GSA-182: Adding support for BED interval files.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1767 348d0f76-0448-11de-a6fe-93d51630548a

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

@@ -42,6 +42,7 @@ import org.broadinstitute.sting.gatk.walkers.*;
 import org.broadinstitute.sting.gatk.filters.ZeroMappingQualityReadFilter;
 import org.broadinstitute.sting.gatk.io.OutputTracker;
 import org.broadinstitute.sting.utils.*;
+import org.broadinstitute.sting.utils.bed.BedParser;
 import org.broadinstitute.sting.utils.fasta.IndexedFastaSequenceFile;
 import org.broadinstitute.sting.utils.cmdLine.ArgumentException;
 import org.broadinstitute.sting.utils.cmdLine.ArgumentSource;
@@ -75,17 +76,25 @@ public class GenomeAnalysisEngine {
     // our argument collection
     private GATKArgumentCollection argCollection;
 
-    /** Collection of inputs used by the walker. */
+    /**
+     * Collection of inputs used by the walker.
+     */
     private Map<ArgumentSource, Object> inputs = new HashMap<ArgumentSource, Object>();
 
-    /** Collection of outputs used by the walker. */
+    /**
+     * Collection of outputs used by the walker.
+     */
     private Collection<Stub<?>> outputs = new ArrayList<Stub<?>>();
 
 
-    /** our log, which we want to capture anything from this class */
+    /**
+     * our log, which we want to capture anything from this class
+     */
     private static Logger logger = Logger.getLogger(GenomeAnalysisEngine.class);
 
-    /** our walker manager */
+    /**
+     * our walker manager
+     */
     private final WalkerManager walkerManager;
 
     /**
@@ -93,7 +102,6 @@ public class GenomeAnalysisEngine {
      * <p/>
      * legacy traversal types are sent to legacyTraversal function; as we move more of the traversals to the
      * new MicroScheduler class we'll be able to delete that function.
-     *
      */
     public GenomeAnalysisEngine() {
         // make sure our instance variable points to this analysis engine
@@ -103,6 +111,7 @@ public class GenomeAnalysisEngine {
 
     /**
      * Actually run the GATK with the specified walker.
+     *
      * @param args      the argument collection, where we get all our setup information from
      * @param my_walker Walker to run over the dataset.  Must not be null.
      * @return the value of this traversal.
@@ -142,6 +151,7 @@ public class GenomeAnalysisEngine {
 
     /**
      * Add additional, externally managed IO streams for walker input.
+     *
      * @param argumentSource Field in the walker into which to inject the value.
      * @param value          Instance to inject.
      */
@@ -151,6 +161,7 @@ public class GenomeAnalysisEngine {
 
     /**
      * Add additional, externally managed IO streams for walker output.
+     *
      * @param stub Instance to inject.
      */
     public void addOutput(Stub<?> stub) {
@@ -159,6 +170,7 @@ public class GenomeAnalysisEngine {
 
     /**
      * Gets a set of the names of all walkers that the GATK has discovered.
+     *
      * @return A set of the names of all discovered walkers.
      */
     public Set<String> getWalkerNames() {
@@ -167,6 +179,7 @@ public class GenomeAnalysisEngine {
 
     /**
      * Retrieves an instance of the walker based on the walker name.
+     *
      * @param walkerName Name of the walker.  Must not be null.  If the walker cannot be instantiated, an exception will be thrown.
      * @return An instance of the walker.
      */
@@ -210,6 +223,7 @@ public class GenomeAnalysisEngine {
 
