From 9422156e091f626f2bdd35d047b3bbe8e9042aa0 Mon Sep 17 00:00:00 2001
From: sjia <sjia@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 24 Sep 2009 03:12:20 +0000
Subject: [PATCH] Finds closest allele for each read in bam file

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1712 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../HLAcaller/FindClosestAlleleWalker.java    | 66 ++-----------------
 1 file changed, 4 insertions(+), 62 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/FindClosestAlleleWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/FindClosestAlleleWalker.java
index 0cbb120a7..9c2c712db 100644
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/FindClosestAlleleWalker.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/FindClosestAlleleWalker.java
@@ -5,6 +5,7 @@
 package org.broadinstitute.sting.playground.gatk.walkers.HLAcaller;
 
 import net.sf.samtools.SAMRecord;
+import org.broadinstitute.sting.playground.gatk.walkers.HLAcaller.ReadCigarFormatter;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.walkers.*;
 
@@ -40,7 +41,7 @@ public class FindClosestAlleleWalker extends ReadWalker<Integer, Integer> {
 
     Hashtable AlleleFrequencies = new Hashtable();
     int iAstart = -1, iAstop = -1, iBstart = -1, iBstop = -1, iCstart = -1, iCstop = -1;
-
+    ReadCigarFormatter formatter = new ReadCigarFormatter();
 
     public Integer reduceInit() { 
     if (!DatabaseLoaded){
@@ -56,7 +57,7 @@ public class FindClosestAlleleWalker extends ReadWalker<Integer, Integer> {
                     s = strLine.split("\\t");
                     if (s.length>=10){
                         //Parse the reads with cigar parser
-                        HLAreads.add(CigarFormatted(s[5],s[9]));
+                        HLAreads.add(formatter.FormatRead(s[5],s[9]));
                         HLAcigars.add(s[5]);
                         HLAnames.add(s[0]);
                         HLApositions.add(s[3]);
@@ -120,65 +121,6 @@ public class FindClosestAlleleWalker extends ReadWalker<Integer, Integer> {
         return 0;
     }
 
-    private String CigarFormatted(String cigar, String read){
-        // returns a cigar-formatted sequence (removes insertions, inserts 'D' to where deletions occur
-        String formattedRead = ""; char c; String count;
-        int cigarPlaceholder = 0; int subcigarLength = 0;
-        int readPlaceholder = 0; int subreadLength = 0;
-
-        //reads cigar string
-        for (int i = 0; i < cigar.length(); i++){
-            c = cigar.charAt(i);
-            if (c == 'M'){
-                //If reach M for match/mismatch, get number immediately preceeding 'M' and tack on that many characters to sequence
-                subcigarLength = i-cigarPlaceholder;
-                count = cigar.substring(cigarPlaceholder, i);
-
-                subreadLength = Integer.parseInt(count);
-                formattedRead = formattedRead + read.substring(readPlaceholder, readPlaceholder+subreadLength);
-
-                //increment placeholders
-                cigarPlaceholder = i+1;
-                readPlaceholder = readPlaceholder + subreadLength;
-            } else if (c == 'I'){
-                //***NOTE: To be modified later if needed (insertions removed here)***
-
-                //If reaches I for insertion, get number before 'I' and skip that many characters in sequence
-                count = cigar.substring(cigarPlaceholder, i);
-                subreadLength = Integer.parseInt(count);
-
-                //increment placeholders without adding inserted bases to sequence (effectively removes insertion).
-                cigarPlaceholder = i+1;
-                readPlaceholder = readPlaceholder + subreadLength;
-            } else if (c == 'H' || c == 'S'){
-                //(H = Headers or S = Soft clipped removed here)***
-
-                //If reaches H for insertion, get number before 'H' and skip that many characters in sequence
-                count = cigar.substring(cigarPlaceholder, i);
-                subreadLength = Integer.parseInt(count);
-
-                //increment cigar placeholder without adding inserted bases to sequence (effectively removes insertion).
-                cigarPlaceholder = i+1;
-            } else if (c == 'D'){
-                //If reaches D for deletion, insert 'D' into sequence as placeholder
-                count = cigar.substring(cigarPlaceholder, i);
-                subreadLength = Integer.parseInt(count);
-
-                //Add one 'D' for each deleted base
-                String deletion = "";
-                for (int j = 1; j <= subreadLength; j++){
-                    deletion = deletion + "D";
-                }
-
-                //update placeholders
-                formattedRead = formattedRead + deletion;
-                cigarPlaceholder = i+1;
-            }
-
-        }
-        return formattedRead;
-    }
-
 
     public Integer map(char[] ref, SAMRecord read) {
         int readstart = read.getAlignmentStart();
@@ -187,7 +129,7 @@ public class FindClosestAlleleWalker extends ReadWalker<Integer, Integer> {
         double[] concordance = new double[HLAreads.size()];
         double[] numcompared = new double[HLAreads.size()];
         double maxConcordance = 0;
-        String s1 = CigarFormatted(read.getCigarString(), read.getReadString());
+        String s1 = formatter.FormatRead(read.getCigarString(), read.getReadString());
         char c1, c2;
         String s2 = "", name = "";