From d4808433a1e602050a59883adee6481d2acf64ac Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Sun, 16 Aug 2009 03:46:36 +0000
Subject: [PATCH] Added option to output the locations of indels in the
 alternate reference

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1424 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../fasta/FastaAlternateReferenceWalker.java  | 35 ++++++++++++++++++-
 .../gatk/walkers/fasta/FastaSequence.java     |  7 +++-
 2 files changed, 40 insertions(+), 2 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/fasta/FastaAlternateReferenceWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/fasta/FastaAlternateReferenceWalker.java
index 0dd494a5a..7c71a4bda 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/fasta/FastaAlternateReferenceWalker.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/fasta/FastaAlternateReferenceWalker.java
@@ -7,8 +7,10 @@ import org.broadinstitute.sting.gatk.walkers.*;
 import org.broadinstitute.sting.utils.*;
 import org.broadinstitute.sting.utils.cmdLine.Argument;
 
+import java.io.*;
 import java.util.Iterator;
 
+
 // create a fasta sequence file from a reference, intervals, and rod(s) of variants
 // if there are multiple variants at a site, we take the first one seen
 
@@ -20,8 +22,23 @@ public class FastaAlternateReferenceWalker extends FastaReferenceWalker {
     private Boolean MASK_SNPS = false;
     @Argument(fullName="outputSequenomFormat", shortName="sequenom", doc="output results in sequenom format (overrides 'maskSNPs' argument)", required=false)
     private Boolean SEQUENOM = false;
+    @Argument(fullName="outputIndelPositions", shortName="indels", doc="output the positions of the indels in the new reference", required=false)
+    String indelsFile = null;
 
-    int deletionBasesRemaining = 0;
+    private int deletionBasesRemaining = 0;
+    private long basesSeen = 0;
+    private PrintWriter indelsWriter = null;
+
+    public void initialize() {
+        super.initialize();
+        if ( indelsFile != null ) {
+            try {
+                indelsWriter = new PrintWriter(indelsFile);
+            } catch (IOException e) {
+                throw new RuntimeException("Unable to open indel positions output file: " + indelsFile);
+            }
+        }
+    }
 
     public Pair<GenomeLoc, String> map(RefMetaDataTracker rodData, ReferenceContext ref, AlignmentContext context) {
         String refBase = String.valueOf(ref.getBase());
@@ -41,16 +58,32 @@ public class FastaAlternateReferenceWalker extends FastaReferenceWalker {
             AllelicVariant variant = (AllelicVariant)rod;
             if ( variant.isDeletion() ) {
                 deletionBasesRemaining = variant.length();
+                basesSeen++;
+                if ( indelsWriter != null )
+                    indelsWriter.println(fasta.getCurrentID() + ":" + basesSeen + "-" + (basesSeen + variant.length()));
                 // delete the next n bases, not this one
                 return new Pair<GenomeLoc, String>(context.getLocation(), (SEQUENOM ? refBase.concat("[-/") : refBase));
             } else if ( variant.isInsertion() ) {
+                basesSeen++;
+                if ( indelsWriter != null )
+                    indelsWriter.println(fasta.getCurrentID() + ":" + basesSeen + "-" + (basesSeen + variant.length()));
+                basesSeen += variant.length();
                 return new Pair<GenomeLoc, String>(context.getLocation(), (SEQUENOM ? refBase.concat("[+/"+variant.getAltBasesFWD()+"]") : refBase.concat(variant.getAltBasesFWD())));
             } else if ( variant.isSNP() ) {
+                basesSeen++;
                 return new Pair<GenomeLoc, String>(context.getLocation(), (SEQUENOM || MASK_SNPS ? "N" : variant.getAltBasesFWD()));
             }
         }
 
         // if we got here then we're just ref
+        basesSeen++;
         return new Pair<GenomeLoc, String>(context.getLocation(), refBase);
 	}
+
+    public void onTraversalDone(GenomeLoc sum) {
+        super.onTraversalDone(sum);
+        if ( indelsWriter != null )
+            indelsWriter.close();
+    }
+
 }
\ No newline at end of file
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/fasta/FastaSequence.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/fasta/FastaSequence.java
index b82cbdc4c..2c3c72d49 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/fasta/FastaSequence.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/fasta/FastaSequence.java
@@ -25,13 +25,18 @@ public class FastaSequence {
     public void flush() {
         printFasta(true);
         printedHeader = false;
+        sequenceCounter++;
+    }
+
+    public String getCurrentID() {
+        return String.valueOf(sequenceCounter);
     }
 
     private void printFasta(boolean printAll) {
         if ( sb.length() == 0 || (!printAll && sb.length() < 60) )
             return;
         if ( !printedHeader ) {
-            out.println(">" + sequenceCounter++);
+            out.println(">" + sequenceCounter);
             printedHeader = true;
         }
         int lines = sb.length() / 60;