zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Removing fully commented out varianteval evaluators 

- Files were completely commmented out, and were screwing up my license script. Dont like them. Removed them.

GSATDG-5
This commit is contained in:
Mauricio Carneiro 2013-01-10 16:50:43 -05:00
parent 5222f9c397
commit dd177b1714
2 changed files with 0 additions and 450 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

361
protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/genotypePhasingEvaluator/GenotypePhasingEvaluator.java
View File

@ -1,361 +0,0 @@
//package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators.genotypePhasingEvaluator;
//
//import org.apache.log4j.Logger;
//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.phasing.AllelePair;
//import org.broadinstitute.sting.gatk.walkers.phasing.ReadBackedPhasingWalker;
//import org.broadinstitute.sting.gatk.walkers.varianteval.VariantEvalWalker;
//import org.broadinstitute.sting.gatk.walkers.varianteval.evaluators.VariantEvaluator;
//import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis;
//import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint;
//import org.broadinstitute.sting.gatk.walkers.varianteval.util.EvaluationContext;
//import org.broadinstitute.sting.utils.GenomeLoc;
//import org.broadinstitute.sting.utils.MathUtils;
//import org.broadinstitute.variant.variantcontext.Genotype;
//import org.broadinstitute.variant.variantcontext.GenotypesContext;
//import org.broadinstitute.variant.variantcontext.VariantContext;
//
//import java.util.HashMap;
//import java.util.HashSet;
//import java.util.Set;
//
///*
// * 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.
// */
//
//@Analysis(name = "Genotype Phasing Evaluation", description = "Evaluates the phasing of genotypes in different tracks")
//public class GenotypePhasingEvaluator extends VariantEvaluator {
// protected final static Logger logger = Logger.getLogger(GenotypePhasingEvaluator.class);
//
// // a mapping from sample to stats
// @DataPoint(description = "the phasing statistics for each sample")
// public SamplePhasingStatistics samplePhasingStatistics = null;
//
// SamplePreviousGenotypes samplePrevGenotypes = null;
//
// double minPhaseQuality = 10.0;
//
// public void initialize(VariantEvalWalker walker) {
// super.initialize(walker);
// this.samplePhasingStatistics = new SamplePhasingStatistics(walker.getMinPhaseQuality());
// this.samplePrevGenotypes = new SamplePreviousGenotypes();
// }
//
// public String getName() {
// return "GenotypePhasingEvaluator";
// }
//
// public int getComparisonOrder() {
// return 2; // we only need to see pairs of (comp, eval)
// }
//
// public String toString() {
// return getName() + ": <table>";
// }
//
// public void update2(VariantContext eval, VariantContext comp, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
// update2(eval,comp,tracker,ref,context,null);
// }
//
// public String update2(VariantContext eval, VariantContext comp, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context, EvaluationContext group) {
// //public String update2(VariantContext eval, VariantContext comp, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context, VariantEvalWalker.EvaluationContext group) {
// Reasons interesting = new Reasons();
// if (ref == null)
// return interesting.toString();
// GenomeLoc curLocus = ref.getLocus();
//
// logger.debug("update2() locus: " + curLocus);
// logger.debug("comp = " + comp + " eval = " + eval);
//
// Set<String> allSamples = new HashSet<String>();
//
// GenotypesContext compSampGenotypes = null;
// if (isRelevantToPhasing(comp)) {
// allSamples.addAll(comp.getSampleNames());
// compSampGenotypes = comp.getGenotypes();
// }
//
// GenotypesContext evalSampGenotypes = null;
