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Convenience printing 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@968 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
depristo 2009-06-10 17:07:38 +00:00
parent 06e5a765f8
commit 9ebcd6546d
4 changed files with 11 additions and 13 deletions
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2
java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/HardyWeinbergEquilibrium.java
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@ -79,7 +79,7 @@ public class HardyWeinbergEquilibrium extends BasicVariantAnalysis {
List<String> s = new ArrayList<String>();
s.add(String.format("n_calls %d", nSites));
s.add(String.format("n_violations %d", nViolations));
s.add(String.format("violations_rate %.2f", (100.0*nSites) / nViolations));
s.add(String.format("violations_rate %.2f", (100.0*nViolations) / nSites));
return s;
}
}

4
java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/PairwiseDistanceAnalysis.java
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@ -75,10 +75,12 @@ public class PairwiseDistanceAnalysis extends BasicVariantAnalysis {
List<String> s = new ArrayList<String>();
s.add(String.format("snps counted for pairwise distance: %d", pairWiseDistances.size()));
int cumulative = 0;
for ( int i = 0; i < pairWiseBoundries.length; i++ ) {
int maxDist = pairWiseBoundries[i];
int count = pairCounts[i];
s.add(String.format("snps within %8d bp: %d", maxDist, count));
cumulative += count;
s.add(String.format("snps within %8d bp: %d %d", maxDist, count, cumulative));
}
return s;

16
java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantDBCoverage.java
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@ -26,17 +26,10 @@ public class VariantDBCoverage extends BasicVariantAnalysis {
if (inDB && inEval) nOverlapping++;
}
public int nDBSites() {
return nDBObs;
}
public int nEvalSites() {
return nEvalObs;
}
public int nOverlappingSites() {
return nOverlapping;
}
public int nDBSites() { return nDBObs; }
public int nEvalSites() { return nEvalObs; }
public int nOverlappingSites() { return nOverlapping; }
public int nNovelSites() { return Math.abs(nEvalSites() - nOverlappingSites()); }
/**
* What fraction of the evaluated site variants were also found in the db?
@ -70,6 +63,7 @@ public class VariantDBCoverage extends BasicVariantAnalysis {
s.add(String.format("n_db_sites %d", nDBSites()));
s.add(String.format("n_eval_sites %d", nEvalSites()));
s.add(String.format("n_overlapping_sites %d", nOverlappingSites()));
s.add(String.format("n_novel_sites %d", nNovelSites()));
s.add(String.format("per_eval_sites_in_db %.2f", 100*fractionEvalSitesCoveredByDB()));
s.add(String.format("per_db_sites_in_eval %.2f", 100*fractionDBSitesDiscoveredInEval()));
return s;

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantEvalWalker.java
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@ -103,6 +103,8 @@ public class VariantEvalWalker extends RefWalker<Integer, Integer> {
public Integer map(RefMetaDataTracker tracker, char ref, LocusContext context) {
// Iterate over each analysis, and update it
AllelicVariant eval = (AllelicVariant)tracker.lookup("eval", null);
//if ( eval!=null ) System.out.printf("Eval: %f %d %b%n", eval.getVariationConfidence(), minDiscoveryQ, eval.getVariationConfidence() < minDiscoveryQ);
if ( eval != null && eval.getVariationConfidence() < minDiscoveryQ )
eval = null;