From 62be55376b452ffa297a52cad79427b9e9cfea67 Mon Sep 17 00:00:00 2001 From: depristo Date: Mon, 15 Nov 2010 17:53:33 +0000 Subject: [PATCH] no longer useful git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4677 348d0f76-0448-11de-a6fe-93d51630548a --- .../TestVariantRecalibrator.java | 143 ------------------ 1 file changed, 143 deletions(-) delete mode 100644 java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/TestVariantRecalibrator.java diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/TestVariantRecalibrator.java b/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/TestVariantRecalibrator.java deleted file mode 100644 index d481840dc..000000000 --- a/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/TestVariantRecalibrator.java +++ /dev/null @@ -1,143 +0,0 @@ -/* - * Copyright (c) 2010 The Broad Institute - * - * Permission is hereby granted, free of charge, to any person - * obtaining a copy of this software and associated documentation - * files (the "Software"), to deal in the Software without - * restriction, including without limitation the rights to use, - * copy, modify, merge, publish, distribute, sublicense, and/or sell - * copies of the Software, and to permit persons to whom the - * Software is furnished to do so, subject to the following - * conditions: - * - * The above copyright notice and this permission notice shall be - * included in all copies or substantial portions of the Software. - * - * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, - * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES - * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND - * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT - * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, - * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING - * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR - * THE USE OR OTHER DEALINGS IN THE SOFTWARE. - */ - -package org.broadinstitute.sting.gatk.walkers.variantrecalibration; - -import org.broad.tribble.dbsnp.DbSNPFeature; -import org.broad.tribble.util.variantcontext.VariantContext; -import org.broad.tribble.vcf.*; -import org.broadinstitute.sting.commandline.*; -import org.broadinstitute.sting.gatk.contexts.AlignmentContext; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils; -import org.broadinstitute.sting.gatk.datasources.simpleDataSources.ReferenceOrderedDataSource; -import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.refdata.utils.helpers.DbSNPHelper; -import org.broadinstitute.sting.gatk.walkers.RodWalker; -import org.broadinstitute.sting.utils.*; -import org.broadinstitute.sting.utils.text.XReadLines; -import org.broadinstitute.sting.utils.collections.ExpandingArrayList; -import org.broadinstitute.sting.utils.collections.NestedHashMap; -import org.broadinstitute.sting.utils.exceptions.UserException; -import org.broadinstitute.sting.utils.exceptions.StingException; -import org.broadinstitute.sting.utils.vcf.VCFUtils; - -import java.io.File; -import java.io.FileNotFoundException; -import java.io.PrintStream; -import java.util.*; - -/** - * Applies calibrated variant cluster parameters to variant calls to produce an accurate and informative variant quality score - * - * @author rpoplin - * @since Mar 17, 2010 - * - * @help.summary Applies calibrated variant cluster parameters to variant calls to produce an accurate and informative variant quality score - */ - -public class TestVariantRecalibrator extends RodWalker, ExpandingArrayList> { - - ///////////////////////////// - // Inputs - ///////////////////////////// - @Input(fullName="dataFile", shortName="dataFile", doc="The input cluster file generated by GenerateVariantClusters", required=true) - private File dataFile; - - @Argument(fullName="target_titv", shortName="titv", doc="The expected novel Ti/Tv ratio to use when calculating FDR tranches and for display on optimization curve output figures. (~~2.07 for whole genome experiments)", required=true) - private double TARGET_TITV = 2.07; - @Argument(fullName="FDRtranche", shortName="tranche", doc="The levels of novel false discovery rate (FDR, implied by ti/tv) at which to slice the data. (in percent, that is 1.0 for 1 percent)", required=false) - private double[] FDR_TRANCHES = null; - - @Argument(fullName="maxElements", shortName="maxElements", doc="The expected novel Ti/Tv ratio to use when calculating FDR tranches and for display on optimization curve output figures. (~~2.07 for whole genome experiments)", required=false) - private double maxElements = -1; - - @Argument(fullName="sixElementFile", shortName="sixElementFile", doc="", required=false) - private File sixElementFile = null; - - @Argument(fullName="fourElementFile", shortName="fourElementFile", doc="", required=false) - private File fourElementFile = null; - - public void initialize() { - List vd = new ArrayList(); - try { - for ( String line : new XReadLines(dataFile, true) ) { - String[] parts = line.split(" "); - if ( ! parts[0].equals("QUAL") ) { - VariantDatum datum = new VariantDatum(); - datum.qual = Double.valueOf(parts[0]); - datum.isTransition = parts[1].equals("1"); - datum.isKnown = parts[2].equals("1"); - vd.add(datum); - - if ( maxElements != -1 && vd.size() > maxElements ) - break; - } - } - } catch (FileNotFoundException e) { - throw new StingException("foo", e); - } - - List tranches = VariantGaussianMixtureModel.findTranches(vd.toArray(new VariantDatum[0]), FDR_TRANCHES, TARGET_TITV); - System.out.printf(Tranche.tranchesString(tranches)); - - if ( sixElementFile != null ) { - List six = Tranche.readTraches(sixElementFile); - System.out.printf("six%n"); - System.out.printf(Tranche.tranchesString(six)); - } - - if ( fourElementFile != null ) { - List four = Tranche.readTraches(fourElementFile); - System.out.printf("four%n"); - System.out.printf(Tranche.tranchesString(four)); - } - - System.exit(0); - } - - public ExpandingArrayList map( RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context ) { - return null; - } - - //--------------------------------------------------------------------------------------------------------------- - // - // reduce - // - //--------------------------------------------------------------------------------------------------------------- - - public ExpandingArrayList reduceInit() { - return new ExpandingArrayList(); - } - - public ExpandingArrayList reduce( final ExpandingArrayList mapValue, final ExpandingArrayList reduceSum ) { - reduceSum.addAll( mapValue ); - return reduceSum; - } - - public void onTraversalDone( ExpandingArrayList reduceSum ) { - - } -} \ No newline at end of file