// if (isRelevantToPhasing(eval)) {
// allSamples.addAll(eval.getSampleNames());
// evalSampGenotypes = eval.getGenotypes();
// }
//
// for (String samp : allSamples) {
// logger.debug("sample = " + samp);
//
// Genotype compSampGt = null;
// if (compSampGenotypes != null)
// compSampGt = compSampGenotypes.get(samp);
//
// Genotype evalSampGt = null;
// if (evalSampGenotypes != null)
// evalSampGt = evalSampGenotypes.get(samp);
//
// if (compSampGt == null || evalSampGt == null || compSampGt.isNoCall() || evalSampGt.isNoCall()) { // Since either comp or eval (or both) are missing the site, the best we can do is hope to preserve phase [if the non-missing one preserves phase]
// // Having an unphased site breaks the phasing for the sample [does NOT permit "transitive phasing"] - hence, must reset phasing knowledge for both comp and eval [put a null CompEvalGenotypes]:
// if (isNonNullButUnphased(compSampGt) || isNonNullButUnphased(evalSampGt))
// samplePrevGenotypes.put(samp, null);
// }
// else { // Both comp and eval have a non-null Genotype at this site:
// AllelePair compAllelePair = new AllelePair(compSampGt);
// AllelePair evalAllelePair = new AllelePair(evalSampGt);
//
// boolean breakPhasing = false;
// if (compSampGt.isHet() != evalSampGt.isHet() || compSampGt.isHom() != evalSampGt.isHom())
// breakPhasing = true; // since they are not both het or both hom
// else { // both are het, or both are hom:
// boolean topMatchesTopAndBottomMatchesBottom = (topMatchesTop(compAllelePair, evalAllelePair) && bottomMatchesBottom(compAllelePair, evalAllelePair));
// boolean topMatchesBottomAndBottomMatchesTop = (topMatchesBottom(compAllelePair, evalAllelePair) && bottomMatchesTop(compAllelePair, evalAllelePair));
// if (!topMatchesTopAndBottomMatchesBottom && !topMatchesBottomAndBottomMatchesTop)
// breakPhasing = true; // since the 2 VCFs have different diploid genotypes for this sample
// }
//
// if (breakPhasing) {
// samplePrevGenotypes.put(samp, null); // nothing to do for this site, AND must remove any history for the future
// }
// else if (compSampGt.isHet() && evalSampGt.isHet()) {
// /* comp and eval have the HET same Genotype at this site:
// [Note that if both are hom, then nothing is done here, but the het history IS preserved].
// */
// CompEvalGenotypes prevCompAndEval = samplePrevGenotypes.get(samp);
// if (prevCompAndEval != null && !prevCompAndEval.getLocus().onSameContig(curLocus)) // exclude curLocus if it is "phased" relative to a different chromosome
// prevCompAndEval = null;
//
// // Replace the previous hets with the current hets:
// samplePrevGenotypes.put(samp, curLocus, compSampGt, evalSampGt);
//
// if (prevCompAndEval != null) {
// GenomeLoc prevLocus = prevCompAndEval.getLocus();
// logger.debug("Potentially phaseable het locus: " + curLocus + " [relative to previous het locus: " + prevLocus + "]");
// PhaseStats ps = samplePhasingStatistics.ensureSampleStats(samp);
//
// boolean compSampIsPhased = genotypesArePhasedAboveThreshold(compSampGt);
// boolean evalSampIsPhased = genotypesArePhasedAboveThreshold(evalSampGt);
// if (compSampIsPhased || evalSampIsPhased) {
// if (!evalSampIsPhased) {
// ps.onlyCompPhased++;
// //interesting.addReason("ONLY_COMP", samp, group, prevLocus, "");
// }
// else if (!compSampIsPhased) {
// ps.onlyEvalPhased++;
// //interesting.addReason("ONLY_EVAL", samp, group, prevLocus, "");
// }
// else { // both comp and eval are phased:
// AllelePair prevCompAllelePair = new AllelePair(prevCompAndEval.getCompGenotpye());
// AllelePair prevEvalAllelePair = new AllelePair(prevCompAndEval.getEvalGenotype());
//
// // Sufficient to check only the top of comp, since we ensured that comp and eval have the same diploid genotypes for this sample:
