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deal with reverse complemented reads 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@115 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2009-03-20 16:01:49 +00:00
parent 9ec96414c7
commit f3f1b47808
1 changed files with 5 additions and 4 deletions
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9
playground/java/src/org/broadinstitute/sting/gatk/walkers/MismatchHistoWalker.java
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@ -54,9 +54,11 @@ public class MismatchHistoWalker extends BasicReadWalker<Integer, Integer> {
String refStr = Utils.baseList2string(refSeq).toUpperCase();
String readStr = Utils.baseList2string(readBases).toUpperCase();
boolean reverseFlag = read.getReadNegativeStrandFlag();
for ( int i = 0; i < refStr.length(); i++) {
if ( refStr.charAt(i) != readStr.charAt(i) )
mismatchCounts[i]++;
mismatchCounts[(reverseFlag ? (refStr.length()-1-i) : i)]++;
}
}
@ -70,9 +72,8 @@ public class MismatchHistoWalker extends BasicReadWalker<Integer, Integer> {
}
public void onTraversalDone() {
for ( int i = 0; i < mismatchCounts.length; i++ ) {
System.out.printf("%3d %10d%n", (i+1), mismatchCounts[i]);
}
for ( int i = 0; i < mismatchCounts.length; i++ )
System.out.println((i+1) + "\t" + mismatchCounts[i]);
}
private static Object resizeArray (Object oldArray, int newSize) {