Moving some useful and stable walkers to core:

- ClipReads
- PrintRODs (generalized to print all RODs that are Variations)
- FixBAMSortOrderTag (added documentation to walker so that people know what it does and why)



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2238 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/gatk/walkers/ClipReadsWalker.java

@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.playground.gatk.walkers;
+package org.broadinstitute.sting.gatk.walkers;
 
 import net.sf.samtools.*;
 import net.sf.picard.reference.ReferenceSequenceFileFactory;
@@ -8,9 +8,6 @@ import org.broadinstitute.sting.utils.cmdLine.Argument;
 import org.broadinstitute.sting.utils.Utils;
 import org.broadinstitute.sting.utils.Pair;
 import org.broadinstitute.sting.utils.BaseUtils;
-import org.broadinstitute.sting.gatk.walkers.Requires;
-import org.broadinstitute.sting.gatk.walkers.DataSource;
-import org.broadinstitute.sting.gatk.walkers.ReadWalker;
 
 import java.util.*;
 import java.util.regex.Pattern;

java/src/org/broadinstitute/sting/gatk/walkers/FixBAMSortOrderTag.java

@@ -1,6 +1,17 @@
-package org.broadinstitute.sting.playground.gatk.walkers;
+package org.broadinstitute.sting.gatk.walkers;
+
+/*  Motivation: BAM files created by samtools which are sorted often don't
+ *   have the sort order set to 'coordinate' in the BAM header (instead it's
+ *   marked as 'unsorted'.  Because BAMs are binary files, there's no way to
+ *   easily change the tag.
+ *
+ *  This walker rewrites a BAM file so that the output is identical to the input
+ *   except that the sort order tag is set to 'coordinate'.
+ *
+ *  Important note: to run properly in the GATK, the '-U' flag must be used so that
+ *   the input BAM file not be rejected by the system.
+ */
 
-import org.broadinstitute.sting.gatk.walkers.ReadWalker;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 import org.broadinstitute.sting.utils.cmdLine.Argument;
 import net.sf.samtools.SAMFileWriter;
@@ -16,7 +27,7 @@ import java.io.File;
  * Date: Oct 9, 2009
  * Time: 2:21:08 PM
  */
-public class UpdateSAMSortOrderWalker extends ReadWalker<SAMRecord, SAMFileWriter> {
+public class FixBAMSortOrderTag extends ReadWalker<SAMRecord, SAMFileWriter> {
 
     @Argument(required=true, shortName="out_bam", doc="The samfile to output to")
     public File SAM_FILE_OUTPUT_LOCATION;

java/src/org/broadinstitute/sting/gatk/walkers/PrintRODsWalker.java

@@ -23,18 +23,18 @@
  * OTHER DEALINGS IN THE SOFTWARE.
  */
 
-package org.broadinstitute.sting.playground.gatk.walkers;
+package org.broadinstitute.sting.gatk.walkers;
 
-import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
+import org.broadinstitute.sting.gatk.contexts.*;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.*;
-import org.broadinstitute.sting.gatk.walkers.*;
+import org.broadinstitute.sting.utils.genotype.Variation;
+
+import java.util.Iterator;
 
 /**
  * PrintRODsWalker prints out all of the RODs that it sees (using the ROD's toString method)
  */
-@Requires(value={DataSource.REFERENCE},referenceMetaData=@RMD(name="variant",type=ReferenceOrderedDatum.class))
+public class PrintRODsWalker extends RodWalker<Integer, Integer> {
-public class PrintRODsWalker extends RefWalker<Integer, Integer> {
 
     /**
      * Initialize the number of loci processed to zero.
@@ -52,10 +52,15 @@ public class PrintRODsWalker extends RefWalker<Integer, Integer> {
      * @return 1 if the locus was successfully processed, 0 if otherwise
      */
     public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
-        ReferenceOrderedDatum variant = tracker.lookup("variant", null);
+        if ( tracker == null )
+            return 0;
 
-        if (variant != null )
+        Iterator<ReferenceOrderedDatum> rods = tracker.getAllRods().iterator();
-            out.println(variant);
+        while ( rods.hasNext() ) {
+            ReferenceOrderedDatum rod = rods.next();
+            if ( rod instanceof Variation )
+                out.println(rod.toString());
+        }
 
         return 1;
     }