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Some utility methods for creating pileups of secondary bases and secondary quals. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@397 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
kiran 2009-04-14 13:57:54 +00:00
parent 8b2c2e677b
commit 998fad76c6
1 changed files with 70 additions and 0 deletions
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70
java/src/org/broadinstitute/sting/utils/Utils.java
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@ -169,6 +169,76 @@ public class Utils {
return quals.toString();
}
public static ArrayList<Byte> secondaryBasePileup( List<SAMRecord> reads, List<Integer> offsets ) {
ArrayList<Byte> bases2 = new ArrayList<Byte>(reads.size());
boolean hasAtLeastOneSQField = 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;
//byte qual2;
if (compressedQuals != null) {
base2 = (byte) BaseUtils.baseIndexToSimpleBase(QualityUtils.compressedQualityToBaseIndex(compressedQuals[offset]));
//qual2 = QualityUtils.probToQual(QualityUtils.compressedQualityToProb(compressedQuals[offset]));
hasAtLeastOneSQField = true;
} else {
base2 = (byte) '.';
}
bases2.add(base2);
}
return (hasAtLeastOneSQField ? bases2 : null);
}
public static String secondaryBasePileupAsString( List<SAMRecord> reads, List<Integer> offsets ) {
StringBuilder bases2 = new StringBuilder();
ArrayList<Byte> sqbases = secondaryBasePileup(reads, offsets);
if (sqbases == null) { return null; }
for (byte base2 : secondaryBasePileup(reads, offsets)) {
bases2.append((char) base2);
}
return bases2.toString();
}
public static ArrayList<Byte> secondaryQualPileup( List<SAMRecord> reads, List<Integer> offsets ) {
ArrayList<Byte> quals2 = new ArrayList<Byte>(reads.size());
boolean hasAtLeastOneSQField = 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 qual2;
if (compressedQuals != null) {
qual2 = QualityUtils.probToQual(QualityUtils.compressedQualityToProb(compressedQuals[offset]));
hasAtLeastOneSQField = true;
} else {
qual2 = 0;
}
quals2.add(qual2);
}
return (hasAtLeastOneSQField ? quals2 : null);
}
public static String secondaryQualPileupAsString( List<SAMRecord> reads, List<Integer> offsets ) {
StringBuilder quals2 = new StringBuilder();
ArrayList<Byte> sqquals = secondaryQualPileup(reads, offsets);
if (sqquals == null) { return null; }
for (byte qual2 : secondaryQualPileup(reads, offsets)) {
quals2.append(qual2);
}
return quals2.toString();
}
public static ArrayList<Byte> subseq(byte[] fullArray) {
return subseq(fullArray, 0, fullArray.length);
}