Added ability to downsample to a particular coverage

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@250 348d0f76-0448-11de-a6fe-93d51630548a

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

@@ -107,8 +107,8 @@ public class GenomeAnalysisTK extends CommandLineProgram {
         m_parser.addOptionalFlag("threaded_IO", "P", "If set, enables threaded I/O operations", "ENABLED_THREADED_IO");
         m_parser.addOptionalFlag("unsafe", "U", "If set, enables unsafe operations, nothing will be checked at runtime.", "UNSAFE");
         m_parser.addOptionalArg("sort_on_the_fly", "sort", "Maximum number of reads to sort on the fly", "MAX_ON_FLY_SORTS");
-        m_parser.addOptionalArg("downsample_to_fraction", "dfrac", "Fraction of reads to downsample to", "DOWNSAMPLE_FRACTION");
+        m_parser.addOptionalArg("downsample_to_fraction", "dfrac", "Fraction [0.0-1.0] of reads to downsample to", "DOWNSAMPLE_FRACTION");
-        m_parser.addOptionalArg("downsample_to_coverage", "dcov", "Coverage to downsample to", "DOWNSAMPLE_COVERAGE");
+        m_parser.addOptionalArg("downsample_to_coverage", "dcov", "Coverage [integer] to downsample to", "DOWNSAMPLE_COVERAGE");
         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");
         m_parser.addOptionalArg("out", "o", "An output file presented to the walker.  Will overwrite contents if file exists.", "outFileName" );
@@ -241,7 +241,7 @@ public class GenomeAnalysisTK extends CommandLineProgram {
         }
 
         if (DOWNSAMPLE_COVERAGE != null) {
-            ; // TO DO: (Double.parseDouble(DOWNSAMPLE_COVERAGE));
+            engine.setDownsampleByCoverage(Integer.parseInt(DOWNSAMPLE_COVERAGE));
         }
 
         engine.setSafetyChecking(!UNSAFE);

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

@@ -3,7 +3,10 @@ package org.broadinstitute.sting.gatk;
 import net.sf.samtools.SAMRecord;
 
 import java.util.List;
-import java.lang.ref.Reference;
+import java.util.ArrayList;
+import java.util.Iterator;
+import java.util.TreeSet;
+import java.util.Random;
 
 import org.broadinstitute.sting.utils.GenomeLoc;
 import edu.mit.broad.picard.reference.ReferenceSequence;
@@ -98,4 +101,37 @@ public class LocusContext {
     public void setReferenceContig(final ReferenceSequence contig) {
         refContig = contig;
     }
+
+    public void downsampleToCoverage(int coverage) {
+        if ( numReads() <= coverage )
+            return;
+
+        // randomly choose numbers corresponding to positions in the reads list
+        Random generator = new Random();
+        TreeSet positions = new TreeSet();
+        int i = 0;
+        while ( i < coverage ) {
+            if (positions.add(new Integer(generator.nextInt(reads.size()))))
+                i++;
+        }
+
+        ArrayList downsampledReads = new ArrayList();
+        Iterator positionIter = positions.iterator();
+        Iterator readsIter = reads.iterator();
+        int currentRead = 0;
+        while ( positionIter.hasNext() ) {
+            int nextReadToKeep = (Integer)positionIter.next();
+
+            // fast-forward to the right read
+            while ( currentRead < nextReadToKeep ) {
+                readsIter.next();
+                currentRead++;
+            }
+
+            downsampledReads.add(readsIter.next());
+            currentRead++;
+        }
+
+        reads = downsampledReads;
+    }
 }

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

@@ -80,10 +80,12 @@ public abstract class TraversalEngine {
     protected boolean beSafeP = true;
     protected boolean SORT_ON_FLY = false;
     protected boolean DOWNSAMPLE_BY_FRACTION = false;
+    protected boolean DOWNSAMPLE_BY_COVERAGE = false;
     protected boolean FILTER_UNSORTED_READS = false;
     protected boolean walkOverAllSites = false;
     protected int maxOnFlySorts = 100000;
     protected double downsamplingFraction = 1.0;
+    protected int downsamplingCoverage = 0;
     protected long N_RECORDS_TO_PRINT = 100000;
     protected boolean THREADED_IO = false;
     protected int THREADED_IO_BUFFER_SIZE = 10000;
@@ -169,6 +171,12 @@ public abstract class TraversalEngine {
         downsamplingFraction = fraction;
     }
 
+    public void setDownsampleByCoverage(final int coverage) {
+        logger.info("Downsampling to coverage " + coverage);
+        DOWNSAMPLE_BY_COVERAGE = true;
+        downsamplingCoverage = coverage;
+    }
+
     // --------------------------------------------------------------------------------------------------------------
     //
     // functions for dealing locations (areas of the genome we're traversing over)

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

@@ -110,6 +110,8 @@ public class TraverseByLoci extends TraversalEngine {
 
             // actually get the read and hand it to the walker
             LocusContext locus = iter.next();
+            if ( DOWNSAMPLE_BY_COVERAGE )
+                locus.downsampleToCoverage(downsamplingCoverage);
 
             // if we don't have a particular interval we're processing, check them all, otherwise only operate at this
             // location

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

@@ -77,6 +77,8 @@ public class TraverseByLociByReference extends TraverseByLoci {
                 locus = new LocusContext(current, NO_READS, NO_OFFSETS);    // make the empty locus that has no reads
 
             locus.setReferenceContig(refSite.getCurrentContig());            
+            if ( DOWNSAMPLE_BY_COVERAGE )
+                locus.downsampleToCoverage(downsamplingCoverage);
             sum = walkAtLocus( walker, sum, locus, refSite, rodData );
 
             if (this.maxReads > 0 && this.nRecords > this.maxReads) {