Significant output formatting improvements. SNPs as indels analysis. heterozygosity rate calculations
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1478 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
depristo
parent
bde67428fd
commit
6ab9ddf9f5
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@ -20,14 +20,16 @@ import java.util.ArrayList;
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*/
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public abstract class BasicVariantAnalysis implements VariantAnalysis {
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protected String name;
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protected PrintStream out;
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protected VariantEvalWalker master;
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protected PrintStream out, callOut;
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private VariantEvalWalker master;
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protected String filename;
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public BasicVariantAnalysis(String name) {
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this.name = name;
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}
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public VariantEvalWalker getMaster() { return master; }
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public String getName() {
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return name;
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}
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@ -36,9 +38,10 @@ public abstract class BasicVariantAnalysis implements VariantAnalysis {
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return new ArrayList<String>();
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}
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public void initialize(VariantEvalWalker master, PrintStream out, String filename) {
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public void initialize(VariantEvalWalker master, PrintStream out, PrintStream callOut, String filename) {
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this.master = master;
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this.out = out;
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this.callOut = callOut;
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this.filename = filename;
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}
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@ -47,7 +50,7 @@ public abstract class BasicVariantAnalysis implements VariantAnalysis {
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}
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public PrintStream getCallPrintStream() {
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return out;
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return callOut;
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}
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public List<String> done() {
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@ -22,6 +22,7 @@ import java.util.HashSet;
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*/
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public class ClusterCounterAnalysis extends BasicVariantAnalysis implements GenotypeAnalysis, PopulationAnalysis {
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ArrayList<HashSet<GenomeLoc>> variantsWithClusters;
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int minDistanceForFlagging = 5;
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int[] neighborWiseBoundries = {1, 2, 5, 10, 20, 50, 100};
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AllelicVariant lastVariant = null;
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GenomeLoc lastVariantInterval = null;
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@ -60,7 +61,7 @@ public class ClusterCounterAnalysis extends BasicVariantAnalysis implements Geno
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variantsWithClusters.get(i).add(eL);
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}
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}
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r = String.format("snp_within_cluster %d %s %s %s", d, eL, lvL, s.toString());
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r = d <= minDistanceForFlagging ? String.format("snp_within_cluster %d %s %s %s", d, eL, lvL, s.toString()) : null;
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}
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}
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}
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@ -22,7 +22,7 @@ import cern.jet.math.Arithmetic;
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* the Broad Institute nor MIT can be responsible for its use, misuse, or functionality.
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*
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*/
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public class HardyWeinbergEquilibrium extends ViolationVariantAnalysis implements PopulationAnalysis {
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public class HardyWeinbergEquilibrium extends BasicVariantAnalysis implements PopulationAnalysis {
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private double threshold;
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int nSites = 0;
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int nViolations = 0;
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@ -21,8 +21,9 @@ import java.io.PrintStream;
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* the Broad Institute nor MIT can be responsible for its use, misuse, or functionality.
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*
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*/
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public class NeighborDistanceAnalysis extends ViolationVariantAnalysis implements GenotypeAnalysis, PopulationAnalysis {
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public class NeighborDistanceAnalysis extends BasicVariantAnalysis implements GenotypeAnalysis, PopulationAnalysis {
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ArrayList<Long> neighborWiseDistances;
