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

implementation of the truth allele, different cases for REF , HOMVAR, FILTERED and HET. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6051 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
droazen 2011-06-22 22:54:51 +00:00
parent 3f974c62e6
commit 082abfd84f
1 changed files with 42 additions and 13 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

55
java/src/org/broadinstitute/sting/playground/gatk/walkers/replication_validation/ReplicationValidationWalker.java
View File

@ -1,8 +1,10 @@
package org.broadinstitute.sting.playground.gatk.walkers.replication_validation;
import com.google.common.collect.ArrayListMultimap;
import com.sun.xml.internal.ws.client.BindingProviderProperties;
import net.sf.samtools.SAMFileHeader;
import net.sf.samtools.SAMReadGroupRecord;
import org.broad.tribble.util.variantcontext.VariantContext;
import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.commandline.Output;
import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
@ -34,26 +36,33 @@ import java.util.regex.Pattern;
*/
public class ReplicationValidationWalker extends LocusWalker<Integer, Long> implements TreeReducible<Long> {
@Argument(shortName="refsample", fullName="reference_sample_name", doc="Reference sample name.", required=true)
String referenceSampleName;
@Argument(shortName="nsamples", fullName="number_of_samples", doc="Number of samples in the dataset (not counting the reference sample).", required=true)
int nSamples = -1;
@Argument(shortName="nchr", fullName="number_of_chromosomes", doc="Number of chromosomes per sample (in case you're not dealing with diploids). Default: 2.", required=false)
int nChromosomes = 2;
@Argument(shortName="maxac", fullName="max_allele_count", doc="Max number of alleles expected in a site. Default: 2 * number of samples. Smaller numbers process faster.", required=false)
@Argument(shortName="maxac", fullName="max_allele_count", doc="Max number of alleles expected in a site. Smaller numbers process faster. Default: 2 * number of samples. ", required=false)
int overrideMaxAlleleCount = -1;
@Argument(shortName="maxqs", fullName="max_quality_score", doc="Max quality score to consider. Default: Q40. Smaller numbers process faster.", required=false)
@Argument(shortName="maxqs", fullName="max_quality_score", doc="Max quality score to consider. Smaller numbers process faster. Default: Q40.", required=false)
int maxQualityScore= 40;
@Argument(shortName="prior", fullName="site_quality_prior", doc="Phred-Scaled prior quality of the site. Default: Q20.", required=false)
byte defaultPrior= 20;
@Argument(shortName="ef", fullName="exclude_filtered_reference_sites", doc="Don't include in the analysis sites where the reference sample VCF is filtered. Default: false.", required=false)
boolean EXCLUDE_FILTERED_REFERENCE_SITES = false;
@Output(doc="Write output to this file instead of STDOUT")
PrintStream out;
int maxAlleleCount;
String referenceSampleName;
boolean USE_TRUTH_ROD;
final String REFERENCE_ROD_NAME = "reference";
@ -145,6 +154,36 @@ public class ReplicationValidationWalker extends LocusWalker<Integer, Long> impl
}
public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
// Get reference base from VCF or Reference
VariantContext referenceContext = tracker.getVariantContext(ref, REFERENCE_ROD_NAME, context.getLocation());
byte trueReferenceBase;
// Site is not a variant, take from the reference
if (referenceContext == null) {
trueReferenceBase = ref.getBase();
}
// Site has a VCF entry -- is variant
else {
// Site is filtered, don't mess with it if option is set
if (referenceContext.isFiltered() && EXCLUDE_FILTERED_REFERENCE_SITES) {
return 0;
}
// Site is HomVar -- easy, take the only alt allele.
else if (referenceContext.getGenotype(referenceSampleName).isHomVar()) {
trueReferenceBase = referenceContext.getAlternateAllele(0).getBases()[0];
}
// TODO: treat HET cases specially?
else {
return 0;
}
}
ReadBackedPileup contextPileup = context.getBasePileup();
Set<String> lanesInLocus = getLaneIDs(contextPileup.getReadGroups());
for (String laneID : lanesInLocus) {
@ -167,8 +206,6 @@ public class ReplicationValidationWalker extends LocusWalker<Integer, Long> impl
if (referenceSamplePileup != null && !referenceSamplePileup.isEmpty() && !poolPileup.isEmpty()) {
// Build error model
//TODO: Build a reference sample VCF and get true reference base from there.
byte trueReferenceBase = referenceSamplePileup.getBases()[0]; // THIS IS A QUICK FIX JUST TO BE ABLE TO TEST -- IT IS WRONG!
double [] errorModel = buildErrorModel(referenceSamplePileup.getBases(), trueReferenceBase, defaultPrior);
// Debug error model
@ -185,10 +222,6 @@ public class ReplicationValidationWalker extends LocusWalker<Integer, Long> impl
return 1;
}
public Long reduceInit() {
return 0l;
}
@ -197,10 +230,6 @@ public class ReplicationValidationWalker extends LocusWalker<Integer, Long> impl
return value + sum;
}
/**
* Reduces two subtrees together. In this case, the implementation of the tree reduce
* is exactly the same as the implementation of the single reduce.
*/
public Long treeReduce(Long lhs, Long rhs) {
return lhs + rhs;
}