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Fix for MISSING floats 

-- Restructured code to separate the MISSING value in java (currently everywhere a null) from the byte representation on disk (an int).
-- Now handles correctly MISSING qual fields
This commit is contained in:
Mark DePristo 2012-05-10 11:29:57 -04:00
parent 931b575748
commit 81bd7646d6
1 changed files with 4 additions and 2 deletions
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6
public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java
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@ -1225,8 +1225,10 @@ public class VariantContext implements Feature { // to enable tribble integratio
}
public String toString() {
return String.format("[VC %s @ %s of type=%s alleles=%s attr=%s GT=%s",
getSource(), contig + ":" + (start - stop == 0 ? start : start + "-" + stop), this.getType(),
return String.format("[VC %s @ %s Q%s of type=%s alleles=%s attr=%s GT=%s",
getSource(), contig + ":" + (start - stop == 0 ? start : start + "-" + stop),
hasLog10PError() ? String.format("%.2f", getPhredScaledQual()) : ".",
this.getType(),
ParsingUtils.sortList(this.getAlleles()),
ParsingUtils.sortedString(this.getAttributes()),
this.getGenotypes());