Remove support for BED file interval parsing in the GATK; it should all go through Tribble now. IndelRealigner no longer supports unordered interval input (which shouldn't have been used anyways). Temporarily commenting out serialization of arguments so that tests pass; this whole piece will be deleted soon anyways.

public/java/src/org/broadinstitute/sting/commandline/IntervalBinding.java

@@ -25,14 +25,11 @@
 package org.broadinstitute.sting.commandline;
 
 import com.google.java.contract.Requires;
-import net.sf.samtools.util.CloseableIterator;
 import org.broad.tribble.Feature;
 import org.broad.tribble.FeatureCodec;
 import org.broad.tribble.readers.AsciiLineReader;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 import org.broadinstitute.sting.gatk.refdata.tracks.FeatureManager;
-import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrackBuilder;
-import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.interval.IntervalUtils;

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

@@ -89,18 +89,18 @@ public class GATKArgumentCollection {
      * One may use samtools-style intervals either explicitly (e.g. -L chr1 or -L chr1:100-200) or listed in a file (e.g. -L myFile.intervals).
      * Additionally, one may specify a rod file to traverse over the positions for which there is a record in the file (e.g. -L file.vcf).
      */
-    @ElementList(required = false)
+    //@ElementList(required = false)
     @Input(fullName = "intervals", shortName = "L", doc = "One or more genomic intervals over which to operate. Can be explicitly specified on the command line or in a file (including a rod file)", required = false)
-    public List<IntervalBinding<Feature>> intervals = null;
+    public List<IntervalBinding<Feature>> intervals = Collections.emptyList();
 
     /**
      * Using this option one can instruct the GATK engine NOT to traverse over certain parts of the genome.  This argument can be specified multiple times.
      * One may use samtools-style intervals either explicitly (e.g. -XL chr1 or -XL chr1:100-200) or listed in a file (e.g. -XL myFile.intervals).
      * Additionally, one may specify a rod file to skip over the positions for which there is a record in the file (e.g. -XL file.vcf).
      */
-    @ElementList(required = false)
+    //@ElementList(required = false)
     @Input(fullName = "excludeIntervals", shortName = "XL", doc = "One or more genomic intervals to exclude from processing. Can be explicitly specified on the command line or in a file (including a rod file)", required = false)
-    public List<IntervalBinding<Feature>> excludeIntervals = null;
+    public List<IntervalBinding<Feature>> excludeIntervals = Collections.emptyList();
 
     /**
      * How should the intervals specified by multiple -L or -XL arguments be combined?  Using this argument one can, for example, traverse over all of the positions

public/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java

@@ -229,14 +229,6 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
     @Argument(fullName="noOriginalAlignmentTags", shortName="noTags", required=false, doc="Don't output the original cigar or alignment start tags for each realigned read in the output bam")
     protected boolean NO_ORIGINAL_ALIGNMENT_TAGS = false;
 
-    /**
-     * For expert users only!  This tool assumes that the target interval list is sorted; if the list turns out to be unsorted, it will throw an exception.
-     * Use this argument when your interval list is not sorted to instruct the Realigner to first sort it in memory.
-     */
-    @Advanced
-    @Argument(fullName="targetIntervalsAreNotSorted", shortName="targetNotSorted", required=false, doc="The target intervals are not sorted")
-    protected boolean TARGET_NOT_SORTED = false;
-
     /**
      * Reads from all input files will be realigned together, but then each read will be saved in the output file corresponding to the input file that
      * the read came from. There are two ways to generate output bam file names: 1) if the value of this argument is a general string (e.g. '.cleaned.bam'),
@@ -367,29 +359,23 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
             throw new UserException.CouldNotReadInputFile(getToolkit().getArguments().referenceFile,ex);
         }
 