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int minDistanceForFlagging = 5;
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int[] neighborWiseBoundries = {1, 2, 5, 10, 20, 50, 100, 1000, 10000};
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AllelicVariant lastVariant = null;
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@ -51,7 +52,7 @@ public class NeighborDistanceAnalysis extends ViolationVariantAnalysis implement
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//out.printf("# Excluding %d %s %s vs. %s %s%n", d, eL, interval, lvL, lastVariantInterval);
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} else {
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neighborWiseDistances.add(d);
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r = String.format("neighbor-distance %d %s %s", d, eL, lvL);
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r = d <= minDistanceForFlagging ? String.format("neighbor-distance %d %s %s", d, eL, lvL) : null;
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}
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}
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}
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@ -22,7 +22,7 @@ public interface VariantAnalysis {
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public PrintStream getSummaryPrintStream();
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public PrintStream getCallPrintStream();
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public List<String> getParams();
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public void initialize(VariantEvalWalker master, PrintStream out, String filename);
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public void initialize(VariantEvalWalker master, PrintStream out, PrintStream callOut, String filename);
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public String update(AllelicVariant eval, RefMetaDataTracker tracker, char ref, AlignmentContext context);
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public void finalize(long nSites);
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public List<String> done();
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@ -3,6 +3,7 @@ package org.broadinstitute.sting.playground.gatk.walkers.varianteval;
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import org.broadinstitute.sting.gatk.refdata.AllelicVariant;
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import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
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import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
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import org.broadinstitute.sting.utils.GenotypeUtils;
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import java.util.List;
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import java.util.ArrayList;
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@ -20,6 +21,7 @@ import java.util.ArrayList;
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public class VariantCounter extends BasicVariantAnalysis implements GenotypeAnalysis, PopulationAnalysis {
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long nBasesCovered = 0;
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int nSNPs = 0;
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int nHets = 0;
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public VariantCounter() {
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super("variant_counts");
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@ -27,6 +29,10 @@ public class VariantCounter extends BasicVariantAnalysis implements GenotypeAnal
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public String update(AllelicVariant eval, RefMetaDataTracker tracker, char ref, AlignmentContext context) {
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nSNPs += eval == null ? 0 : 1;
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if ( this.getMaster().evalContainsGenotypes && eval != null && eval.isSNP() && GenotypeUtils.isHet(eval) )
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nHets++;
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return null;
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}
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@ -38,12 +44,31 @@ public class VariantCounter extends BasicVariantAnalysis implements GenotypeAnal
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nBasesCovered = nSites;
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}
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private double variantRate(int n) {
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return n / (1.0 * Math.max(nBasesCovered, 1));
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}
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private long variantRateInverse(int n) {
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return nBasesCovered / Math.max(n, 1);
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}
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public List<String> done() {
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List<String> s = new ArrayList<String>();
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s.add(String.format("n bases covered: %d", nBasesCovered));
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s.add(String.format("sites: %d", nSNPs));
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s.add(String.format("variant rate: %.5f confident variants per base", nSNPs / (1.0 * Math.max(nBasesCovered, 1))));
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s.add(String.format("variant rate: 1 / %d confident variants per base", nBasesCovered / Math.max(nSNPs, 1)));
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s.add(String.format("n bases covered %d", nBasesCovered));
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s.add(String.format("variants %d", nSNPs));
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s.add(String.format("variant rate %.5f confident variants per base", variantRate(nSNPs)));
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s.add(String.format("variant rate 1 / %d confident variants per base [human single sample genome-wide expectation is ~1 / 666]", variantRateInverse(nSNPs)));
