From 3b79f9eddcae83769c4a17a1bcfd75388e4dd8ae Mon Sep 17 00:00:00 2001
From: hanna <hanna@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 24 Sep 2009 21:41:30 +0000
Subject: [PATCH] Support 'N's and other mismatch characters in the reference.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1721 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../alignment/bwa/AlignerTestHarness.java     | 25 ++-----------------
 .../sting/alignment/bwa/LowerBound.java       | 11 +++++---
 2 files changed, 10 insertions(+), 26 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/alignment/bwa/AlignerTestHarness.java b/java/src/org/broadinstitute/sting/alignment/bwa/AlignerTestHarness.java
index 4e11e4e2c..43aad684e 100644
--- a/java/src/org/broadinstitute/sting/alignment/bwa/AlignerTestHarness.java
+++ b/java/src/org/broadinstitute/sting/alignment/bwa/AlignerTestHarness.java
@@ -20,9 +20,6 @@ import net.sf.samtools.SAMFileReader;
  * @version 0.1
  */
 public class AlignerTestHarness {
-    private static BWT bwt;
-    private static SuffixArray suffixArray;
-
     public static void main( String argv[] ) throws FileNotFoundException {
         if( argv.length != 5 ) {
             System.out.println("PerfectAlignerTestHarness <fasta> <bwt> <rbwt> <sa> <bam>");
@@ -49,29 +46,11 @@ public class AlignerTestHarness {
 
         for(SAMRecord read: reader) {
             count++;
-            //if( count > 5000 ) break;
-            //if( count != 10959 ) continue;
+            //if( count > 39 ) break;
+            //if( count != 39 ) continue;
             //if( !read.getReadName().endsWith("1507:1636#0") )
             //    continue;
 
-            boolean skipRead = false;
-
-            /*
-            for( CigarElement cigarElement: read.getCigar().getCigarElements() ) {
-                if( cigarElement.getOperator() != CigarOperator.M ) {
-                    System.out.printf("Skipping read %s because it features indels%n", read.getReadName());
-                    skipRead = true;
-                }
-            }
-            */
-
-            if(read.getReadString().indexOf("N") >= 0) {
-                System.out.printf("Skipping read %s because it contains Ns%n", read.getReadName());
-                skipRead = true;
-            }
-
-            if(skipRead) continue;
-
             List<Alignment> alignments = aligner.align(read);
             if(alignments.size() == 0 )
                 throw new StingException(String.format("Unable to align read %s to reference; count = %d",read.getReadName(),count));
diff --git a/java/src/org/broadinstitute/sting/alignment/bwa/LowerBound.java b/java/src/org/broadinstitute/sting/alignment/bwa/LowerBound.java
index 82e654ce1..cd091b69a 100644
--- a/java/src/org/broadinstitute/sting/alignment/bwa/LowerBound.java
+++ b/java/src/org/broadinstitute/sting/alignment/bwa/LowerBound.java
@@ -54,9 +54,14 @@ public class LowerBound {
         int loIndex = 0, hiIndex = bwt.length(), mismatches = 0;
         for( int i = bases.length-1; i >= 0; i-- ) {
             Base base = Base.fromASCII(bases[i]);
-            loIndex = bwt.counts(base) + bwt.occurrences(base,loIndex-1) + 1;
-            hiIndex = bwt.counts(base) + bwt.occurrences(base,hiIndex);
-            if( loIndex > hiIndex ) {
+
+            // Ignore non-ACGT bases.
+            if( base != null ) {
+                loIndex = bwt.counts(base) + bwt.occurrences(base,loIndex-1) + 1;
+                hiIndex = bwt.counts(base) + bwt.occurrences(base,hiIndex);            
+            }
+
+            if( base == null || loIndex > hiIndex ) {
                 loIndex = 0;
                 hiIndex = bwt.length();
                 mismatches++;