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Several cleanups to IndelMetricsByAC: 

- No longer a standard eval module to keep integration tests happy
- Remove class name overlaps with SimpleMetricsByAC so that modules don't overwrite each other's files, and to make it easier to grep results.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4978 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
delangel 2011-01-12 18:35:24 +00:00
parent 8fe5641b2e
commit 8a6b126ea8
1 changed files with 11 additions and 12 deletions
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23
java/src/org/broadinstitute/sting/gatk/walkers/varianteval/IndelMetricsByAC.java
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@ -3,7 +3,6 @@ package org.broadinstitute.sting.gatk.walkers.varianteval;
import org.broad.tribble.util.variantcontext.VariantContext; import org.broad.tribble.util.variantcontext.VariantContext;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.utils.report.tags.Analysis; import org.broadinstitute.sting.utils.report.tags.Analysis;
import org.broadinstitute.sting.utils.report.tags.DataPoint; import org.broadinstitute.sting.utils.report.tags.DataPoint;
@ -43,10 +42,10 @@ import java.util.ArrayList;
*/ */
@Analysis(name = "Indel Metrics by allele count", description = "Shows various stats binned by allele count") @Analysis(name = "Indel Metrics by allele count", description = "Shows various stats binned by allele count")
public class IndelMetricsByAC extends VariantEvaluator implements StandardEval { public class IndelMetricsByAC extends VariantEvaluator {
// a mapping from quality score histogram bin to Ti/Tv ratio // a mapping from quality score histogram bin to Ti/Tv ratio
@DataPoint(name="Indel Metrics by AC", description = "Indel Metrics by allele count") @DataPoint(name="Indel Metrics by AC", description = "Indel Metrics by allele count")
MetricsByAc metrics = null; IndelMetricsByAc metrics = null;
//@DataPoint(name="Quality by Allele Count", description = "average variant quality for each allele count") //@DataPoint(name="Quality by Allele Count", description = "average variant quality for each allele count")
//AlleleCountStats alleleCountStats = null; //AlleleCountStats alleleCountStats = null;
@ -74,11 +73,11 @@ public class IndelMetricsByAC extends VariantEvaluator implements StandardEval {
METRIC_COLUMNS[k] = "indel_size_len"+Integer.valueOf(index2len(k)); METRIC_COLUMNS[k] = "indel_size_len"+Integer.valueOf(index2len(k));
} }
class MetricsAtAC { class IndelMetricsAtAC {
public int ac = -1, nIns =0, nDel = 0, nComplex = 0, nLong; public int ac = -1, nIns =0, nDel = 0, nComplex = 0, nLong;
public int sizeCount[] = new int[2*INDEL_SIZE_LIMIT+1]; public int sizeCount[] = new int[2*INDEL_SIZE_LIMIT+1];
public MetricsAtAC(int ac) { this.ac = ac; } public IndelMetricsAtAC(int ac) { this.ac = ac; }
public void update(VariantContext eval) { public void update(VariantContext eval) {
int eventLength = 0; int eventLength = 0;
@ -120,15 +119,15 @@ public class IndelMetricsByAC extends VariantEvaluator implements StandardEval {
} }
} }
class MetricsByAc implements TableType { class IndelMetricsByAc implements TableType {
ArrayList<MetricsAtAC> metrics = new ArrayList<MetricsAtAC>(); ArrayList<IndelMetricsAtAC> metrics = new ArrayList<IndelMetricsAtAC>();
Object[] rows = null; Object[] rows = null;
public MetricsByAc( int nchromosomes ) { public IndelMetricsByAc( int nchromosomes ) {
rows = new Object[nchromosomes+1]; rows = new Object[nchromosomes+1];
metrics = new ArrayList<MetricsAtAC>(nchromosomes+1); metrics = new ArrayList<IndelMetricsAtAC>(nchromosomes+1);
for ( int i = 0; i < nchromosomes + 1; i++ ) { for ( int i = 0; i < nchromosomes + 1; i++ ) {
metrics.add(new MetricsAtAC(i)); metrics.add(new IndelMetricsAtAC(i));
rows[i] = "ac" + i; rows[i] = "ac" + i;
} }
} }
@ -142,7 +141,7 @@ public class IndelMetricsByAC extends VariantEvaluator implements StandardEval {
} }
public String getName() { public String getName() {
return "MetricsByAc"; return "IndelMetricsByAc";
} }
// //
@ -197,7 +196,7 @@ public class IndelMetricsByAC extends VariantEvaluator implements StandardEval {
if ( metrics == null ) { if ( metrics == null ) {
int nSamples = this.getVEWalker().getNSamplesForEval(eval); int nSamples = this.getVEWalker().getNSamplesForEval(eval);
if ( nSamples != -1 ) if ( nSamples != -1 )
metrics = new MetricsByAc(2 * nSamples); metrics = new IndelMetricsByAc(2 * nSamples);
} }
if ( eval.isIndel() && eval.isBiallelic() && if ( eval.isIndel() && eval.isBiallelic() &&