From 6db9a00a0baa286b625bd40240c46da583b7af8f Mon Sep 17 00:00:00 2001
From: kiran <kiran@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 8 Apr 2009 21:48:24 +0000
Subject: [PATCH] SAMFileWriter doesn't appear to flush the buffer when its
 destructor is called.  You have to call the close() method.  Also, choose a
 random base for Ns in the forward and reverse strands so that samtools
 doesn't pitch a fit.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@338 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../RepairBadlyCombinedSamFile.java           | 32 ++++++++++++++++---
 1 file changed, 28 insertions(+), 4 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/playground/fourbasecaller/RepairBadlyCombinedSamFile.java b/java/src/org/broadinstitute/sting/playground/fourbasecaller/RepairBadlyCombinedSamFile.java
index 2b09b718a..f70c8cc46 100644
--- a/java/src/org/broadinstitute/sting/playground/fourbasecaller/RepairBadlyCombinedSamFile.java
+++ b/java/src/org/broadinstitute/sting/playground/fourbasecaller/RepairBadlyCombinedSamFile.java
@@ -4,6 +4,7 @@ import org.broadinstitute.sting.utils.cmdLine.CommandLineProgram;
 import org.broadinstitute.sting.utils.QualityUtils;
 
 import java.io.File;
+import java.util.Random;
 
 import net.sf.samtools.SAMFileReader;
 import net.sf.samtools.SAMRecord;
@@ -15,6 +16,7 @@ public class RepairBadlyCombinedSamFile extends CommandLineProgram {
 
     public File ASAM;
     public File OSAM;
+    private Random rg;
 
     public static void main(String[] argv) {
         Instance = new RepairBadlyCombinedSamFile();
@@ -27,19 +29,21 @@ public class RepairBadlyCombinedSamFile extends CommandLineProgram {
     }
 
     protected int execute() {
+        rg = new Random();
+        
         SAMFileReader asamr = new SAMFileReader(ASAM);
         asamr.setValidationStringency(SAMFileReader.ValidationStringency.SILENT);
 
         SAMFileWriter osamw = new SAMFileWriterFactory().makeSAMOrBAMWriter(asamr.getFileHeader(), false, OSAM);
 
-
         for (SAMRecord samRecord : asamr) {
+            byte[] bases = samRecord.getReadBases();
+            byte[] newbases = new byte[bases.length];
+
             if (samRecord.getReadNegativeStrandFlag()) {
-                byte[] bases = samRecord.getReadBases();
                 byte[] quals = samRecord.getBaseQualities();
                 byte[] sq    = (byte[]) samRecord.getAttribute("SQ");
 
-                byte[] newbases = new byte[bases.length];
                 byte[] newquals = new byte[bases.length];
                 byte[] newsq    = new byte[bases.length];
 
@@ -50,7 +54,7 @@ public class RepairBadlyCombinedSamFile extends CommandLineProgram {
                         case 'C': newbase = 'G'; break;
                         case 'G': newbase = 'C'; break;
                         case 'T': newbase = 'A'; break;
-                        default: newbase = 'A'; // hack.  This is so downstream applications don't barf on an ambiguous base 'matching' the reference
+                        default: newbase = getRandomBase(); // hack.  This is so downstream applications don't barf on an ambiguous base 'matching' the reference
                     }
                     newbases[i] = newbase;
                     newquals[i] = quals[bases.length - i - 1];
@@ -60,11 +64,31 @@ public class RepairBadlyCombinedSamFile extends CommandLineProgram {
                 samRecord.setReadBases(newbases);
                 samRecord.setBaseQualities(newquals);
                 samRecord.setAttribute("SQ", newsq);
+            } else {
+                for (int i = 0; i < bases.length; i++) {
+                    newbases[i] = (bases[i] == 'A' || bases[i] == 'C' || bases[i] == 'G' || bases[i] == 'T') ? bases[i] : getRandomBase();
+                }
+
+                samRecord.setReadBases(newbases);
             }
             
             osamw.addAlignment(samRecord);
         }
 
+        osamw.close();
+
         return 0;
     }
+
+    private byte getRandomBase() {
+        int baseIndex = rg.nextInt(4);
+
+        switch (baseIndex) {
+            case 0: return 'A';
+            case 1: return 'C';
+            case 2: return 'G';
+            case 3: return 'T';
+            default: return '.'; // unreachable
+        }
+    }
 }