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Now can read E2 or SQ tag. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2027 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
mmelgar 2009-11-12 15:18:21 +00:00
parent c3c001e02e
commit 3742a05760
1 changed files with 29 additions and 10 deletions
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39
java/src/org/broadinstitute/sting/utils/BasicPileup.java
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@ -145,24 +145,43 @@ abstract public class BasicPileup implements Pileup {
public static ArrayList<Byte> secondaryBasePileup( List<SAMRecord> reads, List<Integer> offsets ) {
ArrayList<Byte> bases2 = new ArrayList<Byte>(reads.size());
boolean hasAtLeastOneSQField = false;
boolean hasAtLeastOneSQorE2Field = false;
for ( int i = 0; i < reads.size(); i++ ) {
SAMRecord read = reads.get(i);
int offset = offsets.get(i);
byte[] compressedQuals = (byte[]) read.getAttribute("SQ");
byte base2;
if (read.getAttribute("SQ") != null) {
byte[] compressedQuals = (byte[]) read.getAttribute("SQ");
byte base2;
if (offset != -1 && compressedQuals != null && compressedQuals.length == read.getReadLength()) {
base2 = (byte) BaseUtils.baseIndexToSimpleBase(QualityUtils.compressedQualityToBaseIndex(compressedQuals[offset]));
hasAtLeastOneSQField = true;
} else {
base2 = (byte) '.';
if (offset != -1 && compressedQuals != null && compressedQuals.length == read.getReadLength()) {
base2 = (byte) BaseUtils.baseIndexToSimpleBase(QualityUtils.compressedQualityToBaseIndex(compressedQuals[offset]));
hasAtLeastOneSQorE2Field = true;
}
else {
base2 = (byte) '.';
}
bases2.add((byte) base2);
}
else if (read.getAttribute("E2") != null) {
String secondaries = (String) read.getAttribute("E2");
char base2;
if (offset != -1 && secondaries != null && secondaries.length() == read.getReadLength()) {
base2 = secondaries.charAt(offset);
hasAtLeastOneSQorE2Field = true;
}
else {
base2 = '.';
}
bases2.add((byte) base2);
}
else {
byte base2 = 'N';
bases2.add(base2);
}
bases2.add(base2);
}
return (hasAtLeastOneSQField ? bases2 : null);
return (hasAtLeastOneSQorE2Field ? bases2 : null);
}
public static String secondaryBasePileupAsString( List<SAMRecord> reads, List<Integer> offsets ) {