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actually checking in the first pass 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@795 348d0f76-0448-11de-a6fe-93d51630548a
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depristo 2009-05-22 17:13:27 +00:00
parent 8773b3a430
commit d9fc84f1e3
1 changed files with 85 additions and 0 deletions
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java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantEvalWalker.java 100755
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package org.broadinstitute.sting.playground.gatk.walkers.varianteval;
import org.broadinstitute.sting.gatk.walkers.*;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.refdata.rodDbSNP;
import org.broadinstitute.sting.gatk.refdata.AllelicVariant;
import org.broadinstitute.sting.gatk.LocusContext;
import org.broadinstitute.sting.utils.BaseUtils;
import java.util.EnumMap;
/**
* Created by IntelliJ IDEA.
* User: mdepristo
* Date: Feb 22, 2009
* Time: 2:52:28 PM
* To change this template use File | Settings | File Templates.
*/
@By(DataSource.REFERENCE)
@Requires(DataSource.REFERENCE)
@Allows(DataSource.REFERENCE)
public class VariantEvalWalker extends RefWalker<Integer, Integer> {
int N_TRANSITION_TRANVERSION_BINS = 100;
EnumMap<BaseUtils.BaseSubstitutionType, Integer> transition_transversion_counts[];
public void initialize() {
transition_transversion_counts = new EnumMap[N_TRANSITION_TRANVERSION_BINS];
for ( int i = 0; i < N_TRANSITION_TRANVERSION_BINS; i++ ) {
transition_transversion_counts[i] = new EnumMap<BaseUtils.BaseSubstitutionType, Integer>(BaseUtils.BaseSubstitutionType.class);
for ( BaseUtils.BaseSubstitutionType t : BaseUtils.BaseSubstitutionType.values() ) {
transition_transversion_counts[i].put(t, 0);
}
}
}
private int transition_transversion_bin(double MAF) {
return (int)Math.floor(MAF * N_TRANSITION_TRANVERSION_BINS);
}
private double transition_transversion_bin2MAF(int bin) {
return (bin + 0.5) / N_TRANSITION_TRANVERSION_BINS;
}
public Integer map(RefMetaDataTracker tracker, char ref, LocusContext context) {
AllelicVariant dbsnp = (AllelicVariant)tracker.lookup("dbSNP", null);
if ( dbsnp != null && dbsnp.isSNP() ) {
char refBase = dbsnp.getRefSnpFWD();
char altBase = dbsnp.getAltSnpFWD();
//System.out.printf("%c %c%n", refBase, altBase);
int i = transition_transversion_bin(dbsnp.getMAF());
//System.out.printf("MAF = %f => %d%n", dbsnp.getMAF(), i);
EnumMap<BaseUtils.BaseSubstitutionType, Integer> bin = transition_transversion_counts[i];
BaseUtils.BaseSubstitutionType subType = BaseUtils.SNPSubstitutionType(refBase, altBase);
bin.put(subType, bin.get(subType) + 1);
int sit = bin.get(BaseUtils.BaseSubstitutionType.TRANSITION);
int ver = bin.get(BaseUtils.BaseSubstitutionType.TRANSVERSION);
out.printf("%s %d %d %.2f %s%n", subType, sit, ver, (float)sit/ver, dbsnp.toString());
}
return 1;
}
// Given result of map function
public Integer reduceInit() { return 0; }
public Integer reduce(Integer value, Integer sum) {
return treeReduce(sum,value);
}
public Integer treeReduce(Integer lhs, Integer rhs) {
return lhs + rhs;
}
public void onTraversalDone(Integer result) {
for ( int i = 0; i < N_TRANSITION_TRANVERSION_BINS; i++ ) {
double averageMAF = transition_transversion_bin2MAF(i);
EnumMap<BaseUtils.BaseSubstitutionType, Integer> bin = transition_transversion_counts[i];
int sit = bin.get(BaseUtils.BaseSubstitutionType.TRANSITION);
int ver = bin.get(BaseUtils.BaseSubstitutionType.TRANSVERSION);
double ratio = (float)sit/ver;
out.printf("%.2f %d %d %f%n", averageMAF, sit, ver, ratio);
}
}
}