zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Transpose rows/cols in AF table to make it molten (so I can plot easily in R)

This commit is contained in:
Eric Banks 2012-02-06 16:23:32 -05:00
parent fbbd04621d
commit 91897f5fe7
1 changed files with 21 additions and 14 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

35
public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/MultiallelicSummary.java
View File

@ -91,25 +91,31 @@ public class MultiallelicSummary extends VariantEvaluator { // implements Standa
//@DataPoint(description = "Multi-allelic Indel Novelty Rate")
public String indelNoveltyRate = "NA";
@DataPoint(description="Histogram of allele frequencies for most common alternate allele")
AFHistogram AFhistogramMax = new AFHistogram();
@DataPoint(description="Histogram of allele frequencies for most common SNP alternate allele")
AFHistogram AFhistogramMaxSnp = new AFHistogram();
@DataPoint(description="Histogram of allele frequencies for less common alternate alleles")
AFHistogram AFhistogramMin = new AFHistogram();
@DataPoint(description="Histogram of allele frequencies for less common SNP alternate alleles")
AFHistogram AFhistogramMinSnp = new AFHistogram();
@DataPoint(description="Histogram of allele frequencies for most common Indel alternate allele")
AFHistogram AFhistogramMaxIndel = new AFHistogram();
@DataPoint(description="Histogram of allele frequencies for less common Indel alternate alleles")
AFHistogram AFhistogramMinIndel = new AFHistogram();
/*
* AF histogram table object
*/
static class AFHistogram implements TableType {
private Object[] colKeys, rowKeys = {"pairwise_AF"};
private Object[] rowKeys, colKeys = {"count"};
private int[] AFhistogram;
private static final double AFincrement = 0.01;
private static final int numBins = (int)(1.00 / AFincrement);
public AFHistogram() {
colKeys = initColKeys();
AFhistogram = new int[colKeys.length];
rowKeys = initRowKeys();
AFhistogram = new int[rowKeys.length];
}
public Object[] getColumnKeys() {
@ -121,10 +127,10 @@ public class MultiallelicSummary extends VariantEvaluator { // implements Standa
}
public Object getCell(int row, int col) {
return AFhistogram[col];
return AFhistogram[row];
}
private static Object[] initColKeys() {
private static Object[] initRowKeys() {
ArrayList<String> keyList = new ArrayList<String>(numBins + 1);
for ( double a = 0.00; a <= 1.01; a += AFincrement ) {
keyList.add(String.format("%.2f", a));
@ -164,6 +170,7 @@ public class MultiallelicSummary extends VariantEvaluator { // implements Standa
nMultiSNPs++;
calculatePairwiseTiTv(eval);
calculateSNPPairwiseNovelty(eval, comp);
updateAFhistogram(eval, AFhistogramMaxSnp, AFhistogramMinSnp);
}
break;
case INDEL:
@ -171,13 +178,13 @@ public class MultiallelicSummary extends VariantEvaluator { // implements Standa
if ( !eval.isBiallelic() ) {
nMultiIndels++;
calculateIndelPairwiseNovelty(eval, comp);
updateAFhistogram(eval, AFhistogramMaxIndel, AFhistogramMinIndel);
}
break;
default:
throw new UserException.BadInput("Unexpected variant context type: " + eval);
}
updateAFhistogram(eval);
return null; // we don't capture any interesting sites
}
@ -209,7 +216,7 @@ public class MultiallelicSummary extends VariantEvaluator { // implements Standa
private void calculateIndelPairwiseNovelty(VariantContext eval, VariantContext comp) {
}
private void updateAFhistogram(VariantContext vc) {
private void updateAFhistogram(VariantContext vc, AFHistogram max, AFHistogram min) {
final Object obj = vc.getAttribute(VCFConstants.ALLELE_FREQUENCY_KEY, null);
if ( obj == null || !(obj instanceof List) )
@ -222,9 +229,9 @@ public class MultiallelicSummary extends VariantEvaluator { // implements Standa
}
Collections.sort(AFs);
AFhistogramMax.update(AFs.get(AFs.size()-1));
max.update(AFs.get(AFs.size()-1));
for ( int i = 0; i < AFs.size() - 1; i++ )
AFhistogramMin.update(AFs.get(i));
min.update(AFs.get(i));
}
private final String noveltyRate(final int all, final int known) {