Reads cigar files

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1713 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/ReadCigarFormatter.java

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+/*
+ * To change this template, choose Tools | Templates
+ * and open the template in the editor.
+ */
+
+package org.broadinstitute.sting.playground.gatk.walkers.HLAcaller;
+
+/**
+ * Returns formatted read given read string and cigar string
+ * Essentially removes header bases, soft clipped bases, and currently removes insertions
+ * Deletions coded as "D"
+ *
+ * @author shermanjia
+ */
+public class ReadCigarFormatter {
+    public String FormatRead(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;
+    }
+
+}