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High performance pileup code and utilities 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@242 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
depristo 2009-04-01 00:47:47 +00:00
parent ad63633b1c
commit 385736469c
2 changed files with 44 additions and 10 deletions
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14
java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java
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@ -4,9 +4,11 @@ import org.broadinstitute.sting.gatk.LocusContext;
import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum; import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
import org.broadinstitute.sting.gatk.refdata.rodDbSNP; import org.broadinstitute.sting.gatk.refdata.rodDbSNP;
import org.broadinstitute.sting.utils.cmdLine.Argument; import org.broadinstitute.sting.utils.cmdLine.Argument;
import org.broadinstitute.sting.utils.Utils;
import net.sf.samtools.SAMRecord; import net.sf.samtools.SAMRecord;
import java.util.List; import java.util.List;
import java.util.ArrayList;
/** /**
* Created by IntelliJ IDEA. * Created by IntelliJ IDEA.
@ -26,19 +28,11 @@ public class PileupWalker extends LocusWalker<Integer, Integer> {
return true; // We are keeping all the reads return true; // We are keeping all the reads
} }
// Map over the org.broadinstitute.sting.gatk.LocusContext
public Integer map(List<ReferenceOrderedDatum> rodData, char ref, LocusContext context) { public Integer map(List<ReferenceOrderedDatum> rodData, char ref, LocusContext context) {
List<SAMRecord> reads = context.getReads(); List<SAMRecord> reads = context.getReads();
List<Integer> offsets = context.getOffsets(); List<Integer> offsets = context.getOffsets();
String bases = ""; String bases = Utils.basePileupAsString(reads, offsets);
String quals = ""; String quals = Utils.qualPileupAsString(reads, offsets);
for ( int i = 0; i < reads.size(); i++ ) {
SAMRecord read = reads.get(i);
int offset = offsets.get(i);
bases += read.getReadString().charAt(offset);
quals += read.getBaseQualityString().charAt(offset);
}
if ( bases.equals("") && FLAG_UNCOVERED_BASES ) { if ( bases.equals("") && FLAG_UNCOVERED_BASES ) {
bases = "*** UNCOVERED SITE ***"; bases = "*** UNCOVERED SITE ***";

40
java/src/org/broadinstitute/sting/utils/Utils.java
View File

@ -118,6 +118,46 @@ public class Utils {
return c; return c;
} }
public static String basePileupAsString( List<SAMRecord> reads, List<Integer> offsets ) {
StringBuilder bases = new StringBuilder();
for ( byte base : basePileup(reads, offsets)) {
bases.append((char)base);
}
return bases.toString();
}
public static ArrayList<Byte> basePileup( List<SAMRecord> reads, List<Integer> offsets ) {
ArrayList<Byte> bases = new ArrayList(reads.size());
for ( int i = 0; i < reads.size(); i++ ) {
SAMRecord read = reads.get(i);
int offset = offsets.get(i);
bases.add(read.getReadBases()[offset]);
}
return bases;
}
public static ArrayList<Byte> qualPileup( List<SAMRecord> reads, List<Integer> offsets ) {
ArrayList<Byte> quals = new ArrayList(reads.size());
for ( int i = 0; i < reads.size(); i++ ) {
SAMRecord read = reads.get(i);
int offset = offsets.get(i);
byte qual = (byte)read.getBaseQualities()[offset];
quals.add(qual);
}
return quals;
}
public static String qualPileupAsString( List<SAMRecord> reads, List<Integer> offsets ) {
StringBuilder quals = new StringBuilder();
for ( int qual : qualPileup(reads, offsets)) {
qual = Math.min(qual, 63); // todo: fixme, this isn't a good idea
char qualChar = (char) (33 + qual); // todo: warning, this is illegal for qual > 63
quals.append(qualChar);
}
return quals.toString();
}
public static ArrayList<Byte> subseq(byte[] fullArray) { public static ArrayList<Byte> subseq(byte[] fullArray) {
return subseq(fullArray, 0, fullArray.length); return subseq(fullArray, 0, fullArray.length);
} }