BWA: odds and ends. Get rid of some spurious debug code that was accidentally

checked in.  Add a better way to write out unmapped reads (thanks Kiran!)  Add 
a pre-built version of the shared library to the repository for early adoption.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2111 348d0f76-0448-11de-a6fe-93d51630548a

c/bwa/org_broadinstitute_sting_alignment_bwa_c_BWACAligner.cpp

@@ -228,7 +228,6 @@ JNIEXPORT jobjectArray JNICALL Java_org_broadinstitute_sting_alignment_bwa_c_BWA
   Alignment* alignments = NULL;
   unsigned num_alignments = 0;
   bwa->generate_alignments_from_paths((const char*)read_bases,read_length,paths,num_paths,best_count,second_best_count,alignments,num_alignments);
-  num_alignments = 0;
 
   jobjectArray java_alignments = env->NewObjectArray(num_alignments, env->FindClass("org/broadinstitute/sting/alignment/Alignment"), NULL);  
   if(java_alignments == NULL) return NULL;

java/src/org/broadinstitute/sting/alignment/Alignment.java

@@ -202,7 +202,7 @@ public class Alignment {
             read.setMappingQuality(alignment.getMappingQuality());
             read.setCigar(alignment.getCigar());
             if(alignment.isNegativeStrand()) {
-                read.setReadBases(BaseUtils.reverse(read.getReadBases()));
+                read.setReadBases(BaseUtils.simpleReverseComplement(read.getReadBases()));
                 read.setBaseQualities(BaseUtils.reverse(read.getBaseQualities()));
             }
             read.setAttribute("NM",alignment.getEditDistance());

java/src/org/broadinstitute/sting/alignment/AlignmentValidationWalker.java

@@ -29,11 +29,6 @@ public class AlignmentValidationWalker extends ReadWalker<Integer,Integer> {
      */
     private BWACAligner aligner = null;
 
-    /**
-     * Number of reads processed.
-     */
-    private int count = 0;
-
     /**
      * Create an aligner object.  The aligner object will load and hold the BWT until close() is called.
      */
@@ -105,10 +100,6 @@ public class AlignmentValidationWalker extends ReadWalker<Integer,Integer> {
             throw new StingException(String.format("Read %s mismatches!", read.getReadName()));
         }
 
-        if(++count % 10000 == 0) {
-            logger.info(String.format("Processed %d reads", count));
-        }
-
         return 1;
     }
 

java/src/org/broadinstitute/sting/alignment/AlignmentWalker.java

@@ -1,7 +1,6 @@
 package org.broadinstitute.sting.alignment;
 
 import org.broadinstitute.sting.utils.cmdLine.Argument;
-import org.broadinstitute.sting.utils.Utils;
 import org.broadinstitute.sting.gatk.walkers.ReadWalker;
 import org.broadinstitute.sting.gatk.walkers.WalkerName;
 import org.broadinstitute.sting.alignment.bwa.c.BWACAligner;
@@ -10,6 +9,8 @@ import org.broadinstitute.sting.alignment.bwa.BWTFiles;
 import net.sf.samtools.*;
 import net.sf.picard.reference.ReferenceSequenceFileFactory;
 
+import java.io.File;
+
 /**
  * Align reads to the reference specified by BWTPrefix.
  *
@@ -25,7 +26,7 @@ public class AlignmentWalker extends ReadWalker<Integer,Integer> {
     String outputBamFile = null;
 
     @Argument(fullName = "bam_compression", shortName = "compress", doc = "Compression level to use for writing BAM files", required = false)
-    public Integer bamCompression = 5;        
+    Integer bamCompression = 5;
 
     /**
      * The actual aligner.
@@ -40,7 +41,7 @@ public class AlignmentWalker extends ReadWalker<Integer,Integer> {
     /**
      * New header to use, if desired.
      */
-    private SAMFileHeader header = null;
+    private SAMFileHeader header;
 
     /** Must return true for reads that need to be processed. Reads, for which this method return false will
      * be skipped by the engine and never passed to the walker.
@@ -59,21 +60,16 @@ public class AlignmentWalker extends ReadWalker<Integer,Integer> {
         BWAConfiguration configuration = new BWAConfiguration();
         aligner = new BWACAligner(bwtFiles,configuration);
 
-        // HACK: If the sequence dictionary in the existing header is null, stuff the contents of the current reference
+        // Take the header of the SAM file, tweak it by adding in the reference dictionary and specifying that the target file is unsorted.
-        //       into it, so that the sequence has something to which to back-align.
+        header = getToolkit().getSAMFileHeader().clone();
-        SAMFileHeader originalHeader = getToolkit().getSAMFileHeader();
+        SAMSequenceDictionary referenceDictionary =
-        if(originalHeader.getSequenceDictionary().isEmpty()) {
+                ReferenceSequenceFileFactory.getReferenceSequenceFile(getToolkit().getArguments().referenceFile).getSequenceDictionary();
-            header = originalHeader.clone();
+        header.setSequenceDictionary(referenceDictionary);
-            SAMSequenceDictionary referenceDictionary =
+        header.setSortOrder(SAMFileHeader.SortOrder.unsorted);
-                    ReferenceSequenceFileFactory.getReferenceSequenceFile(getToolkit().getArguments().referenceFile).getSequenceDictionary();
-            header.setSequenceDictionary(referenceDictionary);            
-        }
-        else
-            header = originalHeader;
 
-        if ( outputBamFile != null ) {
+        if (outputBamFile != null) {
-            // Stuff the header from the fasta into that of the sequence dictionary.
+            SAMFileWriterFactory factory = new SAMFileWriterFactory();
-            outputBam = Utils.createSAMFileWriterWithCompression(header, false, outputBamFile, bamCompression);
+            outputBam = factory.makeBAMWriter(header, false, new File(outputBamFile), bamCompression);
         }
     }
 
@@ -119,6 +115,8 @@ public class AlignmentWalker extends ReadWalker<Integer,Integer> {
     @Override
     public void onTraversalDone(Integer result) {
         aligner.close();
+        if (outputBam != null)
+            outputBam.close();
         super.onTraversalDone(result);
     }