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removed the hashmap from Genotype Concordance, moved it into a table 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3133 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
aaron 2010-04-07 21:24:48 +00:00
parent e55f27b3b1
commit 20cc2a85a4
1 changed files with 28 additions and 17 deletions
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45
java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/GenotypeConcordance.java
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@ -27,7 +27,7 @@ public class GenotypeConcordance extends VariantEvaluator {
// a mapping from allele count to stats // a mapping from allele count to stats
@DataPoint(description = "the frequency statistics for each allele") @DataPoint(description = "the frequency statistics for each allele")
private HashMap<Integer, FrequencyStats> alleleCountStats = new HashMap<Integer, FrequencyStats>(); FrequencyStats alleleFreqStats = new FrequencyStats();
// a mapping from sample to stats // a mapping from sample to stats
@DataPoint(name="samples", description = "the concordance statistics for each sample") @DataPoint(name="samples", description = "the concordance statistics for each sample")
@ -41,11 +41,18 @@ public class GenotypeConcordance extends VariantEvaluator {
class FrequencyStats implements TableType { class FrequencyStats implements TableType {
long nFound = 0; class Stats {
long nMissed = 0; public Stats(int found, int missed) { nFound = found; nMissed = missed; }
public long nFound = 0;
public long nMissed = 0;
}
public HashMap<Integer, Stats> alleleCountStats = new HashMap<Integer, Stats>();
public Object[] getRowKeys() { public Object[] getRowKeys() {
return new String[]{"sample"}; String rows[] = new String[alleleCountStats.size()];
int index = 0;
for (int i : alleleCountStats.keySet()) rows[index++] = "Allele Count " + i;
return rows;
} }
public Object[] getColumnKeys() { public Object[] getColumnKeys() {
@ -57,13 +64,23 @@ public class GenotypeConcordance extends VariantEvaluator {
} }
public String getCell(int x, int y) { public String getCell(int x, int y) {
if (y == 0) return String.valueOf(nFound); if (x >= alleleCountStats.size()) throw new IllegalStateException(x + " is greater than the max index of " + (alleleCountStats.size()-1));
else return String.valueOf(nMissed); if (y == 0) return String.valueOf(alleleCountStats.get(alleleCountStats.keySet().toArray(new Integer[alleleCountStats.size()])[x]).nFound);
else return String.valueOf(alleleCountStats.get(alleleCountStats.keySet().toArray(new Integer[alleleCountStats.size()])[x]).nMissed);
} }
public String toString() { public void incrementFoundCount(int alleleFreq) {
long total = nFound + nMissed; if (!alleleCountStats.containsKey(alleleFreq))
return String.format("%d %d %.2f ", nFound, nMissed, total == 0 ? 0.0 : (100.0 * rate(nFound, total))); alleleCountStats.put(alleleFreq,new Stats(1,0));
else
alleleCountStats.get(alleleFreq).nFound++;
}
public void incrementMissedCount(int alleleFreq) {
if (!alleleCountStats.containsKey(alleleFreq))
alleleCountStats.put(alleleFreq,new Stats(0,1));
else
alleleCountStats.get(alleleFreq).nMissed++;
} }
} }
@ -281,16 +298,10 @@ public class GenotypeConcordance extends VariantEvaluator {
for (final Allele a : validation.getAlternateAlleles()) { for (final Allele a : validation.getAlternateAlleles()) {
trueAlleleCount += validation.getChromosomeCount(a); trueAlleleCount += validation.getChromosomeCount(a);
} }
if (!alleleCountStats.containsKey(trueAlleleCount)) {
alleleCountStats.put(trueAlleleCount, new FrequencyStats());
}
final FrequencyStats stats = alleleCountStats.get(trueAlleleCount);
if (eval != null) { if (eval != null) {
stats.nFound++; alleleFreqStats.incrementFoundCount(trueAlleleCount);
} else { } else {
stats.nMissed++; alleleFreqStats.incrementMissedCount(trueAlleleCount);
} }
} }