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misc cleanup 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2933 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2010-03-04 21:34:13 +00:00
parent 706d49d84c
commit 9eb122924f
1 changed files with 8 additions and 3 deletions
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11
java/src/org/broadinstitute/sting/playground/gatk/walkers/variantstovcf/PlinkToVCF.java
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@ -194,6 +194,9 @@ public class PlinkToVCF extends RodWalker<VCFRecord,Integer> {
}
}
// TODO -- REWRITE THIS TO WORK WITH VARIANT CONTEXT
/******
private String smartHardy(ReferenceContext ref, VCFRecord rec) {
HashMap<String,ArrayList<Genotype>> genotypesByPopulation = new HashMap<String,ArrayList<Genotype>>(10);
HashMap<String,String> hardyWeinbergByPopulation = new HashMap<String,String>(10);
@ -211,8 +214,8 @@ public class PlinkToVCF extends RodWalker<VCFRecord,Integer> {
for ( String population : samplesToPopulation.values() ) {
VCFVariationCall v = new VCFVariationCall(ref.getBase(),ref.getLocus(),VCFVariationCall.VARIANT_TYPE.SNP);
// TODO -- v.setGenotypeCalls(genotypesByPopulation.get(population));
// TODO -- hardyWeinbergByPopulation.put(population,HWCalc.annotate(null,ref,null,v));
v.setGenotypeCalls(genotypesByPopulation.get(population));
hardyWeinbergByPopulation.put(population,HWCalc.annotate(null,ref,null,v));
}
return smartHardyString(hardyWeinbergByPopulation);
@ -228,6 +231,8 @@ public class PlinkToVCF extends RodWalker<VCFRecord,Integer> {
return String.format("%s",maxH);
}
*********/
private HashMap<String,String> parsePopulationFile(File file) {
HashMap<String,String> samplesToPopulation = new HashMap<String,String>();
try {
@ -237,7 +242,7 @@ public class PlinkToVCF extends RodWalker<VCFRecord,Integer> {
String[] populationSamples = line.split("\t");
String population = populationSamples[0];
for ( int i = 1; i < populationSamples.length; i ++ ) {
samplesToPopulation.put(populationSamples[i],population);
samplesToPopulation.put(populationSamples[i], population);
}
}
} catch ( IOException e) {