From 8bd345ba002f7d7f1f97435f995d00a7f974e3a1 Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Tue, 29 Sep 2009 15:58:43 +0000
Subject: [PATCH] Generalized deletions in pileup

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1739 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/utils/BasicPileup.java              | 19 ++++++++++++++++---
 .../sting/utils/ReadBackedPileup.java         |  9 +++------
 2 files changed, 19 insertions(+), 9 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/utils/BasicPileup.java b/java/src/org/broadinstitute/sting/utils/BasicPileup.java
index bb2066465..6de07b1c3 100755
--- a/java/src/org/broadinstitute/sting/utils/BasicPileup.java
+++ b/java/src/org/broadinstitute/sting/utils/BasicPileup.java
@@ -15,6 +15,15 @@ import java.util.Random;
  * To change this template use File | Settings | File Templates.
  */
 abstract public class BasicPileup implements Pileup {
+
+    public static final char DELETION_CHAR = 'D';
+
+    protected boolean includeDeletions = false;
+
+    public void setIncludeDeletionsInPileupString(boolean value) {
+	includeDeletions = value;
+    }
+
     public String getPileupString()
     {
         return String.format("%s: %s %s %s", getLocation(), getRef(), getBases(), getQuals());
@@ -29,8 +38,12 @@ abstract public class BasicPileup implements Pileup {
     }
 
     public static String basePileupAsString( List<SAMRecord> reads, List<Integer> offsets ) {
+	return basePileupAsString( reads, offsets, false );
+    }
+
+    public static String basePileupAsString( List<SAMRecord> reads, List<Integer> offsets, boolean includeDeletions ) {
         StringBuilder bases = new StringBuilder();
-        for ( byte base : basePileup(reads, offsets)) {
+        for ( byte base : basePileup(reads, offsets, includeDeletions)) {
             bases.append((char)base);
         }
         return bases.toString();
@@ -50,7 +63,7 @@ abstract public class BasicPileup implements Pileup {
 	    char base;
 	    if ( offset == -1 ) {
 		if ( includeDeletions )
-		    base = 'D';
+		    base = DELETION_CHAR;
 		else
 		    continue;
 	    } else {
@@ -79,7 +92,7 @@ abstract public class BasicPileup implements Pileup {
             int offset = offsets.get(i);
 	    if ( offset == -1 ) {
 		if ( includeDeletions )
-		    bases.add((byte)'D');
+		    bases.add((byte)DELETION_CHAR);
 	    } else {
 		bases.add(read.getReadBases()[offset]);
 	    }
diff --git a/java/src/org/broadinstitute/sting/utils/ReadBackedPileup.java b/java/src/org/broadinstitute/sting/utils/ReadBackedPileup.java
index 60a2fecaf..36ea48f89 100755
--- a/java/src/org/broadinstitute/sting/utils/ReadBackedPileup.java
+++ b/java/src/org/broadinstitute/sting/utils/ReadBackedPileup.java
@@ -17,7 +17,6 @@ public class ReadBackedPileup extends BasicPileup {
     char ref;
     List<SAMRecord> reads;
     List<Integer> offsets;
-    boolean includeDeletions = false;
 
     public ReadBackedPileup(char ref, AlignmentContext context ) {
         this(context.getLocation(), ref, context.getReads(), context.getOffsets());
@@ -38,8 +37,6 @@ public class ReadBackedPileup extends BasicPileup {
     public List<SAMRecord> getReads() { return reads; }
     public List<Integer> getOffsets() { return offsets; }
 
-    public void includeDeletionsInPileupString() { includeDeletions = true; }
-
     public GenomeLoc getLocation() {
         return loc;
     }
@@ -49,11 +46,11 @@ public class ReadBackedPileup extends BasicPileup {
     }
 
     public String getBases() {
-        return basePileupAsString(reads, offsets);
+        return basePileupAsString(reads, offsets, includeDeletions);
     }
 
     public String getBasesWithStrand() {
-        return baseWithStrandPileupAsString(reads, offsets);
+        return baseWithStrandPileupAsString(reads, offsets, includeDeletions);
     }
 
     public String getQuals() {
@@ -82,7 +79,7 @@ public class ReadBackedPileup extends BasicPileup {
     }
 
     public String getBasePileupAsCountsString() {
-        String bases = basePileupAsString(reads, offsets);
+        String bases = basePileupAsString(reads, offsets, includeDeletions);
 
 	int[] counts = new int[4];
 	for (int i = 0; i < reads.size(); i++)