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Added utility shortcut method: getOriginalQualsInCycleOrder(read) 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3851 348d0f76-0448-11de-a6fe-93d51630548a
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asivache 2010-07-22 15:44:25 +00:00
parent 473ec91633
commit 3308d956f4
1 changed files with 14 additions and 0 deletions
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14
java/src/org/broadinstitute/sting/utils/sam/AlignmentUtils.java
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@ -350,6 +350,20 @@ public class AlignmentUtils {
return Utils.reverse(read.getBaseQualities()); return Utils.reverse(read.getBaseQualities());
} }
/** Returns the array of original base qualitites (before recalibration) in the order the bases were read on the machine (i.e. always starting from
* cycle 1). In other words, if the read is unmapped or aligned in the forward direction, the read's own base
* qualities are returned as stored in the SAM record; if the read is aligned in the reverse direction, the array
* of read's base qualitites is inverted (in this case new array is allocated and returned). If no original base qualities
* are available this method will throw a runtime exception.
* @param read
* @return
*/
public static byte [] getOriginalQualsInCycleOrder(SAMRecord read) {
if ( isReadUnmapped(read) || ! read.getReadNegativeStrandFlag() ) return read.getOriginalBaseQualities();
return Utils.reverse(read.getOriginalBaseQualities());
}
/** Takes the alignment of the read sequence <code>readSeq</code> to the reference sequence <code>refSeq</code> /** Takes the alignment of the read sequence <code>readSeq</code> to the reference sequence <code>refSeq</code>
* starting at 0-based position <code>refIndex</code> on the <code>refSeq</code> and specified by its <code>cigar</code>. * starting at 0-based position <code>refIndex</code> on the <code>refSeq</code> and specified by its <code>cigar</code>.
* The last argument <code>readIndex</code> specifies 0-based position on the read where the alignment described by the * The last argument <code>readIndex</code> specifies 0-based position on the read where the alignment described by the