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misc minor update to HC debug output for when there are a lot of samples

This commit is contained in:
Ryan Poplin 2012-06-07 10:56:41 -04:00
parent b6a7c3f780
commit 0b4281fdd0
2 changed files with 9 additions and 1 deletions
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1
public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java
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@ -553,7 +553,6 @@ public class ReadUtils {
return true; return true;
} }
/** /**
* Checks if a read starts with an insertion. It looks beyond Hard and Soft clips * Checks if a read starts with an insertion. It looks beyond Hard and Soft clips
* if there are any. * if there are any.

9
public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java
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@ -1264,6 +1264,15 @@ public class VariantContext implements Feature { // to enable tribble integratio
this.getGenotypes()); this.getGenotypes());
} }
public String toStringWithoutGenotypes() {
return String.format("[VC %s @ %s Q%s of type=%s alleles=%s attr=%s",
getSource(), contig + ":" + (start - stop == 0 ? start : start + "-" + stop),
hasLog10PError() ? String.format("%.2f", getPhredScaledQual()) : ".",
this.getType(),
ParsingUtils.sortList(this.getAlleles()),
ParsingUtils.sortedString(this.getAttributes()));
}
// protected basic manipulation routines // protected basic manipulation routines
private static List<Allele> makeAlleles(Collection<Allele> alleles) { private static List<Allele> makeAlleles(Collection<Allele> alleles) {
final List<Allele> alleleList = new ArrayList<Allele>(alleles.size()); final List<Allele> alleleList = new ArrayList<Allele>(alleles.size());