// boolean topsMatch = (topMatchesTop(prevCompAllelePair, prevEvalAllelePair) && topMatchesTop(compAllelePair, evalAllelePair));
// boolean topMatchesBottom = (topMatchesBottom(prevCompAllelePair, prevEvalAllelePair) && topMatchesBottom(compAllelePair, evalAllelePair));
//
// if (topsMatch || topMatchesBottom) {
// ps.phasesAgree++;
//
// Double compPQ = getPQ(compSampGt);
// Double evalPQ = getPQ(evalSampGt);
// if (compPQ != null && evalPQ != null && MathUtils.compareDoubles(compPQ, evalPQ) != 0) {
// //interesting.addReason("PQ_CHANGE", samp, group, prevLocus, compPQ + " -> " + evalPQ);
// }
// }
// else {
// ps.phasesDisagree++;
// logger.debug("SWITCHED locus: " + curLocus);
// //interesting.addReason("SWITCH", samp, group, prevLocus, toString(prevCompAllelePair, compAllelePair) + " -> " + toString(prevEvalAllelePair, evalAllelePair));
// }
// }
// }
// else {
// ps.neitherPhased++;
// }
// }
// }
// }
// }
// logger.debug("\n" + samplePhasingStatistics + "\n");
//
// return interesting.toString();
// }
//
// public static boolean isRelevantToPhasing(VariantContext vc) {
// return (vc != null && !vc.isFiltered());
// }
//
// public boolean isNonNullButUnphased(Genotype gt) {
// return (gt != null && !gt.isNoCall() && !genotypesArePhasedAboveThreshold(gt));
// }
//
// public boolean genotypesArePhasedAboveThreshold(Genotype gt) {
// if (gt.isHom()) // Can always consider a hom site to be phased to its predecessor, since its successor will only be phased to it if it's hom or "truly" phased
// return true;
//
// if (!gt.isPhased())
// return false;
//
// Double pq = getPQ(gt);
// return (pq == null || pq >= minPhaseQuality);
// }
//
// public static Double getPQ(Genotype gt) {
// Double d = gt.getAttributeAsDouble(ReadBackedPhasingWalker.PQ_KEY, -1);
// return d == -1 ? null : d;
// }
//
// public static boolean topMatchesTop(AllelePair b1, AllelePair b2) {
// return b1.getTopAllele().equals(b2.getTopAllele());
// }
//
// public static boolean topMatchesBottom(AllelePair b1, AllelePair b2) {
// return b1.getTopAllele().equals(b2.getBottomAllele());
// }
//
// public static boolean bottomMatchesTop(AllelePair b1, AllelePair b2) {
// return topMatchesBottom(b2, b1);
// }
//
// public static boolean bottomMatchesBottom(AllelePair b1, AllelePair b2) {
// return b1.getBottomAllele().equals(b2.getBottomAllele());
// }
//
// public String toString(AllelePair prev, AllelePair cur) {
// return prev.getTopAllele().getBaseString() + "+" + cur.getTopAllele().getBaseString() + "|" + prev.getBottomAllele().getBaseString() + "+" + cur.getBottomAllele().getBaseString();
// }
//
// public void finalizeEvaluation() {
// }
//
// private static class Reasons {
// private StringBuilder sb;
//
// public Reasons() {
// sb = new StringBuilder();
// }
//
//// public void addReason(String category, String sample, VariantEvalWalker.EvaluationContext evalGroup, GenomeLoc prevLoc, String reason) {
//// sb.append(category + "(" + sample + ", previous: " + prevLoc + " [" + evalGroup.compTrackName + ", " + evalGroup.evalTrackName + "]): " + reason + ";");
//// }
//
// public String toString() {
// if (sb.length() == 0)
// return null;
//
// return "reasons=" + sb.toString();
// }
// }
//}
//
//class CompEvalGenotypes {
// private GenomeLoc loc;
// private Genotype compGt;
// private Genotype evalGt;
//
// public CompEvalGenotypes(GenomeLoc loc, Genotype compGt, Genotype evalGt) {
// this.loc = loc;
// this.compGt = compGt;
// this.evalGt = evalGt;
// }
//
// public GenomeLoc getLocus() {
// return loc;
// }
//
// public Genotype getCompGenotpye() {
// return compGt;
// }
// public Genotype getEvalGenotype() {
// return evalGt;
// }
//}
//
//class SamplePreviousGenotypes {
// private HashMap<String, CompEvalGenotypes> sampleGenotypes = null;
//
// public SamplePreviousGenotypes() {
