Quick fix for Danny Lieber: flesh out the additional functionality required

to align to a reference other than what's specified in the header.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5133 348d0f76-0448-11de-a6fe-93d51630548a

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

@@ -195,6 +195,12 @@ public class Alignment {
         if(newSAMHeader != null)
             read.setHeader(newSAMHeader);
 
+        // If we're realigning a previously aligned record, strip out the placement of the alignment.
+        read.setReferenceName(SAMRecord.NO_ALIGNMENT_REFERENCE_NAME);
+        read.setAlignmentStart(SAMRecord.NO_ALIGNMENT_START);
+        read.setMateReferenceName(SAMRecord.NO_ALIGNMENT_REFERENCE_NAME);
+        read.setMateAlignmentStart(SAMRecord.NO_ALIGNMENT_START);        
+
         if(alignment != null) {
             read.setReadUmappedFlag(false);
             read.setReferenceIndex(alignment.getContigIndex());

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

@@ -25,6 +25,7 @@
 
 package org.broadinstitute.sting.alignment;
 
+import org.broadinstitute.sting.gatk.io.StingSAMFileWriter;
 import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Output;
@@ -49,28 +50,19 @@ import java.io.PrintStream;
  */
 @WalkerName("Align")
 public class AlignmentWalker extends ReadWalker<Integer,Integer> {
-    @Argument(fullName="BWTPrefix",shortName="BWT",doc="Index files generated by bwa index -d bwtsw",required=false)
+    @Argument(fullName="target_reference",shortName="target_ref",doc="The reference to which reads in the source file should be aligned.  Alongside this reference should sit index files " +
-    private String prefix = null;
+                                                                     "generated by bwa index -d bwtsw.  If unspecified, will default " +
-
+                                                                     "to the reference specified via the -R argument.",required=false)
-    @Argument(fullName = "outputBam", shortName = "ob", doc = "Write output to this BAM filename instead of STDOUT", required = false)
+    private File targetReferenceFile = null;
-    private String outputBamFile = null;
 
     @Output
-    private PrintStream out = null;
+    private StingSAMFileWriter out = null;
-
-    @Argument(fullName = "bam_compression", shortName = "compress", doc = "Compression level to use for writing BAM files", required = false)
-    private Integer bamCompression = 5;
 
     /**
      * The actual aligner.
      */
     private BWACAligner aligner = null;
 
-    /**
-     * Target for reads to output.
-     */
-    private SAMFileWriter outputBam = null;
-
     /**
      * New header to use, if desired.
      */
@@ -81,23 +73,20 @@ public class AlignmentWalker extends ReadWalker<Integer,Integer> {
      */    
     @Override
     public void initialize() {
-        if(prefix == null)
+        if(targetReferenceFile == null)
-            prefix = getToolkit().getArguments().referenceFile.getAbsolutePath();        
+            targetReferenceFile = getToolkit().getArguments().referenceFile;
-        BWTFiles bwtFiles = new BWTFiles(prefix);
+        BWTFiles bwtFiles = new BWTFiles(targetReferenceFile.getAbsolutePath());
         BWAConfiguration configuration = new BWAConfiguration();
         aligner = new BWACAligner(bwtFiles,configuration);
 
         // Take the header of the SAM file, tweak it by adding in the reference dictionary and specifying that the target file is unsorted.
         header = getToolkit().getSAMFileHeader().clone();
         SAMSequenceDictionary referenceDictionary =
-                ReferenceSequenceFileFactory.getReferenceSequenceFile(getToolkit().getArguments().referenceFile).getSequenceDictionary();
+                ReferenceSequenceFileFactory.getReferenceSequenceFile(targetReferenceFile).getSequenceDictionary();
         header.setSequenceDictionary(referenceDictionary);
         header.setSortOrder(SAMFileHeader.SortOrder.unsorted);
 
-        if (outputBamFile != null) {
+        out.writeHeader(header);
-            SAMFileWriterFactory factory = new SAMFileWriterFactory();
-            outputBam = factory.makeBAMWriter(header, false, new File(outputBamFile), bamCompression);
-        }
     }
 
     /**
@@ -109,11 +98,7 @@ public class AlignmentWalker extends ReadWalker<Integer,Integer> {
     @Override
     public Integer map(ReferenceContext ref, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
         SAMRecord alignedRead = aligner.align(read,header);
-        if (outputBam != null) {
+        out.addAlignment(alignedRead);
-            outputBam.addAlignment(alignedRead);
-        } else {
-            out.println(alignedRead.format());
-        }
         return 1;
     }
 
@@ -142,8 +127,6 @@ public class AlignmentWalker extends ReadWalker<Integer,Integer> {
     @Override
     public void onTraversalDone(Integer result) {
         aligner.close();
-        if (outputBam != null)
-            outputBam.close();
         super.onTraversalDone(result);
     }
 

java/test/org/broadinstitute/sting/alignment/AlignerIntegrationTest.java

@@ -19,7 +19,7 @@ public class AlignerIntegrationTest extends WalkerTest {
                 "-R /humgen/gsa-scr1/GATK_Data/bwa/human_b36_both.fasta" +
                         " -T Align" +
                         " -I " + validationDataLocation + "NA12878_Pilot1_20.trimmed.unmapped.bam" +
-                        " -ob %s",
+                        " -o %s",
                 1, // just one output file
                 Arrays.asList(md5));
         executeTest("testBasicAlignment", spec);