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Choose a random base to stick in the pileup if the 2nd-best base matches the best base. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@578 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
kiran 2009-05-01 06:27:37 +00:00
parent 9800d09608
commit 4f818f5c1c
1 changed files with 20 additions and 2 deletions
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22
java/src/org/broadinstitute/sting/utils/BasicPileup.java
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@ -6,6 +6,7 @@ import net.sf.samtools.SAMRecord;
import java.util.List; import java.util.List;
import java.util.ArrayList; import java.util.ArrayList;
import java.util.Arrays; import java.util.Arrays;
import java.util.Random;
/** /**
* Created by IntelliJ IDEA. * Created by IntelliJ IDEA.
@ -95,13 +96,30 @@ abstract public class BasicPileup implements Pileup {
public static String secondaryBasePileupAsString( List<SAMRecord> reads, List<Integer> offsets ) { public static String secondaryBasePileupAsString( List<SAMRecord> reads, List<Integer> offsets ) {
StringBuilder bases2 = new StringBuilder(); StringBuilder bases2 = new StringBuilder();
ArrayList<Byte> sqbases = secondaryBasePileup(reads, offsets); ArrayList<Byte> sbases = secondaryBasePileup(reads, offsets);
if (sqbases == null) { return null; } if (sbases == null) { return null; }
ArrayList<Byte> pbases = basePileup(reads, offsets);
Random generator = new Random();
for (int pileupIndex = 0; pileupIndex < sbases.size(); pileupIndex++) {
byte pbase = pbases.get(pileupIndex);
byte sbase = sbases.get(pileupIndex);
while (sbase == pbase) {
sbase = (byte) BaseUtils.baseIndexToSimpleBase(generator.nextInt(4));
}
bases2.append((char) sbase);
}
/*
for (byte base2 : secondaryBasePileup(reads, offsets)) { for (byte base2 : secondaryBasePileup(reads, offsets)) {
bases2.append((char) base2); bases2.append((char) base2);
} }
*/
return bases2.toString(); return bases2.toString();
} }