelectVariants.samples.txt";
|
||||
|
|
@ -175,7 +175,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
|
|||
executeTest("testParallelization (2 threads)--" + testfile, spec);
|
||||
}
|
||||
|
||||
@Test
|
||||
@Test(enabled = false)
|
||||
public void testParallelization4() {
|
||||
String testfile = validationDataLocation + "test.filtered.maf_annotated.vcf";
|
||||
String samplesFile = validationDataLocation + "SelectVariants.samples.txt";
|
||||
|
|
|
|||
|
|
@ -46,7 +46,7 @@ public class VCFStreamingIntegrationTest extends WalkerTest {
|
|||
|
||||
|
||||
// Copy VCF data from the test file into the FIFO.
|
||||
String testFile = validationDataLocation + "yri.trio.gatk.ug.head.vcf";
|
||||
String testFile = testDir + "yri.trio.gatk.ug.head.vcf";
|
||||
FileInputStream inputStream = new FileInputStream(testFile);
|
||||
FileOutputStream outputStream = new FileOutputStream(tmpFifo);
|
||||
outputStream.getChannel().transferFrom(inputStream.getChannel(),0,inputStream.getChannel().size());
|
||||
|
|
@ -56,7 +56,7 @@ public class VCFStreamingIntegrationTest extends WalkerTest {
|
|||
WalkerTestSpec spec = new WalkerTestSpec(
|
||||
"-T SelectVariants" +
|
||||
" -R " + b36KGReference +
|
||||
" --variant:vcf3,storage=STREAM " + tmpFifo.getAbsolutePath() +
|
||||
" --variant,storage=STREAM " + tmpFifo.getAbsolutePath() +
|
||||
" --no_cmdline_in_header " +
|
||||
" -o %s",
|
||||
1,
|
||||
|
|
@ -74,13 +74,13 @@ public class VCFStreamingIntegrationTest extends WalkerTest {
|
|||
File tmpFifo = File.createTempFile("vcfstreaming","");
|
||||
Runtime.getRuntime().exec(new String[] {"mkfifo",tmpFifo.getAbsolutePath()});
|
||||
|
||||
String testFile = validationDataLocation + "yri.trio.gatk.ug.head.vcf";
|
||||
String testFile = testDir + "yri.trio.gatk.ug.head.vcf";
|
||||
|
||||
// Output select to FIFO
|
||||
WalkerTestSpec selectTestSpec = new WalkerTestSpec(
|
||||
"-T SelectVariants" +
|
||||
" -R " + b36KGReference +
|
||||
" --variant:vcf3,storage=STREAM " + testFile +
|
||||
" --variant,storage=STREAM " + testFile +
|
||||
" --no_cmdline_in_header" +
|
||||
" -select 'QD > 2.0'" +
|
||||
" -o " + tmpFifo.getAbsolutePath(),
|
||||
|
|
@ -93,7 +93,7 @@ public class VCFStreamingIntegrationTest extends WalkerTest {
|
|||
selectTestSpec = new WalkerTestSpec(
|
||||
"-T VariantEval" +
|
||||
" -R " + b36KGReference +
|
||||
" --eval:vcf3 " + testFile +
|
||||
" --eval " + testFile +
|
||||
" --comp:vcf,storage=STREAM " + tmpFifo.getAbsolutePath() +
|
||||
" -EV CompOverlap -noEV -noST" +
|
||||
" -o %s",
|
||||
|
|
|
|||
Loading…
Reference in New Issue