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Nicer printing out of clustering 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4035 348d0f76-0448-11de-a6fe-93d51630548a
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depristo 2010-08-14 16:02:13 +00:00
parent c85ab9db37
commit 0d209d5442
1 changed files with 12 additions and 4 deletions
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16
java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyVariantCuts.java
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@ -126,17 +126,25 @@ public class ApplyVariantCuts extends RodWalker<Integer, Integer> {
public void initialize() { public void initialize() {
// todo -- ryan, it's always best to use a read data structure, I need to read these in. // todo -- ryan, it's always best to use a data structure, I need to read these in too.
// todo -- I would have updated your code but there's no integration test to protect me from unexpected effects // todo -- I would have updated your code but there's no integration test to protect me from unexpected effects
boolean firstLine = true; boolean firstLine = true;
try { try {
for( final String line : new XReadLines(new File( TRANCHE_FILENAME )) ) { for( final String line : new XReadLines(new File( TRANCHE_FILENAME )) ) {
if( !firstLine ) { if( !firstLine ) {
final String[] vals = line.split(","); final String[] vals = line.split(",");
if(Double.parseDouble(vals[0]) >= FDR_FILTER_LEVEL) { double FDR = Double.parseDouble(vals[0]);
qCuts.add(Double.parseDouble(vals[2])); double TsTv = Double.parseDouble(vals[1]);
filterName.add(vals[4]); double pCut = Double.parseDouble(vals[2]);
String name = vals[4];
//String statusMsg = "Excluding, below FDR level";
if (FDR >= FDR_FILTER_LEVEL) {
qCuts.add(pCut);
filterName.add(name);
//statusMsg = "Keeping, above FDR threshold";
} }
logger.info(String.format("Tranche %s with %.2f FDR, TsTv %.2f and pCut %.2f, threshold %.2f",
name, FDR, TsTv, pCut, FDR_FILTER_LEVEL));
} }
firstLine = false; firstLine = false;
} }