     /**
      * setup a microscheduler
+     *
      * @param my_walker our walker of type LocusWalker
      * @return a new microscheduler
      */
@@ -236,14 +250,19 @@ public class GenomeAnalysisEngine {
      * setup the interval regions, from either the interval file of the genome region string
      *
      * @param intervals the list of intervals to parse
-     *
      * @return a list of genomeLoc representing the interval file
      */
     public static List<GenomeLoc> parseIntervalRegion(final List<String> intervals) {
         List<GenomeLoc> locs = new ArrayList<GenomeLoc>();
         for (String interval : intervals) {
             if (new File(interval).exists()) {
+                // support for the bed style interval format
+                if (interval.endsWith(".bed") || interval.endsWith(".BED")) {
+                    BedParser parser = new BedParser(new File(interval));
+                    locs.addAll(parser.getSortedAndMergedLocations());
+                } else {
                     locs.addAll(GenomeLocParser.intervalFileToList(interval));
+                }
             } else {
                 locs.addAll(GenomeLocParser.parseGenomeLocs(interval));
             }
@@ -257,6 +276,7 @@ public class GenomeAnalysisEngine {
      * individual bam files). For instance: if GATK is run with three input bam files (three -I arguments), then the list
      * returned by this method will contain 3 elements (one for each reader), with each element being a set of sample names
      * found in the corresponding bam file.
+     *
      * @return
      */
     public List<Set<String>> getSamplesByReaders() {
@@ -285,6 +305,7 @@ public class GenomeAnalysisEngine {
      * individual bam files). For instance: if GATK is run with three input bam files (three -I arguments), then the list
      * returned by this method will contain 3 elements (one for each reader), with each element being a set of library names
      * found in the corresponding bam file.
+     *
      * @return
      */
     public List<Set<String>> getLibrariesByReaders() {
@@ -313,6 +334,7 @@ public class GenomeAnalysisEngine {
      * individual bam files). For instance: if GATK is run with three input bam files (three -I arguments), then the list
      * returned by this method will contain 3 elements (one for each reader), with each element being a set of remapped read groups
      * (i.e. as seen by read.getReadGroup().getReadGroupId() in the merged stream) that come from the corresponding bam file.
+     *
      * @return
      */
     public List<Set<String>> getMergedReadGroupsByReaders() {
@@ -348,7 +370,6 @@ public class GenomeAnalysisEngine {
      *
      * @param walker        The walker for which to extract info.
      * @param argCollection The collection of arguments passed to the engine.
-     *
      * @return The reads object providing reads source info.
      */
     private Reads extractSourceInfo(Walker walker, GATKArgumentCollection argCollection) {
@@ -370,6 +391,7 @@ public class GenomeAnalysisEngine {
 
     /**
      * Verifies that the supplied set of reads files mesh with what the walker says it requires.
+     *
      * @param walker    Walker to test.
      * @param arguments Supplied reads files.
      */
@@ -385,6 +407,7 @@ public class GenomeAnalysisEngine {
 
     /**
      * Verifies that the supplied reference file mesh with what the walker says it requires.
+     *
      * @param walker    Walker to test.
      * @param arguments Supplied reads files.
      */
@@ -401,6 +424,7 @@ public class GenomeAnalysisEngine {
     /**
      * Verifies that all required reference-ordered data has been supplied, and any reference-ordered data that was not
      * 'allowed' is still present.
+     *
      * @param walker Walker to test.
      * @param rods   Reference-ordered data to load.
      */
@@ -426,6 +450,7 @@ public class GenomeAnalysisEngine {
 
     /**
      * Now that all files are open, validate the sequence dictionaries of the reads vs. the reference.
+     *
      * @param reads     Reads data source.
      * @param reference Reference data source.
      */
@@ -506,7 +531,6 @@ public class GenomeAnalysisEngine {
      * @param drivingDataSource Data on which to shard.
      * @param intervals         Intervals to use when limiting sharding.
      * @param maxIterations     the maximum number of iterations to run through
-     *
      * @return Sharding strategy for this driving data source.
      */
     protected ShardStrategy getShardStrategy(Walker walker,
@@ -566,7 +590,6 @@ public class GenomeAnalysisEngine {
      * Gets a data source for the given set of reads.
      *
      * @param reads the read source information
-     *
      * @return A data source for the given set of reads.
      */
     private SAMDataSource createReadsDataSource(Reads reads) {
@@ -583,7 +606,6 @@ public class GenomeAnalysisEngine {
      * Opens a reference sequence file paired with an index.
      *
      * @param refFile Handle to a reference sequence file.  Non-null.
-     *
      * @return A thread-safe file wrapper.
      */
     private IndexedFastaSequenceFile openReferenceSequenceFile(File refFile) {
@@ -602,7 +624,6 @@ public class GenomeAnalysisEngine {
      * Open the reference-ordered data sources.
      *
      * @param rods the reference order data to execute using
-     *
      * @return A list of reference-ordered data sources.
      */
     private List<ReferenceOrderedDataSource> getReferenceOrderedDataSources(List<ReferenceOrderedData<? extends ReferenceOrderedDatum>> rods) {
@@ -639,6 +660,7 @@ public class GenomeAnalysisEngine {
     /**
      * Returns data source object encapsulating all essential info and handlers used to traverse
      * reads; header merger, individual file readers etc can be accessed through the returned data source object.
+     *
      * @return
      */
     public SAMDataSource getDataSource() {

