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

java/src/org/broadinstitute/sting/gatk/walkers/PileupWithContextWalker.java

@@ -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 ) {
+        out.printf("%s%s %s%n", pileup.getPileupWithStrandString(qualsAsInts), extras, rodString);
-        //System.out.printf("quals as ints %b%n", qualsAsInts);
-        out.printf("%s%s %s%n", pileup.getPileupString(qualsAsInts), extras, rodString);
-        //}
 
         if ( EXTENDED ) {
             String probDists = pileup.getProbDistPileup();

java/src/org/broadinstitute/sting/utils/BasicPileup.java

@@ -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) '.';

java/src/org/broadinstitute/sting/utils/ReadBackedPileup.java

@@ -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() );
+    }
 }