intervals_file + genome_loc => intervals.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@659 348d0f76-0448-11de-a6fe-93d51630548a

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

@@ -67,10 +67,6 @@ public class GATKArgumentCollection {
     @Argument(fullName = "reference_sequence", shortName = "R", doc = "Reference sequence file", required = false)
     public File referenceFile = null;
 
-    @Element(required=false)
-    @Argument(fullName = "genome_region", shortName = "L", doc = "Genome region to operation on: from chr:start-end", required = false)
-    public String genomeRegion = null;
-
     @Element(required=false)
     @Argument(fullName = "analysis_type", shortName = "T", doc = "Type of analysis to run")
     public String analysisName = null;
@@ -112,8 +108,8 @@ public class GATKArgumentCollection {
     public String downsampleCoverage = null;
 
     @Element(required=false)
-    @Argument(fullName = "intervals_file", shortName = "V", doc = "File containing list of genomic intervals to operate on. line := <contig> <start> <end>", required = false)
+    @Argument(fullName = "intervals", shortName = "L", doc = "A list of genomic intervals over which to operate. Can be explicitly specified on the command line or in a file.", required = false)
-    public String intervalsFile = null;
+    public String intervals = null;
 
     @Element(required=false)
     @Argument(fullName = "all_loci", shortName = "A", doc = "Should we process all loci, not just those covered by reads", required = false)
@@ -222,7 +218,7 @@ public class GATKArgumentCollection {
         if (!other.referenceFile.equals(this.referenceFile)) {
             return false;
         }
-        if (!other.genomeRegion.equals(this.genomeRegion)) {
+        if (!other.intervals.equals(this.intervals)) {
             return false;
         }
         if (!other.analysisName.equals(this.analysisName)) {
@@ -252,9 +248,6 @@ public class GATKArgumentCollection {
         if (!other.downsampleCoverage.equals(this.downsampleCoverage)) {
             return false;
         }
-        if (!other.intervalsFile.equals(this.intervalsFile)) {
-            return false;
-        }
         if (!other.walkAllLoci.equals(this.walkAllLoci)) {
             return false;
         }

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

@@ -16,6 +16,7 @@ import org.broadinstitute.sting.utils.Utils;
 
 import java.util.ArrayList;
 import java.util.List;
+import java.io.File;
 
 public class GenomeAnalysisEngine {
 
@@ -76,7 +77,7 @@ public class GenomeAnalysisEngine {
         ReferenceOrderedData.parseBindings(logger, argCollection.RODBindings, rods);
 
         // create the output streams
-        initializeOutputStreams();
+        initializeOutputStreams( my_walker );
 
         // our microscheduler, which is in charge of running everything
         MicroScheduler microScheduler = null;
@@ -205,12 +206,9 @@ public class GenomeAnalysisEngine {
 
         engine.setMaxReads(Integer.parseInt(argCollection.maximumReads));
 
-        if (argCollection.genomeRegion != null) {
-            engine.setLocation(argCollection.genomeRegion);
-        }
         // we default interval files over the genome region strin
-        if (argCollection.intervalsFile != null) {
+        if (argCollection.intervals != null) {
-            engine.setLocationFromFile(argCollection.intervalsFile);
+            engine.setLocation(setupIntervalRegion());
         }
         // hmm...
         if (argCollection.maximumReadSorts != null) {
@@ -239,11 +237,14 @@ public class GenomeAnalysisEngine {
      */
     private List<GenomeLoc> setupIntervalRegion() {
         List<GenomeLoc> locs;
-        if (argCollection.intervalsFile != null)
+        if( new File(argCollection.intervals).exists() ) {
-            locs = GenomeLoc.IntervalFileToList(argCollection.intervalsFile);
+            logger.info("Intervals argument specifies a file.  Loading intervals from file.");
-        else
+            return GenomeLoc.IntervalFileToList(argCollection.intervals);
-            locs = GenomeLoc.parseGenomeLocs(argCollection.genomeRegion);
+        }
-        return locs;
+        else {
+            logger.info("Intervals argument does not specify a file.  Trying to parse it as a simple string.");
+            return GenomeLoc.parseGenomeLocs(argCollection.intervals);
+        }
     }
 
     /**
@@ -276,9 +277,10 @@ public class GenomeAnalysisEngine {
 
 
     /** Initialize the output streams as specified by the user. */
-    private void initializeOutputStreams() {
+    private void initializeOutputStreams( Walker walker ) {
         outputTracker = (argCollection.outErrFileName != null) ? new OutputTracker(argCollection.outErrFileName, argCollection.outErrFileName)
                 : new OutputTracker(argCollection.outFileName, argCollection.errFileName);
+        walker.initializeOutputStreams(outputTracker);
     }
 