// this.sampleGenotypes = new HashMap<String, CompEvalGenotypes>();
// }
//
// public CompEvalGenotypes get(String sample) {
// return sampleGenotypes.get(sample);
// }
//
// public void put(String sample, CompEvalGenotypes compEvalGts) {
// sampleGenotypes.put(sample, compEvalGts);
// }
//
// public void put(String sample, GenomeLoc locus, Genotype compGt, Genotype evalGt) {
// sampleGenotypes.put(sample, new CompEvalGenotypes(locus, compGt, evalGt));
// }
//}
//
//class PhaseStats {
// public int neitherPhased;
// public int onlyCompPhased;
// public int onlyEvalPhased;
// public int phasesAgree;
// public int phasesDisagree;
//
// public PhaseStats() {
// this.neitherPhased = 0;
// this.onlyCompPhased = 0;
// this.onlyEvalPhased = 0;
// this.phasesAgree = 0;
// this.phasesDisagree = 0;
// }
//
// public String toString() {
// StringBuilder sb = new StringBuilder();
// sb.append("Neither phased: " + neitherPhased + "\tOnly Comp: " + onlyCompPhased + "\tOnly Eval: " + onlyEvalPhased + "\tSame phase: " + phasesAgree + "\tOpposite phase: " + phasesDisagree);
// return sb.toString();
// }
//
// public static String[] getFieldNamesArray() {
// return new String[]{"total", "neither", "only_comp", "only_eval", "both", "match", "switch", "switch_rate"};
// }
//
// public Object getField(int index) {
// switch (index) {
// case (0):
// return (neitherPhased + onlyCompPhased + onlyEvalPhased + phasesAgree + phasesDisagree);
// case (1):
// return neitherPhased;
// case (2):
// return onlyCompPhased;
// case (3):
// return onlyEvalPhased;
// case (4):
// return (phasesAgree + phasesDisagree);
// case (5):
// return phasesAgree;
// case (6):
// return phasesDisagree;
// case (7):
// return ((phasesDisagree == 0) ? 0 : ((double) phasesDisagree) / (phasesAgree + phasesDisagree));
// default:
// return -1;
// }
// }
//}
//

89
protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/genotypePhasingEvaluator/SamplePhasingStatistics.java
View File

@ -1,89 +0,0 @@
///*
// * Copyright (c) 2012, 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.varianteval.evaluators.genotypePhasingEvaluator;
//
//import org.broadinstitute.sting.gatk.walkers.varianteval.util.TableType;
//
//import java.util.HashMap;
//import java.util.Map;
//
///**
// * a table of sample names to genotype phasing statistics
// */
//class SamplePhasingStatistics extends TableType {
// private HashMap<String, PhaseStats> sampleStats = null;
// private double minPhaseQuality;
//
// public SamplePhasingStatistics(double minPhaseQuality) {
// this.sampleStats = new HashMap<String, PhaseStats>();
// this.minPhaseQuality = minPhaseQuality;
// }
//
// public PhaseStats ensureSampleStats(String samp) {
// PhaseStats ps = sampleStats.get(samp);
// if (ps == null) {
// ps = new PhaseStats();
// sampleStats.put(samp, ps);
// }
// return ps;
// }
//
// /**
// * @return one row per sample
// */
// public String[] getRowKeys() {
// return sampleStats.keySet().toArray(new String[sampleStats.size()]);
// }
//
// /**
// * get the column keys
// *
// * @return a list of objects, in this case strings, that are the column names
// */
// public String[] getColumnKeys() {
// return PhaseStats.getFieldNamesArray();
// }
//
// public Object getCell(int x, int y) {
// String[] rowKeys = getRowKeys();
// PhaseStats ps = sampleStats.get(rowKeys[x]);
// return ps.getField(y);
// }
//
// public String getName() {
// return "Sample Phasing Statistics (for PQ >= " + minPhaseQuality + ")";
// }
//
// public String toString() {
// StringBuilder sb = new StringBuilder();
// for (Map.Entry<String, PhaseStats> sampPhaseStatsEnt : sampleStats.entrySet()) {
// String sample = sampPhaseStatsEnt.getKey();
// PhaseStats ps = sampPhaseStatsEnt.getValue();
//
// sb.append(sample + "\t" + ps);
// }
// return sb.toString();
// }
//}