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if ( this.getMaster().evalContainsGenotypes ) {
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s.add(String.format("heterozygotes %d", nHets));
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s.add(String.format("homozygotes %d", nSNPs - nHets));
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s.add(String.format("heterozygosity %.5f confident hets per base", variantRate(nHets)));
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s.add(String.format("heterozygosity 1 / %d confident hets per base [human single sample expectation is ~1 / 1000]", variantRateInverse(nHets)));
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s.add(String.format("het to hom ratio %.2f confident hets per confident homozygote non-refs [human single sample genome-wide expectation is 2:1]",
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((double)nHets) / (Math.max(nSNPs - nHets, 1))));
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}
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return s;
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}
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}
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@ -19,10 +19,12 @@ import java.util.ArrayList;
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*/
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public class VariantDBCoverage extends BasicVariantAnalysis implements GenotypeAnalysis, PopulationAnalysis {
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private String dbName;
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private int nDBObs = 0;
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private int nDBSNPs = 0;
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private int nDBIndels = 0;
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private int nEvalObs = 0;
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private int nOverlapping = 0;
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private int nConcordant = 0;
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private int nSNPsCalledAtIndels = 0;
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public VariantDBCoverage(final String name) {
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super("db_coverage");
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@ -33,33 +35,38 @@ public class VariantDBCoverage extends BasicVariantAnalysis implements GenotypeA
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boolean inDB = dbSNP != null;
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boolean inEval = eval != null;
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if (inDB) nDBObs++;
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if (inDB ) {
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if ( dbSNP.isSNP() ) nDBSNPs++;
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if ( dbSNP.isIndel() ) nDBIndels++;
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//System.out.printf("snp=%b ins=%b del=%b indel=%b %s%n", dbSNP.isSNP(), dbSNP.isInsertion(), dbSNP.isDeletion(), dbSNP.isIndel(), dbSNP);
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}
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if (inEval) nEvalObs++;
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if (inDB && inEval) {
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nOverlapping++;
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if ( dbSNP.isSNP() ) { // changes the calculation a bit
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nOverlapping++;
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if ( ! discordantP(dbSNP, eval) )
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nConcordant++;
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if ( ! discordantP(dbSNP, eval) )
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nConcordant++;
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}
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if ( dbSNP.isIndel() && eval.isSNP() )
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nSNPsCalledAtIndels++;
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}
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}
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public int nDBSites() { return nDBObs; }
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public int nDBSNPs() { return nDBSNPs; }
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public int nDBIndels() { return nDBIndels; }
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public int nEvalSites() { return nEvalObs; }
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public int nOverlappingSites() { return nOverlapping; }
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public int nConcordant() { return nConcordant; }
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public int nNovelSites() { return Math.abs(nEvalSites() - nOverlappingSites()); }
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public int nSNPsAtIndels() { return nSNPsCalledAtIndels; }
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public boolean discordantP(AllelicVariant dbSNP, AllelicVariant eval) {
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if (dbSNP != null && dbSNP.isSNP() && eval != null ) {
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boolean concordant = dbSNP.getAltSnpFWD() == eval.getAltSnpFWD() || dbSNP.getRefSnpFWD() == eval.getAltSnpFWD();
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//System.out.printf("dbSNP=%s | %c, eval=%s | %c, concordant=%b %s %s%n",
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// dbSNP.getGenotype().get(0), dbSNP.getAltSnpFWD(),
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// eval.getGenotype().get(0), eval.getAltSnpFWD(),
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// concordant,
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// dbSNP, eval);
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return ! concordant;
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return ! (dbSNP.getAltSnpFWD() == eval.getAltSnpFWD() || dbSNP.getRefSnpFWD() == eval.getAltSnpFWD());
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} else {
