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New method: getBasesAtLocus(int n); for the windowed reference context, this method extracts n bases starting at the current locus (NOT at the window start, so this method is an extension of getBase()) 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3210 348d0f76-0448-11de-a6fe-93d51630548a
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asivache 2010-04-20 17:35:09 +00:00
parent cac125b35c
commit 4723cad1be
1 changed files with 22 additions and 0 deletions
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22
java/src/org/broadinstitute/sting/gatk/contexts/ReferenceContext.java
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@ -107,4 +107,26 @@ public class ReferenceContext {
public char[] getBases() {
return bases;
}
/** Extracts from the current window and returns n bases starting at this context's locus (NOT
* from the window start!). The returned array of chars is newly allocated. If n is too large (runs beyond
* the right boundary of this context's window), an exception will be thrown. If n==(-1), all bases starting
* from this context's locus through the end of the window will be returned.
* @param n number of requested bases including and starting from the current locus
* @return
*/
public char[] getBasesAtLocus(int n) {
int start = (int)(locus.getStart()-window.getStart());
int stop = ( n==(-1) ? bases.length : start+n );
char[] b = new char[stop-start];
if ( stop > bases.length )
throw new StingException("Bases beyond the current window requested: window="+window+", requested="+n);
int i = 0;
for ( int j = start ; j < stop ; j++) b[i++]=bases[j];
return b;
}
}