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Now can generate verbose String representation of deletions (e.g. "-AAT") if reference bases are provided as an argument to getEventStringWithCounts(). 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2488 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
asivache 2009-12-30 21:54:50 +00:00
parent 89791d730e
commit a41cb0701b
1 changed files with 35 additions and 1 deletions
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36
java/src/org/broadinstitute/sting/utils/pileup/ReadBackedExtendedEventPileup.java
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@ -304,7 +304,24 @@ public class ReadBackedExtendedEventPileup implements Iterable<ExtendedEventPile
return v;
}
/** A shortcut for getEventStringsWithCounts(null);
*
* @return
*/
public List<Pair<String,Integer>> getEventStringsWithCounts() {
return getEventStringsWithCounts(null);
}
/** Returns String representation of all distinct extended events (indels) at the site along with
* observation counts (numbers of reads) for each distinct event. If refBases is null, a simple string representation for
* deletions will be generated as "<length>D" (i.e. "5D"); if the reference bases are provided, the actual
* deleted sequence will be used in the string representation (e.g. "-AAC").
* @param refBases reference bases, starting with the current locus (i.e. the one immediately before the indel), and
* extending far enough to accomodate the longest deletion (i.e. size of refBases must be at least 1+<length of longest deletion>)
* @return list of distinct events; first element of a pair is a string representation of the event, second element
* gives the number of reads, in which that event was observed
*/
public List<Pair<String,Integer>> getEventStringsWithCounts(char[] refBases) {
Map<String, Integer> events = new HashMap<String,Integer>();
for ( ExtendedEventPileupElement e : this ) {
@ -315,7 +332,7 @@ public class ReadBackedExtendedEventPileup implements Iterable<ExtendedEventPile
indel = "+"+e.getEventBases();
break;
case DELETION:
indel = Integer.toString(e.getEventLength())+"D";
indel = getDeletionString(e.getEventLength(),refBases);
break;
case NOEVENT: continue;
default: throw new StingException("Unknown event type encountered: "+e.getType());
@ -333,6 +350,23 @@ public class ReadBackedExtendedEventPileup implements Iterable<ExtendedEventPile
return eventList;
}
/**
* Builds string representation of the deletion event. If refBases is null, the representation will be
* "<length>D" (e.g. "5D"); if the reference bases are provided, a verbose representation (e.g. "-AAC")
* will be generated. NOTE: refBases must start with the base prior to the actual deletion (i.e. deleted
* base(s) are refBase[1], refBase[2], ...), and the length of the passed array must be sufficient to accomodate the
* deletion length (i.e. size of refBase must be at least length+1).
* @param length
* @param refBases
* @return
*/
private String getDeletionString(int length, char[] refBases) {
if ( refBases == null ) {
return Integer.toString(length)+"D"; // if we do not have reference bases, we can only report something like "5D"
} else {
return "-"+new String(refBases,1,length);
}
}
/**
* Get an array of the mapping qualities