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return false;
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}
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@ -83,8 +90,20 @@ public class VariantDBCoverage extends BasicVariantAnalysis implements GenotypeA
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// There are four cases here:
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AllelicVariant dbsnp = (AllelicVariant)tracker.lookup(dbName, null);
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boolean isSNP = dbsnp != null && dbsnp.isSNP();
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inc(isSNP ? dbsnp : null, eval);
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return ! isSNP && eval != null ? "Novel " + eval : (discordantP(dbsnp, eval) ? (String.format("Discordant DBSNP=%s %s", dbsnp.getGenotype().get(0), eval)) : null);
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inc(dbsnp, eval);
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if ( dbsnp != null && eval != null ) {
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if ( dbsnp.isSNP() && eval.isSNP() && discordantP(dbsnp, eval) ) {
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return String.format("Discordant [DBSNP %s] [EVAL %s]", dbsnp, eval);
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} else if ( dbsnp.isIndel() && eval.isSNP() ) {
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return String.format("SNP-at-indel DBSNP=%s %s", dbsnp.getGenotype().get(0), eval);
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} else {
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return null;
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// return "Novel " + eval;
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}
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} else {
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return null;
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}
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}
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/**
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@ -93,21 +112,30 @@ public class VariantDBCoverage extends BasicVariantAnalysis implements GenotypeA
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* @return
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*/
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public double fractionDBSitesDiscoveredInEval() {
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return nOverlappingSites() / (1.0 * nDBSites());
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return nOverlappingSites() / (1.0 * nDBSNPs());
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}
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public List<String> done() {
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List<String> s = new ArrayList<String>();
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s.add(String.format("%d\t%d\t%d\t%.2f\t%.2f", nDBSites(), nEvalSites(), nOverlappingSites(), fractionEvalSitesCoveredByDB(), fractionDBSitesDiscoveredInEval()));
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s.add(String.format("name %s", dbName));
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s.add(String.format("n_db_sites %d", nDBSites()));
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s.add(String.format("n_eval_sites %d", nEvalSites()));
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s.add(String.format("n_overlapping_sites %d", nOverlappingSites()));
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s.add(String.format("n_concordant %d", nConcordant()));
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s.add(String.format("n_novel_sites %d", nNovelSites()));
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s.add(String.format("per_eval_sites_in_db %.2f", 100*fractionEvalSitesCoveredByDB()));
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s.add(String.format("concordance_rate %.2f", 100*concordanceRate()));
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s.add(String.format("per_db_sites_in_eval %.2f", 100*fractionDBSitesDiscoveredInEval()));
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//s.add(String.format("%d\t%d\t%d\t%.2f\t%.2f", nDBSNPs(), nEvalSites(), nOverlappingSites(), fractionEvalSitesCoveredByDB(), fractionDBSitesDiscoveredInEval()));
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s.add(String.format("name %s", dbName));
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s.add(String.format("n_db_sites %d", nDBSNPs() + nDBIndels()));
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s.add(String.format("n_db_snps %d", nDBSNPs()));
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s.add(String.format("n_db_indels %d", nDBIndels()));
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s.add(String.format("n_eval_sites %d", nEvalSites()));
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s.add(String.format("n_overlapping_sites %d", nOverlappingSites()));
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s.add(String.format("n_concordant %d", nConcordant()));
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s.add(String.format("n_novel_sites %d", nNovelSites()));
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s.add(String.format("percent_eval_sites_in_db %.2f", 100*fractionEvalSitesCoveredByDB()));
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s.add(String.format("concordance_rate %.2f", 100*concordanceRate()));
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s.add(String.format("percent_db_sites_in_eval %.2f", 100*fractionDBSitesDiscoveredInEval()));
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s.add(String.format("n_snp_calls_at_indels %d", nSNPsAtIndels()));
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s.add(String.format("percent_calls_at_indels %.2f", nSNPsAtIndels() / (0.01 * nEvalSites())));
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return s;
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}
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}
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@ -5,6 +5,7 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
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import org.broadinstitute.sting.gatk.refdata.AllelicVariant;