     /**

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

@@ -87,7 +87,7 @@ public abstract class TraversalEngine {
 
 
     // Locations we are going to process during the traversal
-    private ArrayList<GenomeLoc> locs = null;
+    private List<GenomeLoc> locs = null;
 
     // --------------------------------------------------------------------------------------------------------------
     //
@@ -194,33 +194,13 @@ public abstract class TraversalEngine {
     }
 
     /**
-     * Parses the location string locStr and sets the traversal engine to only process
+     * Sets the intervals over which the traversal(s) should happen.
-     * regions specified by the location string.  The string is of the form:
+     * @param locs
-     * Of the form: loc1;loc2;...
-     * Where each locN can be:
-     * 'chr2', 'chr2:1000000' or 'chr2:1,000,000-2,000,000'
-     *
-     * @param locStr
      */
-    public void setLocation(final String locStr) {
+    public void setLocation(final List<GenomeLoc> locs) {
-        this.locs = GenomeLoc.parseGenomeLocs(locStr);
+        this.locs = locs;
     }
 
-    /**
-     * Read a file of genome locations to process.
-     * regions specified by the location string.  The string is of the form:
-     * Of the form: loc1;loc2;...
-     * Where each locN can be:
-     * 'chr2', 'chr2:1000000' or 'chr2:1,000,000-2,000,000'
-     *
-     * @param file_name
-     */
-    public void setLocationFromFile(final String file_name) {
-
-      this.locs = GenomeLoc.IntervalFileToList(file_name);
-    }
-
-
 
     public boolean hasLocations() {
         return this.locs != null;
@@ -533,7 +513,7 @@ public abstract class TraversalEngine {
             }
             walker.onTraversalDone(map);
         } else {
-            ArrayList<GenomeLoc> l = new ArrayList<GenomeLoc>();
+            List<GenomeLoc> l = new ArrayList<GenomeLoc>();
             if ( hasLocations() )
                 l = locs;
             sum = traverse(walker, l);
@@ -543,7 +523,7 @@ public abstract class TraversalEngine {
         return sum;
     }
 
-    public <M, T> T traverse(Walker<M, T> walker, ArrayList<GenomeLoc> locations) {
+    public <M, T> T traverse(Walker<M, T> walker, List<GenomeLoc> locations) {
         return null;
     }
 

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

@@ -6,6 +6,7 @@ import java.util.Map;
 import java.util.List;
 
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
+import org.broadinstitute.sting.gatk.OutputTracker;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.Pair;
 import org.apache.log4j.Logger;
@@ -33,15 +34,11 @@ public abstract class Walker<MapType, ReduceType> {
     protected PrintStream err = null;
 
     protected Walker() {
-        if( GenomeAnalysisEngine.instance != null ) {
+    }
-            GenomeAnalysisEngine gatk = GenomeAnalysisEngine.instance;
+
-            out = new PrintStream( gatk.getOutputTracker().getOutStream() );
+    public void initializeOutputStreams( OutputTracker outputTracker ) {
-            err = new PrintStream( gatk.getOutputTracker().getErrStream() );
+        out = new PrintStream( outputTracker.getOutStream() );
-        }
+        err = new PrintStream( outputTracker.getErrStream() );
-        else {
-            out = System.out;
-            err = System.err;
-        }
     }
 
     /**

java/test/org/broadinstitute/sting/gatk/GATKArgumentCollectionTest.java

@@ -76,7 +76,6 @@ public class GATKArgumentCollectionTest extends BaseTest {
         collect.maximumReads = "-1";
         collect.strictnessLevel = "strict";
         collect.referenceFile = new File("referenceFile".toLowerCase());
-        collect.genomeRegion = "genomeRegion".toLowerCase();
         collect.analysisName = "analysisName".toLowerCase();
         collect.DBSNPFile = "DBSNPFile".toLowerCase();
         collect.HAPMAPFile = "HAPMAPFile".toLowerCase();
@@ -86,7 +85,7 @@ public class GATKArgumentCollectionTest extends BaseTest {
         collect.maximumReadSorts = "maximumReadSorts".toLowerCase();
         collect.downsampleFraction = "downsampleFraction".toLowerCase();
         collect.downsampleCoverage = "downsampleCoverage".toLowerCase();
-        collect.intervalsFile = "intervalsFile".toLowerCase();
+        collect.intervals = "intervals".toLowerCase();
         collect.walkAllLoci = true;
         collect.disableThreading = false;
         collect.outFileName = "outFileName".toLowerCase();