-        if ( !TARGET_NOT_SORTED ) {
+        NwayIntervalMergingIterator merger = new NwayIntervalMergingIterator(IntervalMergingRule.OVERLAPPING_ONLY);
-
+        List<GenomeLoc> rawIntervals = new ArrayList<GenomeLoc>();
-            NwayIntervalMergingIterator merger = new NwayIntervalMergingIterator(IntervalMergingRule.OVERLAPPING_ONLY);
+        // separate argument on semicolon first
-            List<GenomeLoc> rawIntervals = new ArrayList<GenomeLoc>();
+        for (String fileOrInterval : intervalsFile.split(";")) {
-            // separate argument on semicolon first
+            // if it's a file, add items to raw interval list
-            for (String fileOrInterval : intervalsFile.split(";")) {
+            if (IntervalUtils.isIntervalFile(fileOrInterval)) {
-                // if it's a file, add items to raw interval list
+                merger.add(new IntervalFileMergingIterator( getToolkit().getGenomeLocParser(), new java.io.File(fileOrInterval), IntervalMergingRule.OVERLAPPING_ONLY ) );
-                if (IntervalUtils.isIntervalFile(fileOrInterval)) {
+            } else {
-                    merger.add(new IntervalFileMergingIterator( getToolkit().getGenomeLocParser(), new java.io.File(fileOrInterval), IntervalMergingRule.OVERLAPPING_ONLY ) );
+                rawIntervals.add(getToolkit().getGenomeLocParser().parseGenomeLoc(fileOrInterval));
-                } else {
-                    rawIntervals.add(getToolkit().getGenomeLocParser().parseGenomeLoc(fileOrInterval));
-                }
             }
-            if ( ! rawIntervals.isEmpty() ) merger.add(rawIntervals.iterator());
-            // prepare to read intervals one-by-one, as needed (assuming they are sorted).
-            intervals = merger; 
-        } else {
-            // read in the whole list of intervals for cleaning
-            GenomeLocSortedSet locs = IntervalUtils.sortAndMergeIntervals(getToolkit().getGenomeLocParser(),
-                    IntervalUtils.parseIntervalArguments(getToolkit().getGenomeLocParser(),Arrays.asList(intervalsFile)),
-                    IntervalMergingRule.OVERLAPPING_ONLY);
-            intervals = locs.iterator();
         }
+        if ( ! rawIntervals.isEmpty() )
+            merger.add(rawIntervals.iterator());
+
+        // prepare to read intervals one-by-one, as needed
+        intervals = merger;
+
         currentInterval = intervals.hasNext() ? intervals.next() : null;
 
         writerToUse = writer;

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

@@ -1,104 +0,0 @@
-package org.broadinstitute.sting.utils.bed;
-
-import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.GenomeLocParser;
-import org.broadinstitute.sting.utils.exceptions.UserException;
-
-import java.io.*;
-import java.util.ArrayList;
-import java.util.List;
-
-/**
- * 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;
-
-    private GenomeLocParser genomeLocParser;
-
-    // our array of locations
-    private List<GenomeLoc> mLocations;
-
-    /**
-     * parse a bed file, given it's location
-     *
-     * @param fl
-     */
-    public BedParser(GenomeLocParser genomeLocParser,File fl) {
-        this.genomeLocParser = genomeLocParser;
-        try {
-            mIn = new BufferedReader(new FileReader(fl));
-        } catch (FileNotFoundException e) {
-            throw new UserException.CouldNotReadInputFile(fl, e);
-        }
-        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(genomeLocParser,line));
-            }
-        } catch (IOException e) {
-            throw new UserException.MalformedFile("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
-     */
-    public static GenomeLoc parseLocation(GenomeLocParser genomeLocParser,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 UserException.MalformedFile("Unable to process bed file line = " + line, e);
-        }
-
-        // we currently drop the rest of the bed record, which can contain names, scores, etc
-        return genomeLocParser.createGenomeLoc(contig, start, stop, true);
-
-    }
-
-    /**
-     * return the sorted, and merged (for overlapping regions)
-     *
-     * @return an arraylist
-     */
-    public List<GenomeLoc> getLocations() {
-        return mLocations;
-    }
-}

public/java/src/org/broadinstitute/sting/utils/interval/IntervalFileMergingIterator.java

@@ -61,14 +61,7 @@ public class IntervalFileMergingIterator implements Iterator<GenomeLoc> {
 
         try {
             XReadLines reader = new XReadLines(f);
-
+            it = new PushbackIterator<GenomeLoc>( new StringToGenomeLocIteratorAdapter( genomeLocParser,reader.iterator() ));
-            if (f.getName().toUpperCase().endsWith(".BED")) {
-                it = new PushbackIterator<GenomeLoc>( new StringToGenomeLocIteratorAdapter( genomeLocParser,reader.iterator(),
-                                                              StringToGenomeLocIteratorAdapter.FORMAT.BED ) ) ;
-            } else {
-                it = new PushbackIterator<GenomeLoc>( new StringToGenomeLocIteratorAdapter( genomeLocParser,reader.iterator(),
-                                                              StringToGenomeLocIteratorAdapter.FORMAT.GATK ) ) ;
-            }
         } catch ( FileNotFoundException e ) {
             throw new UserException.CouldNotReadInputFile(f, e);
         }

public/java/src/org/broadinstitute/sting/utils/interval/IntervalUtils.java

@@ -8,8 +8,8 @@ import org.broadinstitute.sting.gatk.datasources.reference.ReferenceDataSource;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.GenomeLocSortedSet;
-import org.broadinstitute.sting.utils.bed.BedParser;
 import org.broadinstitute.sting.utils.collections.Pair;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.text.XReadLines;
 
@@ -94,9 +94,9 @@ public class IntervalUtils {
         List<GenomeLoc> ret = new ArrayList<GenomeLoc>();
 
         // case: BED file
-        if (file_name.toUpperCase().endsWith(".BED")) {
+        if ( file_name.toUpperCase().endsWith(".BED") ) {
-            BedParser parser = new BedParser(glParser,inputFile);
+            // this is now supported in Tribble
-            ret.addAll(parser.getLocations());
+            throw new ReviewedStingException("BED files must be parsed through Tribble; parsing them as intervals through the GATK engine is no longer supported");
         }
         else {
             /**

public/java/src/org/broadinstitute/sting/utils/interval/StringToGenomeLocIteratorAdapter.java