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import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
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import org.broadinstitute.sting.gatk.refdata.SNPCallFromGenotypes;
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import org.broadinstitute.sting.gatk.refdata.IntervalRod;
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import org.broadinstitute.sting.gatk.walkers.*;
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import org.broadinstitute.sting.utils.StingException;
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import org.broadinstitute.sting.utils.Utils;
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@ -27,8 +28,8 @@ import java.util.*;
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*
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*/
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@By(DataSource.REFERENCE)
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@Requires(DataSource.REFERENCE)
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@Allows(DataSource.REFERENCE)
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@Requires(value={DataSource.REFERENCE},referenceMetaData={@RMD(name="eval",type=AllelicVariant.class)})
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@Allows(value={DataSource.REFERENCE},referenceMetaData = {@RMD(name="eval",type=AllelicVariant.class), @RMD(name="dbsnp",type=AllelicVariant.class),@RMD(name="hapmap-chip",type=AllelicVariant.class), @RMD(name="interval",type=IntervalRod.class)})
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public class VariantEvalWalker extends RefWalker<Integer, Integer> {
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@Argument(shortName="minConfidenceScore", doc="Minimum confidence score to consider an evaluation SNP a variant", required=false)
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public int minConfidenceScore = -1;
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@ -39,18 +40,27 @@ public class VariantEvalWalker extends RefWalker<Integer, Integer> {
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@Argument(shortName="badHWEThreshold", doc="XXX", required=false)
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public double badHWEThreshold = 1e-3;
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@Argument(shortName="evalContainsGenotypes", doc="If true, the input list of variants will be treated as a genotyping file, containing assertions of actual genotype values for a particular person. Analyses that only make sense on at the population level will be disabled, while those operating on genotypes will be enabled", required=false)
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@Argument(fullName="evalContainsGenotypes", shortName = "G", doc="If true, the input list of variants will be treated as a genotyping file, containing assertions of actual genotype values for a particular person. Analyses that only make sense on at the population level will be disabled, while those operating on genotypes will be enabled", required=false)
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public boolean evalContainsGenotypes = false;
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String analysisFilenameBase = null;
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@Argument(fullName="explode", shortName = "E", doc="Old style formatting, with each analysis split into separate files.", required=false)
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public boolean explode = false;
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String COMMENT_STRING = "";
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@Argument(fullName="includeViolations", shortName = "V", doc="If provided, violations will be written out along with summary information", required=false)
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public boolean includeViolations = false;
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@Argument(fullName="extensiveSubsets", shortName = "A", doc="If provided, output will be calculated over a lot of subsets, by default we only operate over all variants", required=false)
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public boolean extensiveSubsets = false;
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String analysisFilenameBase = null;
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final String knownSNPDBName = "dbSNP";
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final String genotypeChipName = "hapmap-chip";
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HashMap<String, ArrayList<VariantAnalysis>> analysisSets;
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PrintStream perLocusStream = null;
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long nSites = 0;
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final String ALL_SNPS = "all";
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@ -60,10 +70,13 @@ public class VariantEvalWalker extends RefWalker<Integer, Integer> {
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final String NOVEL_SNPS = "novel";
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final String[] POPULATION_ANALYSIS_NAMES = { ALL_SNPS, SINGLETON_SNPS, TWOHIT_SNPS, KNOWN_SNPS, NOVEL_SNPS };
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final String[] GENOTYPE_ANALYSIS_NAMES = { ALL_SNPS, KNOWN_SNPS, NOVEL_SNPS };
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final String[] SIMPLE_ANALYSIS_NAMES = { ALL_SNPS };
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String[] ALL_ANALYSIS_NAMES = null;
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public void initialize() {
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ALL_ANALYSIS_NAMES = evalContainsGenotypes ? GENOTYPE_ANALYSIS_NAMES : POPULATION_ANALYSIS_NAMES;
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ALL_ANALYSIS_NAMES = SIMPLE_ANALYSIS_NAMES;
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if ( extensiveSubsets )
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ALL_ANALYSIS_NAMES = evalContainsGenotypes ? GENOTYPE_ANALYSIS_NAMES : POPULATION_ANALYSIS_NAMES;
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// setup the path to the analysis