java/src/org/broadinstitute/sting/utils/GenomeLocSortedSet.java

@@ -247,9 +247,7 @@ public class GenomeLocSortedSet extends AbstractSet<GenomeLoc> {
      */
     public static GenomeLocSortedSet createSetFromList(List<GenomeLoc> locs) {
         GenomeLocSortedSet set = new GenomeLocSortedSet();
-        for (GenomeLoc l : locs) {
+        set.addAll(locs);
-            set.add(l);
-        }
         return set;
     }
 

java/src/org/broadinstitute/sting/utils/bed/BedParser.java

@@ -0,0 +1,107 @@
+package org.broadinstitute.sting.utils.bed;
+
+import org.broadinstitute.sting.utils.StingException;
+import org.broadinstitute.sting.utils.GenomeLoc;
+import org.broadinstitute.sting.utils.GenomeLocParser;
+
+import java.io.*;
+import java.util.*;
+
+/**
+ * Created by IntelliJ IDEA.
+ * User: aaron
+ * Date: Oct 5, 2009
+ * Time: 5:46:45 PM
+ */
+public class BedParser {
+    // the GATk operates as a one based location, bed files are 0 based
+    static final int TO_ONE_BASED_ADDITION = 1;
+
+    // the buffered reader input
+    private final BufferedReader mIn;
+
+    // our array of locations
+    private List<GenomeLoc> mLocations;
+
+    /**
+     * parse a bed file, given it's location
+     *
+     * @param fl
+     */
+    public BedParser(File fl) {
+        try {
+            mIn = new BufferedReader(new FileReader(fl));
+        } catch (FileNotFoundException e) {
+            throw new StingException("Unable to open the bed file = " + fl);
+        }
+        mLocations = parseLocations();
+    }
+
+    /**
+     * parse a bed file, given an input reader
+     *
+     * @param fl the bed file
+     */
+    public BedParser(BufferedReader fl) {
+        mIn = fl;
+        mLocations = parseLocations();
+    }
+
+    /**
+     * parse out the locations
+     *
+     * @return a list of GenomeLocs, sorted and merged
+     */
+    private List<GenomeLoc> parseLocations() {
+        String line = null;
+        List<GenomeLoc> locArray = new ArrayList<GenomeLoc>();
+        try {
+            while ((line = mIn.readLine()) != null) {
+                locArray.add(parseLocation(line));
+            }
+        } catch (IOException e) {
+            throw new StingException("Unable to parse line in BED file.");
+        }
+        return locArray;
+    }
+
+    /**
+     * parse a single location
+     *
+     * @param line the line, as a string
+     * @return a parsed genome loc
+     */
+    private GenomeLoc parseLocation(String line) {
+        String contig;
+        int start;
+        int stop;
+        try {
+            String parts[] = line.split("\\s+");
+            contig = parts[0];
+            start = Integer.valueOf(parts[1]) + TO_ONE_BASED_ADDITION;
+            stop = Integer.valueOf(parts[2]); // the ending point is an open interval
+        } catch (Exception e) {
+            throw new StingException("Unable to process bed file line = " + line);
+        }
+
+        // we currently drop the rest of the bed record, which can contain names, scores, etc
+        return GenomeLocParser.createGenomeLoc(contig, start, stop);
+
+    }
+
+    /**
+     * return the sorted, and merged (for overlapping regions)
+     *
+     * @return an arraylist
+     */
+    public List<GenomeLoc> getLocations() {
+        return mLocations;
+    }
+
+    public List<GenomeLoc> getSortedAndMergedLocations() {
+        List<GenomeLoc> locs = new ArrayList<GenomeLoc>();
+        locs.addAll(mLocations);
+        Collections.sort(locs);
+        return GenomeLocParser.mergeOverlappingLocations(locs);
+    }
+}

