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

CalculateChromosomeCounts() now only calculates AC, AF, and AN when there are genotypes. Can now combine variants with headers that differ in only whether a field is a integer or a float. Updated CombineVariants integrationtest, as incorrect AC values where being calculated in the previous GS outputs. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5383 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
depristo 2011-03-06 19:25:52 +00:00
parent 5b8fdc5b1f
commit af71576a07
3 changed files with 28 additions and 19 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

38
java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextUtils.java
View File

@ -113,26 +113,28 @@ public class VariantContextUtils {
return;
}
attributes.put(VCFConstants.ALLELE_NUMBER_KEY, vc.getChromosomeCount());
if ( vc.hasGenotypes() ) {
attributes.put(VCFConstants.ALLELE_NUMBER_KEY, vc.getChromosomeCount());
// if there are alternate alleles, record the relevant tags
if ( vc.getAlternateAlleles().size() > 0 ) {
ArrayList<String> alleleFreqs = new ArrayList<String>();
ArrayList<Integer> alleleCounts = new ArrayList<Integer>();
double totalChromosomes = (double)vc.getChromosomeCount();
for ( Allele allele : vc.getAlternateAlleles() ) {
int altChromosomes = vc.getChromosomeCount(allele);
alleleCounts.add(altChromosomes);
String freq = String.format(makePrecisionFormatStringFromDenominatorValue(totalChromosomes), ((double)altChromosomes / totalChromosomes));
alleleFreqs.add(freq);
// if there are alternate alleles, record the relevant tags
if ( vc.getAlternateAlleles().size() > 0 ) {
ArrayList<String> alleleFreqs = new ArrayList<String>();
ArrayList<Integer> alleleCounts = new ArrayList<Integer>();
double totalChromosomes = (double)vc.getChromosomeCount();
for ( Allele allele : vc.getAlternateAlleles() ) {
int altChromosomes = vc.getChromosomeCount(allele);
alleleCounts.add(altChromosomes);
String freq = String.format(makePrecisionFormatStringFromDenominatorValue(totalChromosomes), ((double)altChromosomes / totalChromosomes));
alleleFreqs.add(freq);
}
attributes.put(VCFConstants.ALLELE_COUNT_KEY, alleleCounts.size() == 1 ? alleleCounts.get(0) : alleleCounts);
attributes.put(VCFConstants.ALLELE_FREQUENCY_KEY, alleleFreqs.size() == 1 ? alleleFreqs.get(0) : alleleFreqs);
}
else {
attributes.put(VCFConstants.ALLELE_COUNT_KEY, 0);
attributes.put(VCFConstants.ALLELE_FREQUENCY_KEY, 0.0);
}
attributes.put(VCFConstants.ALLELE_COUNT_KEY, alleleCounts);
attributes.put(VCFConstants.ALLELE_FREQUENCY_KEY, alleleFreqs);
}
else {
attributes.put(VCFConstants.ALLELE_COUNT_KEY, 0);
attributes.put(VCFConstants.ALLELE_FREQUENCY_KEY, 0.0);
}
}

7
java/src/org/broadinstitute/sting/utils/vcf/VCFUtils.java
View File

@ -156,6 +156,13 @@ public class VCFUtils {
// values varies, is unknown, or is unbounded, then this value should be '.'.
if ( logger != null ) logger.warn("Promoting header field Number to . due to number differences in header lines: " + line + " " + other);
compOther.setNumberToUnbounded();
} else if ( compLine.getType() == VCFHeaderLineType.Integer && compOther.getType() == VCFHeaderLineType.Float ) {
// promote key to Float
if ( logger != null ) logger.warn("Promoting Integer to Float in header: " + compOther);
map.put(key, compOther);
} else if ( compLine.getType() == VCFHeaderLineType.Float && compOther.getType() == VCFHeaderLineType.Integer ) {
// promote key to Float
if ( logger != null ) logger.warn("Promoting Integer to Float in header: " + compOther);
} else {
throw new IllegalStateException("Incompatible header types, collision between these two types: " + line + " " + other );
}

2
java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsIntegrationTest.java
View File

@ -87,7 +87,7 @@ public class CombineVariantsIntegrationTest extends WalkerTest {
" -priority NA19240_BGI,NA19240_ILLUMINA,NA19240_WUGSC,denovoInfo" +
" -genotypeMergeOptions UNIQUIFY -L 1"),
1,
Arrays.asList("00c431243201e7dec99c2c1a1a863438"));
Arrays.asList("a07995587b855f3214fb71940bf23c0f"));
executeTest("threeWayWithRefs", spec);
}