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Removed experimental "master merging" from CombineVariants 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5138 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
fromer 2011-01-31 17:13:05 +00:00
parent b0432ee1e2
commit c59b2a8296
3 changed files with 7 additions and 74 deletions
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64
java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextUtils.java
View File

@ -316,71 +316,9 @@ public class VariantContextUtils {
}
public enum VariantMergeType {
UNION, INTERSECT, MASTER
UNION, INTERSECT
}
/**
* Performs a master merge on the VCs. Here there is a master input [contains all of the information] and many
* VCs containing partial, extra genotype information which should be added to the master. For example,
* we scatter out the phasing algorithm over some samples in the master, producing a minimal VCF with phasing
* information per genotype. The master merge will add the PQ information from each genotype record, where
* appropriate, to the master VC.
*
* @param genomeLocParser
* @param unsortedVCs
* @param masterName
* @param refBase
* @return
*/
public static VariantContext masterMerge(Collection<VariantContext> unsortedVCs, String masterName) {
VariantContext master = findMaster(unsortedVCs, masterName);
Map<String, Genotype> genotypes = master.getGenotypes();
for ( Genotype g : genotypes.values() ) {
genotypes.put(g.getSampleName(), new MutableGenotype(g));
}
for ( VariantContext vc : unsortedVCs ) {
if ( ! vc.getSource() .equals(masterName) ) {
for ( Genotype g : vc.getGenotypes().values() ) {
MutableGenotype masterG = (MutableGenotype)genotypes.get(g.getSampleName());
for ( Map.Entry<String, Object> attr : g.getAttributes().entrySet() ) {
if ( ! masterG.hasAttribute(attr.getKey()) ) {
//System.out.printf("Adding attribute %s to masterG %s, new %s%n", attr, masterG, g);
masterG.putAttribute(attr.getKey(), attr.getValue());
}
}
if ( masterG.isPhased() != g.isPhased() ) {
// System.out.printf("Updating phasing %s to masterG %s, new %s%n", g.isPhased(), masterG, g);
masterG.setPhase(g.isPhased());
}
// if ( MathUtils.compareDoubles(masterG.getNegLog10PError(), g.getNegLog10PError()) != 0 ) {
// System.out.printf("Updating GQ %s to masterG %s, new %s%n", g.getNegLog10PError(), masterG, g);
// masterG.setNegLog10PError(g.getNegLog10PError());
// }
// TODO -- WARNING -- THIS CODE DOES NOT ACTUALLY LOOK AT ALL OF THE GENOTYPE ATTRIBUTES, ONLY THOSE
// TODO -- WARNING -- IMMEDIATELY USEFUL TO PHASING. A COMPLETE IMPLEMENTATION WILL NEED TO HANDLE
// TODO -- WARNING -- ALL OF THE FIELDS LIKE ALLELES, ETC
}
}
}
return new VariantContext(master.getSource(), master.getChr(), master.getStart(), master.getEnd(), master.getAlleles(), genotypes, master.getNegLog10PError(), master.getFilters(), master.getAttributes());
}
private static final VariantContext findMaster(Collection<VariantContext> unsortedVCs, String masterName) {
for ( VariantContext vc : unsortedVCs ) {
if ( vc.getSource() .equals(masterName) ) {
return vc;
}
}
throw new ReviewedStingException(String.format("Couldn't find master VCF %s at %s", masterName, unsortedVCs.iterator().next()));
}
public static VariantContext simpleMerge(GenomeLocParser genomeLocParser, Collection<VariantContext> unsortedVCs, byte refBase) {
return simpleMerge(genomeLocParser, unsortedVCs, null, VariantMergeType.INTERSECT, GenotypeMergeType.UNSORTED, false, false, refBase);
}

15
java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java
View File

@ -120,29 +120,24 @@ public class CombineVariants extends RodWalker<Integer, Integer> {
}
public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
if ( tracker == null ) // RodWalkers can make funky map calls
if (tracker == null) // RodWalkers can make funky map calls
return 0;
// get all of the vcf rods at this locus
// Need to provide reference bases to simpleMerge starting at current locus
Collection<VariantContext> vcs = tracker.getAllVariantContexts(ref, context.getLocation());
VariantContext mergedVC = null;
if ( variantMergeOption == VariantContextUtils.VariantMergeType.MASTER ) {
mergedVC = VariantContextUtils.masterMerge(vcs, "master");
} else {
mergedVC = VariantContextUtils.simpleMerge(getToolkit().getGenomeLocParser(),vcs, priority, variantMergeOption,
genotypeMergeOption, true, printComplexMerges, ref.getBase(), SET_KEY, filteredAreUncalled);
}
VariantContext mergedVC = VariantContextUtils.simpleMerge(getToolkit().getGenomeLocParser(), vcs, priority, variantMergeOption,
genotypeMergeOption, true, printComplexMerges, ref.getBase(), SET_KEY, filteredAreUncalled);
//out.printf(" merged => %s%nannotated => %s%n", mergedVC, annotatedMergedVC);
if ( mergedVC != null ) { // only operate at the start of events
if (mergedVC != null) { // only operate at the start of events
HashMap<String, Object> attributes = new HashMap<String, Object>(mergedVC.getAttributes());
// re-compute chromosome counts
VariantContextUtils.calculateChromosomeCounts(mergedVC, attributes, false);
VariantContext annotatedMergedVC = VariantContext.modifyAttributes(mergedVC, attributes);
if ( minimalVCF )
if (minimalVCF)
annotatedMergedVC = VariantContextUtils.pruneVariantContext(annotatedMergedVC, new HashSet(Arrays.asList(SET_KEY)));
vcfWriter.add(annotatedMergedVC, ref.getBase());
}

2
java/src/org/broadinstitute/sting/oneoffprojects/walkers/phasing/ComparePhasingToTrioPhasingNoRecombinationWalker.java
View File

@ -497,7 +497,7 @@ class CompareTrioAndPhasingTracks {
out.println("");
}
private static String percentString(double numerator, double denominator) {
private static String percentString(int numerator, int denominator) {
int NUM_DECIMAL_PLACES = 1;
String percent = new Formatter().format("%." + NUM_DECIMAL_PLACES + "f", MathUtils.percentage(numerator, denominator)).toString();