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if ( this.getToolkit().getArguments().outFileName != null ) {
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@ -77,7 +90,7 @@ public class VariantEvalWalker extends RefWalker<Integer, Integer> {
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}
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private ArrayList<VariantAnalysis> getAnalysisSet(final String name) {
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return analysisSets.get(name);
|
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return analysisSets.containsKey(name) ? analysisSets.get(name) : null;
|
||||
}
|
||||
|
||||
private ArrayList<VariantAnalysis> initializeAnalysisSet(final String setName) {
|
||||
|
|
@ -137,12 +150,20 @@ public class VariantEvalWalker extends RefWalker<Integer, Integer> {
|
|||
|
||||
public void initializeAnalysisOutputStream(final String setName, VariantAnalysis analysis) {
|
||||
final String filename = getAnalysisFilename(setName + "." + analysis.getName(), analysis.getParams());
|
||||
if ( filename == null )
|
||||
analysis.initialize(this, out, filename);
|
||||
|
||||
try {
|
||||
if ( perLocusStream == null )
|
||||
perLocusStream = filename == null ? out : new PrintStream(new File(analysisFilenameBase + "interesting_sites"));
|
||||
} catch (FileNotFoundException e) {
|
||||
throw new RuntimeException(e);
|
||||
}
|
||||
|
||||
if ( filename == null || ! explode )
|
||||
analysis.initialize(this, out, perLocusStream, filename);
|
||||
else {
|
||||
File file = new File(filename);
|
||||
try {
|
||||
analysis.initialize(this, new PrintStream(new FileOutputStream(file)), filename);
|
||||
analysis.initialize(this, new PrintStream(new FileOutputStream(file)), perLocusStream, filename);
|
||||
} catch (FileNotFoundException e) {
|
||||
throw new StingException("Couldn't open analysis output file " + filename, e);
|
||||
}
|
||||
|
|
@ -191,9 +212,13 @@ public class VariantEvalWalker extends RefWalker<Integer, Integer> {
|
|||
public void updateAnalysisSet(final String analysisSetName, AllelicVariant eval,
|
||||
RefMetaDataTracker tracker, char ref, AlignmentContext context) {
|
||||
// Iterate over each analysis, and update it
|
||||
for ( VariantAnalysis analysis : getAnalysisSet(analysisSetName) ) {
|
||||
String s = analysis.update(eval, tracker, ref, context);
|
||||
if ( s != null ) analysis.getCallPrintStream().println(s);
|
||||
if ( getAnalysisSet(analysisSetName) != null ) {
|
||||
for ( VariantAnalysis analysis : getAnalysisSet(analysisSetName) ) {
|
||||
String s = analysis.update(eval, tracker, ref, context);
|
||||
if ( s != null && includeViolations ) {
|
||||
analysis.getCallPrintStream().println(getLineHeader(analysisSetName, "flagged", analysis.getName()) + s);
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
|
|
@ -212,20 +237,26 @@ public class VariantEvalWalker extends RefWalker<Integer, Integer> {
|
|||
}
|
||||
}
|
||||
|
||||
private String getLineHeader( final String analysisSetName, final String keyword, final String analysis) {
|
||||
String s = Utils.join(",", Arrays.asList(analysisSetName, keyword, analysis));
|
||||
return s + Utils.dupString(' ', 50 - s.length());
|
||||
}
|
||||
|
||||
private void printAnalysisSet( final String analysisSetName ) {
|
||||
out.printf("Writing analysis set %s", analysisSetName);
|
||||
//out.printf("Writing analysis set %s", analysisSetName);
|
||||
Date now = new Date();
|
||||
for ( VariantAnalysis analysis : getAnalysisSet(analysisSetName) ) {
|
||||
String header = getLineHeader(analysisSetName, "summary", analysis.getName());
|
||||
analysis.finalize(nSites);
|
||||
PrintStream stream = analysis.getSummaryPrintStream();
|
||||
stream.printf("%s%s%n", COMMENT_STRING, Utils.dupString('-', 78));
|
||||
stream.printf("%sAnalysis set %s%n", COMMENT_STRING, analysisSetName);
|
||||
stream.printf("%sAnalysis name %s%n", COMMENT_STRING, analysis.getName());
|
||||
stream.printf("%sAnalysis params %s%n", COMMENT_STRING, Utils.join(" ", analysis.getParams()));
|
||||
stream.printf("%sAnalysis class %s%n", COMMENT_STRING, analysis );
|
||||
stream.printf("%sAnalysis time %s%n", COMMENT_STRING, now );
|
||||
stream.printf("%s%s%n", header, Utils.dupString('-', 78));
|
||||
//stream.printf("%s Analysis set %s%n", analysisSetName, , analysisSetName);
|
||||
stream.printf("%sAnalysis name %s%n", header, analysis.getName());
|
||||
stream.printf("%sAnalysis params %s%n", header, Utils.join(" ", analysis.getParams()));
|
||||
stream.printf("%sAnalysis class %s%n", header, analysis);
|
||||
stream.printf("%sAnalysis time %s%n", header, now);
|
||||
for ( String line : analysis.done()) {
|
||||
stream.printf("%s%s%n", COMMENT_STRING, line);
|
||||
stream.printf("%s%s%n", header, line);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
|
|
|||
|
|
@ -1,62 +0,0 @@
|
|||
/*
|
||||
* Copyright (c) 2009 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.playground.gatk.walkers.varianteval;
|
||||
|
||||
import java.io.PrintStream;
|
||||
import java.io.File;
|
||||
import java.io.FileNotFoundException;
|
||||
|
||||
/**
|
||||
* The Broad Institute
|
||||
* SOFTWARE COPYRIGHT NOTICE AGREEMENT
|
||||
* This software and its documentation are copyright 2009 by the
|
||||
* Broad Institute/Massachusetts Institute of Technology. All rights are reserved.
|
||||
*
|
||||
* This software is supplied without any warranty or guaranteed support whatsoever. Neither
|
||||
* the Broad Institute nor MIT can be responsible for its use, misuse, or functionality.
|
||||
*
|
||||
*/
|
||||
public abstract class ViolationVariantAnalysis extends BasicVariantAnalysis {
|
||||
PrintStream violationsOut = null;
|
||||
|
||||
public ViolationVariantAnalysis(final String name) {
|
||||
super(name);
|
||||
}
|
||||
|
||||
public void initialize(VariantEvalWalker master, PrintStream out, String filename) {
|
||||
super.initialize(master, out, filename);
|
||||
|
||||
try {
|
||||
violationsOut = filename == null ? out : new PrintStream(new File(filename + ".violations"));
|
||||
} catch (FileNotFoundException e) {
|
||||
throw new RuntimeException(e);
|
||||
}
|
||||
}
|
||||
|
||||
public PrintStream getCallPrintStream() {
|
||||
return violationsOut;
|
||||
}
|
||||
}
|
||||
Loading…
Reference in New Issue