From 5c5151c4e747c094397103b07e718040d8bbc6a7 Mon Sep 17 00:00:00 2001
From: sjia <sjia@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 24 Sep 2009 02:48:29 +0000
Subject: [PATCH] Creates ped file from reads

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1711 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../HLAcaller/CreatePedFileWalker.java        | 94 +++++++++++++++++++
 1 file changed, 94 insertions(+)
 create mode 100644 java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/CreatePedFileWalker.java

diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/CreatePedFileWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/CreatePedFileWalker.java
new file mode 100644
index 000000000..41bc1f173
--- /dev/null
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/CreatePedFileWalker.java
@@ -0,0 +1,94 @@
+/*
+ * Creates a ped file given reads (for SNP analysis, imputation, etc)
+ */
+
+package org.broadinstitute.sting.playground.gatk.walkers.HLAcaller;
+import net.sf.samtools.SAMRecord;
+import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
+import org.broadinstitute.sting.playground.gatk.walkers.HLAcaller.ReadCigarFormatter;
+import org.broadinstitute.sting.gatk.walkers.*;
+
+import java.io.FileInputStream;
+import java.io.BufferedReader;
+import java.io.DataInputStream;
+import java.io.InputStreamReader;
+import java.util.ArrayList;
+import java.util.Hashtable;
+import java.util.List;
+import java.lang.Math;
+/**
+ *
+ * @author shermanjia
+ */
+@Requires({DataSource.READS, DataSource.REFERENCE})
+public class CreatePedFileWalker extends ReadWalker<Integer, Integer> {
+    ReadCigarFormatter formatter = new ReadCigarFormatter();
+    char c;
+    boolean DEBUG = false;
+    int HLA_A_start = 30018310;
+    int HLA_A_end = 30021211;
+    String[] SNPnames;
+    String SNPname;
+    int start, end;
+    Integer I;
+
+    Hashtable indexer = new Hashtable();
+
+    public Integer reduceInit() {
+        SNPnames = new String[HLA_A_end-HLA_A_start+1];
+        start = HLA_A_start;
+        end = HLA_A_end;
+
+        indexer.put('A', (Integer) 1);
+        indexer.put('C', (Integer) 2);
+        indexer.put('G', (Integer) 3);
+        indexer.put('T', (Integer) 4);
+        indexer.put('D', (Integer) 0); // D for deletion
+        out.print("Reads:\n");
+        return 0;
+    }
+
+
+
+    public Integer map(char[] ref, SAMRecord read) {
+
+        int readstart = read.getAlignmentStart();
+        int readstop = read.getAlignmentEnd();
+
+        if(readstart <= HLA_A_end && readstop >= HLA_A_start){
+            String s = formatter.FormatRead(read.getCigarString(),read.getReadString());
+            String name = read.getReadName();
+
+            out.printf("%s\t%s\t0\t0\tM",name,name);
+
+            for (int i = start; i <= end; i++){
+
+                if (i - readstart < s.length() && i - readstart >= 0){
+                    c = s.charAt(i-readstart);
+                    I = (Integer) indexer.get(c);
+                    out.printf("\t%s %s",I,I);
+                }else{
+                    out.print("\t0 0");
+                }
+            }
+            out.printf("\n");
+        }
+        return 1;
+    }
+
+
+
+    public Integer reduce(Integer value, Integer sum) {
+
+        return value + sum;
+    }
+
+    public void onTraversalDone(Integer value) {
+        out.print("\nSNP names:\n");
+        for (int pos = start; pos <= end; pos++){
+            SNPname = "M CHR6_POS" + String.valueOf(pos);
+            SNPnames[pos-start]=SNPname;
+            out.printf("%s\n",SNPname);
+        }
+    }
+}