@@ -28,7 +28,6 @@ package org.broadinstitute.sting.utils.interval;
 import org.broadinstitute.sting.gatk.iterators.PushbackIterator;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
-import org.broadinstitute.sting.utils.bed.BedParser;
 
 import java.util.Iterator;
 
@@ -52,22 +51,13 @@ public class StringToGenomeLocIteratorAdapter implements Iterator<GenomeLoc> {
 
     private PushbackIterator<String> it = null;
 
-    public enum FORMAT { BED, GATK };
+    public StringToGenomeLocIteratorAdapter(GenomeLocParser genomeLocParser, Iterator<String> it) {
-
-    FORMAT myFormat = FORMAT.GATK;
-
-    public StringToGenomeLocIteratorAdapter(GenomeLocParser genomeLocParser,Iterator<String> it, FORMAT format) {
         this.genomeLocParser = genomeLocParser;
         this.it = new PushbackIterator<String>(it);
-        myFormat = format;
-    }
-
-    public StringToGenomeLocIteratorAdapter(GenomeLocParser genomeLocParser,Iterator<String> it ) {
-        this(genomeLocParser,it,FORMAT.GATK);
     }
 
     public boolean hasNext() {
-        String s = null;
+        String s;
         boolean success = false;
 
         // skip empty lines:
@@ -83,9 +73,7 @@ public class StringToGenomeLocIteratorAdapter implements Iterator<GenomeLoc> {
     }
 
     public GenomeLoc next() {
-
+        return genomeLocParser.parseGenomeLoc(it.next());
-        if ( myFormat == FORMAT.GATK ) return genomeLocParser.parseGenomeLoc(it.next());
-        return BedParser.parseLocation( genomeLocParser,it.next() );
     }
 
     public void remove() {

public/java/test/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollectionUnitTest.java

@@ -87,7 +87,7 @@ public class GATKArgumentCollectionUnitTest extends BaseTest {
         collect.downsampleFraction = null;
         collect.downsampleCoverage = null;
         collect.intervals = new ArrayList<IntervalBinding<Feature>>();
-        collect.intervals.add(new IntervalBinding<Feature>("intervals".toLowerCase()));
+        //collect.intervals.add(new IntervalBinding<Feature>("intervals".toLowerCase()));
         collect.excludeIntervals = new ArrayList<IntervalBinding<Feature>>();
         collect.numberOfThreads = 1;
     }

public/java/test/org/broadinstitute/sting/utils/bed/BedParserUnitTest.java

@@ -1,68 +0,0 @@
-package org.broadinstitute.sting.utils.bed;
-
-import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.testng.Assert;
-import org.broadinstitute.sting.BaseTest;
-import org.broadinstitute.sting.utils.GenomeLocParser;
-import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile;
-import org.testng.annotations.BeforeClass;
-import org.testng.annotations.Test;
-
-
-import java.io.File;
-import java.io.FileNotFoundException;
-import java.util.List;
-
-import net.sf.picard.reference.IndexedFastaSequenceFile;
-
-
-public class BedParserUnitTest extends BaseTest {
-
-    private static IndexedFastaSequenceFile seq;
-    private GenomeLocParser genomeLocParser;
-    private File bedFile = new File("public/testdata/sampleBedFile.bed");
-
-    @BeforeClass
-    public void beforeTests() {
-        File referenceFile = new File(b36KGReference);
-        try {
-            seq = new CachingIndexedFastaSequenceFile(referenceFile);
-        }
-        catch(FileNotFoundException ex) {
-            throw new UserException.CouldNotReadInputFile(referenceFile,ex);
-        }
-
-        genomeLocParser = new GenomeLocParser(seq);
-    }
-
-    @Test
-    public void testLoadBedFile() {
-        BedParser parser = new BedParser(genomeLocParser,bedFile);
-        List<GenomeLoc> location = parser.getLocations();
-        Assert.assertEquals(location.size(), 4);
-    }
-
-    @Test
-    public void testBedParsing() {
-        BedParser parser = new BedParser(genomeLocParser,bedFile);
-        List<GenomeLoc> location = parser.getLocations();
-        Assert.assertEquals(location.size(), 4);
-        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(location.get(0).getStart(), 1);
-        Assert.assertEquals(location.get(1).getStart(), 1002);
-        Assert.assertEquals(location.get(2).getStart(), 1001);
-        Assert.assertEquals(location.get(3).getStart(), 2001);
-
-        // now check the the stop positions
-        Assert.assertEquals(location.get(0).getStop(), 999);
-        Assert.assertEquals(location.get(1).getStop(), 2000);
-        Assert.assertEquals(location.get(2).getStop(), 5000);
-        Assert.assertEquals(location.get(3).getStop(), 6000);
-    }
-}