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Added some methods to format bases such that read bases on the forward strand are in uppercase, while those on the negative strand are lowercase. This does *not* affect the default functionality of the standard PileupWalker 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@969 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
kiran 2009-06-10 17:31:00 +00:00
parent 9ebcd6546d
commit b0cc763eb5
3 changed files with 36 additions and 37 deletions
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37
java/src/org/broadinstitute/sting/gatk/walkers/PileupWithContextWalker.java
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@ -16,30 +16,10 @@ import java.util.List;
import java.io.File;
import java.io.IOException;
/**
* samtools pileup [-f in.ref.fasta] [-t in.ref_list] [-l in.site_list] [-iscg] [-T theta] [-N nHap] [-r pairDiffRate] <in.alignment>
*
* Print the alignment in the pileup format. In the pileup format, each line represents a genomic position,
* consisting of chromosome name, coordinate, reference base, read bases, read qualities and alignment mapping
* qualities. Information on match, mismatch, indel, strand, mapping quality and start and end of a read are all
* encoded at the read base column. At this column, a dot stands for a match to the reference base on the forward strand,
* a comma for a match on the reverse strand, 'ACGTN' for a mismatch on the forward strand and 'acgtn' for a mismatch on the
* reverse strand.
*
* A pattern '\+[0-9]+[ACGTNacgtn]+' indicates there is an insertion between this reference position and the next
* reference position. The length of the insertion is given by the integer in the pattern, followed by the inserted sequence.
* Similarly, a pattern '-[0-9]+[ACGTNacgtn]+' represents a deletion from the reference.
* Also at the read base column, a symbol '^' marks the start of a read segment which is a contiguous subsequence on the read
* separated by 'N/S/H' CIGAR operations. The ASCII of the character following '^' minus 33 gives the mapping quality.
* A symbol '$' marks the end of a read segment.
*/
public class PileupWithContextWalker extends LocusWalker<Integer, Integer> implements TreeReducible<Integer> {
@Argument(fullName="alwaysShowSecondBase",doc="If true, prints dummy bases for the second bases in the BAM file where they are missing",required=false)
public boolean alwaysShowSecondBase = false;
//@Argument(fullName="showSecondBaseQuals",doc="If true, prints out second base qualities in the pileup",required=false)
//public boolean showSecondBaseQuals = false;
@Argument(fullName="qualsAsInts",doc="If true, prints out qualities in the pileup as comma-separated integers",required=false)
public boolean qualsAsInts = false;
@ -68,7 +48,7 @@ public class PileupWithContextWalker extends LocusWalker<Integer, Integer> imple
public Integer map(RefMetaDataTracker tracker, char ref, LocusContext context) {
ReadBackedPileup pileup = new ReadBackedPileup(ref, context);
String bases = pileup.getBases();
String bases = pileup.getBasesWithStrand();
if ( bases.equals("") && FLAG_UNCOVERED_BASES ) {
bases = "***UNCOVERED_SITE***";
@ -82,14 +62,6 @@ public class PileupWithContextWalker extends LocusWalker<Integer, Integer> imple
}
if ( secondBasePileup != null ) extras.append(" ").append(secondBasePileup);
/*
if ( showSecondBaseQuals ) {
String secondQualPileup = pileup.getSecondaryQualPileup();
if ( secondQualPileup == null )
secondQualPileup = Utils.dupString((char)(33), bases.length());
extras.append(" ").append(secondQualPileup);
}
*/
if (contig == null || !context.getContig().equals(contig)) {
contig = context.getContig();
contigSeq = refSeq.getSequence(contig);
@ -109,9 +81,7 @@ public class PileupWithContextWalker extends LocusWalker<Integer, Integer> imple
String rodString = "";
for ( ReferenceOrderedDatum datum : tracker.getAllRods() ) {
if ( datum != null && ! (datum instanceof rodDbSNP)) {
//System.out.printf("rod = %s%n", datum.toSimpleString());
rodString += datum.toSimpleString();
//System.out.printf("Rod string %s%n", rodString);
}
}
@ -122,10 +92,7 @@ public class PileupWithContextWalker extends LocusWalker<Integer, Integer> imple
if ( rodString != "" )
rodString = "[ROD: " + rodString + "]";
//if ( context.getLocation().getStart() % 1 == 0 ) {
//System.out.printf("quals as ints %b%n", qualsAsInts);
out.printf("%s%s %s%n", pileup.getPileupString(qualsAsInts), extras, rodString);
//}
out.printf("%s%s %s%n", pileup.getPileupWithStrandString(qualsAsInts), extras, rodString);
if ( EXTENDED ) {
String probDists = pileup.getProbDistPileup();

23
java/src/org/broadinstitute/sting/utils/BasicPileup.java
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@ -37,6 +37,26 @@ abstract public class BasicPileup implements Pileup {
return bases.toString();
}
public static String baseWithStrandPileupAsString( List<SAMRecord> reads, List<Integer> offsets ) {
StringBuilder bases = new StringBuilder();
for ( int i = 0; i < reads.size(); i++ ) {
SAMRecord read = reads.get(i);
int offset = offsets.get(i);
char base = (char) read.getReadBases()[offset];
base = Character.toUpperCase(base);
if (read.getReadNegativeStrandFlag()) {
base = Character.toLowerCase(base);
}
bases.append(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++ ) {
@ -97,10 +117,9 @@ abstract public class BasicPileup implements Pileup {
byte[] compressedQuals = (byte[]) read.getAttribute("SQ");
byte base2;
//byte qual2;
if (compressedQuals != null && compressedQuals.length == read.getReadLength()) {
base2 = (byte) BaseUtils.baseIndexToSimpleBase(QualityUtils.compressedQualityToBaseIndex(compressedQuals[offset]));
//qual2 = QualityUtils.probToQual(QualityUtils.compressedQualityToProb(compressedQuals[offset]));
hasAtLeastOneSQField = true;
} else {
base2 = (byte) '.';

13
java/src/org/broadinstitute/sting/utils/ReadBackedPileup.java
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@ -50,6 +50,10 @@ public class ReadBackedPileup extends BasicPileup {
return basePileupAsString(reads, offsets);
}
public String getBasesWithStrand() {
return baseWithStrandPileupAsString(reads, offsets);
}
public String getQuals() {
return qualPileupAsString(reads, offsets);
}
@ -92,4 +96,13 @@ public class ReadBackedPileup extends BasicPileup {
qualsAsInts ? getQualsAsInts() : getQuals(),
qualsAsInts ? getMappingQualsAsInts() : getMappingQuals() );
}
public String getPileupWithStrandString(boolean qualsAsInts) {
return String.format("%s %s %s %s %s %s",
getLocation().getContig(), getLocation().getStart(), // chromosome name and coordinate
getRef(), // reference base
getBasesWithStrand(),
qualsAsInts ? getQualsAsInts() : getQuals(),
qualsAsInts ? getMappingQualsAsInts() : getMappingQuals() );
}
}