java/test/org/broadinstitute/sting/utils/bed/BedParserTest.java

@@ -0,0 +1,75 @@
+package org.broadinstitute.sting.utils.bed;
+
+import org.broadinstitute.sting.BaseTest;
+import org.broadinstitute.sting.utils.fasta.IndexedFastaSequenceFile;
+import org.broadinstitute.sting.utils.StingException;
+import org.broadinstitute.sting.utils.GenomeLocParser;
+import org.broadinstitute.sting.utils.GenomeLoc;
+import org.junit.BeforeClass;
+import org.junit.Test;
+import org.junit.Assert;
+
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.util.ArrayList;
+import java.util.List;
+
+/**
+ * Created by IntelliJ IDEA.
+ * User: aaron
+ * Date: Oct 5, 2009
+ * Time: 9:09:42 PM
+ * To change this template use File | Settings | File Templates.
+ */
+public class BedParserTest extends BaseTest {
+
+    private static IndexedFastaSequenceFile seq;
+    private File bedFile = new File("testdata/sampleBedFile.bed");
+
+    @BeforeClass
+    public static void beforeTests() {
+        try {
+            seq = new IndexedFastaSequenceFile(new File("/broad/1KG/reference/human_b36_both.fasta"));
+        } catch (FileNotFoundException e) {
+            throw new StingException("unable to load the sequence dictionary");
+        }
+        GenomeLocParser.setupRefContigOrdering(seq);
+    }
+
+    @Test
+    public void testLoadBedFile() {
+        BedParser parser = new BedParser(bedFile);
+        List<GenomeLoc> location = parser.getLocations();
+        Assert.assertEquals(4, location.size());
+    }
+
+    @Test
+    public void testBedParsing() {
+        BedParser parser = new BedParser(bedFile);
+        List<GenomeLoc> location = parser.getLocations();
+        Assert.assertEquals(4, location.size());
+        Assert.assertTrue(location.get(0).getContig().equals("20"));
+        Assert.assertTrue(location.get(1).getContig().equals("20"));
+        Assert.assertTrue(location.get(2).getContig().equals("22"));
+        Assert.assertTrue(location.get(3).getContig().equals("22"));
+
+        // now check the the start positions
+        Assert.assertEquals(1, location.get(0).getStart());
+        Assert.assertEquals(1002, location.get(1).getStart());
+        Assert.assertEquals(1001, location.get(2).getStart());
+        Assert.assertEquals(2001, location.get(3).getStart());
+
+        // now check the the stop positions
+        Assert.assertEquals(999, location.get(0).getStop());
+        Assert.assertEquals(2000, location.get(1).getStop());
+        Assert.assertEquals(5000, location.get(2).getStop());
+        Assert.assertEquals(6000, location.get(3).getStop());
+    }
+
+    @Test
+    public void testLoadBedFileOverlapping() {
+        BedParser parser = new BedParser(bedFile);
+        List<GenomeLoc> location = parser.getSortedAndMergedLocations();
+        Assert.assertEquals(3, location.size());
+    }
+}

testdata/sampleBedFile.bed

@@ -0,0 +1,4 @@
+20 0 999
+20 1001 2000
+22 1000 5000 cloneA 960 + 1000 5000 0 2 567,488, 0,3512
+22 2000 6000 cloneB 900 - 2000 6000 0 2 433,399, 0,3601