Tried to add a poor man's version of seeing all reference sites in an interval, and failed. However, I did add the command line argument and a few pieces of useful code.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@206 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/gatk/GenomeAnalysisTK.java

@@ -47,7 +47,7 @@ public class GenomeAnalysisTK extends CommandLineProgram {
     public String pluginPathName = null;
     private TraversalEngine engine = null;
     public boolean DEBUGGING = false;
-
+    public boolean WALK_ALL_LOCI = false;
 
     /**
      * our log, which we want to capture anything from this class
@@ -61,7 +61,7 @@ public class GenomeAnalysisTK extends CommandLineProgram {
      * Flags don't take an argument, the associated Boolean gets set to true if the flag appears on the command line.
      */
     protected void setupArgs() {
-        m_parser.addRequiredArg("input_file", "I", "SAM or BAM file for validation", "INPUT_FILE");
+        m_parser.addRequiredArg("input_file", "I", "SAM or BAM file", "INPUT_FILE");
         m_parser.addOptionalArg("maximum_reads", "M", "Maximum number of reads to process before exiting", "MAX_READS_ARG");
         m_parser.addOptionalArg("validation_strictness", "S", "How strict should we be with validation", "STRICTNESS_ARG");
         m_parser.addOptionalArg("reference_sequence", "R", "Reference sequence file", "REF_FILE_ARG");
@@ -73,6 +73,7 @@ public class GenomeAnalysisTK extends CommandLineProgram {
         m_parser.addOptionalFlag("unsafe", "U", "If set, enables unsafe operations, nothing will be checked at runtime.", "UNSAFE");
         m_parser.addOptionalFlag("sort_on_the_fly", "F", "If set, enables on fly sorting of reads file.", "ENABLED_SORT_ON_FLY");
         m_parser.addOptionalArg("intervals_file", "V", "File containing list of genomic intervals to operate on. line := <contig> <start> <end>", "INTERVALS_FILE");
+        m_parser.addOptionalArg("all_loci", "A", "Should we process all loci, not just those covered by reads", "WALK_ALL_LOCI");
     }
 
     /**
@@ -177,6 +178,7 @@ public class GenomeAnalysisTK extends CommandLineProgram {
         engine.setSafetyChecking(!UNSAFE);
         engine.setSortOnFly(ENABLED_SORT_ON_FLY);
         engine.setThreadedIO(ENABLED_THREADED_IO);
+        engine.setWalkOverAllSites(WALK_ALL_LOCI);
         engine.initialize();
 
         Walker my_walker = null;

java/src/org/broadinstitute/sting/gatk/TraversalEngine.java

@@ -82,6 +82,7 @@ public class TraversalEngine {
     public boolean beSafeP = true;
     public boolean SORT_ON_FLY = false;
     public boolean FILTER_UNSORTED_READS = false;
+    public boolean walkOverAllSites = false;
     public int MAX_ON_FLY_SORTS = 100000;
     public long N_RECORDS_TO_PRINT = 100000;
     public boolean THREADED_IO = false;
@@ -134,6 +135,10 @@ public class TraversalEngine {
         this.THREADED_IO = threadedIO;
     }
 
+    public void setWalkOverAllSites(final boolean walkOverAllSites) {
+        this.walkOverAllSites = walkOverAllSites;
+    }
+
     public void setDebugging(final boolean d) {
         DEBUGGING = d;
     }
@@ -633,9 +638,7 @@ public class TraversalEngine {
 
                 //System.out.format("Working at %s\n", locus.getLocation().toString());
 
-                // Jump forward in the reference to this locus location
+                ReferenceIterator refSite = refIter.seekForward(locus.getLocation());
-                final ReferenceIterator refSite;
-                refSite = refIter.seekForward(locus.getLocation());
                 final char refBase = refSite.getBaseAsChar();
                 locus.setReferenceContig(refSite.getCurrentContig());
 

java/src/org/broadinstitute/sting/gatk/iterators/ReferenceIterator.java

@@ -50,6 +50,7 @@ public class ReferenceIterator implements Iterator<ReferenceIterator> {
     public char getBaseAsChar() { return getBaseAsString().charAt(0); }
     public ReferenceSequence getCurrentContig() { return currentContig; }
     public long getPosition() { return offset + 1; }
+    public GenomeLoc getLocation() { return new GenomeLoc( getCurrentContig().getName(), getPosition() ); }
     
     // --------------------------------------------------------------------------------------------------------------
     //

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

@@ -54,9 +54,9 @@ public class PileupWalker extends LocusWalker<Integer, Integer> {
         if ( rodString != "" )
             rodString = "[ROD: " + rodString + "]";
 
-        if ( context.getLocation().getStart() % 1 == 0 ) {
+        //if ( context.getLocation().getStart() % 1 == 0 ) {
         System.out.printf("%s: %s %s %s %s%n", context.getLocation(), ref, bases, quals, rodString);
-        }
+        //}
 
         return 1;
     }