From 385736469c70832152b1c2901c1615f13d437846 Mon Sep 17 00:00:00 2001
From: depristo <depristo@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 1 Apr 2009 00:47:47 +0000
Subject: [PATCH] High performance pileup code and utilities

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@242 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/gatk/walkers/PileupWalker.java      | 14 ++-----
 .../org/broadinstitute/sting/utils/Utils.java | 40 +++++++++++++++++++
 2 files changed, 44 insertions(+), 10 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java
index a6063e0d1..4cebc31d7 100644
--- a/java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java
@@ -4,9 +4,11 @@ import org.broadinstitute.sting.gatk.LocusContext;
 import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
 import org.broadinstitute.sting.gatk.refdata.rodDbSNP;
 import org.broadinstitute.sting.utils.cmdLine.Argument;
+import org.broadinstitute.sting.utils.Utils;
 import net.sf.samtools.SAMRecord;
 
 import java.util.List;
+import java.util.ArrayList;
 
 /**
  * Created by IntelliJ IDEA.
@@ -26,19 +28,11 @@ public class PileupWalker extends LocusWalker<Integer, Integer> {
         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) {
         List<SAMRecord> reads = context.getReads();
         List<Integer> offsets = context.getOffsets();
-        String bases = "";
-        String quals = "";
-        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);
-        }
+        String bases = Utils.basePileupAsString(reads, offsets);
+        String quals = Utils.qualPileupAsString(reads, offsets);
 
         if ( bases.equals("") && FLAG_UNCOVERED_BASES ) {
             bases = "*** UNCOVERED SITE ***";
diff --git a/java/src/org/broadinstitute/sting/utils/Utils.java b/java/src/org/broadinstitute/sting/utils/Utils.java
index 65eaa45c1..09b0e86be 100755
--- a/java/src/org/broadinstitute/sting/utils/Utils.java
+++ b/java/src/org/broadinstitute/sting/utils/Utils.java
@@ -118,6 +118,46 @@ public class Utils {
         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) {
         return subseq(fullArray, 0, fullArray.length);
     }