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still in development and testing; kinda works 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@860 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
asivache 2009-05-29 21:59:03 +00:00
parent c252fec1bc
commit c549c34caa
1 changed files with 81 additions and 12 deletions
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93
java/src/org/broadinstitute/sting/playground/gatk/walkers/SomaticMutationFromGenotypeWalker.java
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@ -1,11 +1,10 @@
package org.broadinstitute.sting.playground.gatk.walkers;
import java.io.BufferedOutputStream;
import java.io.FileWriter;
import java.io.OutputStream;
import org.apache.log4j.Logger;
import org.broadinstitute.sting.gatk.GATKArgumentCollection;
import org.broadinstitute.sting.gatk.LocusContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
@ -14,10 +13,13 @@ import org.broadinstitute.sting.gatk.walkers.RefWalker;
import org.broadinstitute.sting.gatk.walkers.Requires;
import org.broadinstitute.sting.gatk.walkers.DataSource;
import org.broadinstitute.sting.gatk.walkers.RMD;
import org.broadinstitute.sting.gatk.refdata.rodRefSeq;
import org.broadinstitute.sting.playground.utils.GenotypingCallStats;
import org.broadinstitute.sting.utils.GenotypeUtils;
import org.broadinstitute.sting.utils.StingException;
import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.cmdLine.Argument;
import org.broadinstitute.sting.utils.cmdLine.ArgumentException;
//@Requires(value=DataSource.REFERENCE,referenceMetaData={@RMD(name="mother",type=rodSAMPileup.class),
@ -38,12 +40,21 @@ public class SomaticMutationFromGenotypeWalker extends RefWalker<SomaticMutatio
required=true)
public String VTYPE_STR;
@Argument(fullName="bed_out", shortName="BED", doc="Write somatic variants into the specified file in BED format",required=false) public java.io.File BED_OUT;
@Argument(fullName="filter", shortName="F",
doc="Report/write variants only inside intervals annotated as: TRANSCRIPT (including UTRs and introns), EXON (including UTRs), or CODING_EXON. If specified, refseq track must be bound. By default, all variants are reported",
required=false) public String FILTER_ARG;
private java.io.Writer bed_stream = null;
private static Logger logger = Logger.getLogger(MendelianInheritanceWalker.class);
private final static String star = new String("*");
private GenotypeUtils.VariantType VARIANT_TYPE;
private static enum FilterType {
NONE,TRANSCRIPT, EXON, CODING_EXON
}
private FilterType filter;
@Override
public SomaticMutationRecord map(RefMetaDataTracker rodData, char ref, LocusContext context) {
@ -51,23 +62,27 @@ public class SomaticMutationFromGenotypeWalker extends RefWalker<SomaticMutatio
ReferenceOrderedDatum rodNormal = rodData.lookup("normal", null);
ReferenceOrderedDatum rodTumor = rodData.lookup("tumor", null);
ReferenceOrderedDatum rodRefseq = rodData.lookup("refseq", null);
rodRefSeq rodRefseq = (rodRefSeq)rodData.lookup("refseq", null);
Genotype normal = GenotypeUtils.extractGenotype(rodNormal,VARIANT_TYPE, defCalls);
Genotype tumor = GenotypeUtils.extractGenotype(rodTumor,VARIANT_TYPE,defCalls);
SomaticMutationRecord r = new SomaticMutationRecord();
if ( rodRefseq == null ) return r;
out.println(context.getLocation() + " " + rodRefseq.toString() );
if ( true ) return r;
if ( filter != FilterType.NONE ) {
// if we request filtering and current position is not annotated, then we have to skip:
if ( rodRefseq == null ) return r;
if ( filter != FilterType.TRANSCRIPT ) {
if ( ! rodRefseq.isExon() ) return r; // if anything but 'transcript' was requested, we must be in an exon
if ( filter == FilterType.CODING_EXON && ! rodRefseq.isCoding() ) return r; // if coding_exon was requested we must also be inside coding seq
}
}
assessGenotype(normal,r.normal);
assessGenotype(tumor, r.tumor);
assessGenotype(tumor, r.tumor);
if ( r.normal.covered == 1 && r.tumor.covered == 1 ) r.mut.covered = 1;
if ( r.normal.assessed == 1 && r.tumor.assessed == 1 ) r.mut.assessed = 1;
@ -141,7 +156,7 @@ public class SomaticMutationFromGenotypeWalker extends RefWalker<SomaticMutatio
protected GenotypingCallStats assessGenotype(Genotype g, GenotypingCallStats stats) {
if ( g != null ) stats.covered = 1;
// if ( g!= null ) System.out.println(g.getLocation()+" is covered");
if ( hasCall(g)) {
stats.assessed = 1;
if ( g.isReference() ) stats.ref = 1;
@ -179,6 +194,21 @@ public class SomaticMutationFromGenotypeWalker extends RefWalker<SomaticMutatio
}
}
VARIANT_TYPE = GenotypeUtils.VariantType.valueOf(VTYPE_STR.toUpperCase());
if ( FILTER_ARG == null ) filter = FilterType.valueOf("NONE");
else {
filter = FilterType.valueOf(FILTER_ARG);
GATKArgumentCollection args = getToolkit().getArguments();
boolean found = false;
for ( String s : args.RODBindings ) {
if ( s.toUpperCase().startsWith("REFSEQ,REFSEQ") ) {
found = true;
break;
}
}
if ( ! found ) throw new ArgumentException("Reference ordered data track 'refseq' of type 'refseq' must be present when --filter is used");
}
}
@ -249,5 +279,44 @@ class SomaticMutationRecord {
return this;
}
public String toString() {
StringBuilder b = new StringBuilder();
b.append("TUMOR-NORMAL PAIR:\n");
b.append( String.format(" covered: %d%n assessed: %d (%3.2f%% covered)%n",
mut.covered, mut.assessed, Utils.percentage(mut.assessed, mut.covered) )
);
b.append( String.format(" ref: %d (%3.2f%% assessed)%n",
mut.ref, Utils.percentage(mut.ref,mut.assessed))
);
b.append( String.format(" somatic variants: %d (%3.2f%% assessed, or 1 per %3.2f kB)%n",
mut.variant, Utils.percentage(mut.variant,mut.assessed), ((double)mut.assessed/mut.variant)/1000.0 )
);
b.append( String.format(" germline variants: %d (%3.2f%% assessed, or 1 per %3.2f kB)%n",
germline, Utils.percentage(germline,mut.assessed), ((double)mut.assessed/germline)/1000.0 )
);
b.append( String.format(" lost variants: %d (%3.2f%% assessed, or 1 per %3.2f kB)%n",
lost_variant, Utils.percentage(lost_variant,mut.assessed), ((double)mut.assessed/lost_variant)/1000.0 )
);
b.append( String.format(" non-matching germline variants: %d (%3.2f%% germline variants)%n",
non_matching_germline, Utils.percentage(non_matching_germline,germline) )
);
b.append( String.format(" variants in tumor with unknown normal status: %d (%d no coverage, %d no confidence)%n",
tumor_variant_without_confident_normal+tumor_variant_without_normal, tumor_variant_without_normal, tumor_variant_without_confident_normal )
);
b.append( String.format(" variants in normal with unknown tumor status: %d (%d no coverage, %d no confidence)%n",
normal_variant_without_confident_tumor+normal_variant_without_tumor, normal_variant_without_tumor, normal_variant_without_confident_tumor )
);
b.append("PER SAMPLE:\n");
b.append(" NORMAL:\n");
b.append(normal.toString());
b.append(" TUMOR:\n");
b.append(tumor.toString());
return b.toString();
}
}