Don't serialize the GATKArgumentCollection for the GATKRunReports (which would have meant dealing with the new IntervalBindings). Also, forgot to remove a test that's no longer relevant to BED parsing.

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

@@ -29,13 +29,11 @@ package org.broadinstitute.sting.gatk.arguments;
 import org.broadinstitute.sting.commandline.Input;
 import org.broadinstitute.sting.commandline.RodBinding;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.simpleframework.xml.*;
 
 /**
  * @author ebanks
  * @version 1.0
  */
-@Root
 public class DbsnpArgumentCollection {
 
     /**

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

@@ -36,24 +36,16 @@ import org.broadinstitute.sting.gatk.DownsamplingMethod;
 import org.broadinstitute.sting.gatk.phonehome.GATKRunReport;
 import org.broadinstitute.sting.gatk.samples.PedigreeValidationType;
 import org.broadinstitute.sting.utils.baq.BAQ;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.interval.IntervalMergingRule;
 import org.broadinstitute.sting.utils.interval.IntervalSetRule;
-import org.simpleframework.xml.*;
-import org.simpleframework.xml.core.Persister;
-import org.simpleframework.xml.stream.Format;
-import org.simpleframework.xml.stream.HyphenStyle;
 
 import java.io.File;
-import java.io.InputStream;
-import java.io.PrintStream;
 import java.util.*;
 
 /**
  * @author aaron
  * @version 1.0
  */
-@Root
 public class GATKArgumentCollection {
 
     /* our version number */
@@ -64,23 +56,18 @@ public class GATKArgumentCollection {
     public GATKArgumentCollection() {
     }
 
-    @ElementMap(entry = "analysis_argument", key = "key", attribute = true, inline = true, required = false)
     public Map<String, String> walkerArgs = new HashMap<String, String>();
 
     // parameters and their defaults
-    @ElementList(required = false)
     @Input(fullName = "input_file", shortName = "I", doc = "SAM or BAM file(s)", required = false)
     public List<String> samFiles = new ArrayList<String>();
 
-    @Element(required = false)
     @Argument(fullName = "read_buffer_size", shortName = "rbs", doc="Number of reads per SAM file to buffer in memory", required = false)
     public Integer readBufferSize = null;
 
-    @Element(required = false)
     @Argument(fullName = "phone_home", shortName = "et", doc="What kind of GATK run report should we generate?  Standard is the default, can be verbose or NO_ET so nothing is posted to the run repository", required = false)
     public GATKRunReport.PhoneHomeOption phoneHomeType = GATKRunReport.PhoneHomeOption.STANDARD;
 
-    @ElementList(required = false)
     @Argument(fullName = "read_filter", shortName = "rf", doc = "Specify filtration criteria to apply to each read individually", required = false)
     public List<String> readFilters = new ArrayList<String>();
 
@@ -106,28 +93,23 @@ public class GATKArgumentCollection {
      * 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
      * for which there is a record in a VCF but just in chromosome 20 (-L chr20 -L file.vcf -isr INTERSECTION).
      */
-    @Element(required = false)
     @Argument(fullName = "interval_set_rule", shortName = "isr", doc = "Indicates the set merging approach the interval parser should use to combine the various -L or -XL inputs", required = false)
     public IntervalSetRule intervalSetRule = IntervalSetRule.UNION;
 
     /**
      * Should abutting (but not overlapping) intervals be treated as separate intervals?
      */
-    @Element(required = false)
     @Argument(fullName = "interval_merging", shortName = "im", doc = "Indicates the interval merging rule we should use for abutting intervals", required = false)
     public IntervalMergingRule intervalMerging = IntervalMergingRule.ALL;
 
-    @Element(required = false)
     @Input(fullName = "reference_sequence", shortName = "R", doc = "Reference sequence file", required = false)
     public File referenceFile = null;
 
     @Deprecated
     @Hidden
-    @ElementList(required = false)
     @Input(fullName = "rodBind", shortName = "B", doc = "Bindings for reference-ordered data, in the form :<name>,<type> <file>", required = false)
     public ArrayList<String> RODBindings = new ArrayList<String>();
 
-    @Element(required = false)
     @Argument(fullName = "nonDeterministicRandomSeed", shortName = "ndrs", doc = "Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run", required = false)
     public boolean nonDeterministicRandomSeed = false;
 
@@ -140,15 +122,12 @@ public class GATKArgumentCollection {
     private static DownsampleType DEFAULT_DOWNSAMPLING_TYPE = DownsampleType.BY_SAMPLE;
     private static int DEFAULT_DOWNSAMPLING_COVERAGE = 1000;
 
-    @Element(required = false)
     @Argument(fullName = "downsampling_type", shortName="dt", doc="Type of reads downsampling to employ at a given locus.  Reads will be selected randomly to be removed from the pile based on the method described here", required = false)
     public DownsampleType downsamplingType = null;
 
-    @Element(required = false)
     @Argument(fullName = "downsample_to_fraction", shortName = "dfrac", doc = "Fraction [0.0-1.0] of reads to downsample to", required = false)
     public Double downsampleFraction = null;
 
-    @Element(required = false)
     @Argument(fullName = "downsample_to_coverage", shortName = "dcov", doc = "Coverage [integer] to downsample to at any given locus; note that downsampled reads are randomly selected from all possible reads at a locus", required = false)
     public Integer downsampleCoverage = null;
 
@@ -182,11 +161,9 @@ public class GATKArgumentCollection {
     // BAQ arguments
     //
     // --------------------------------------------------------------------------------------------------------------
-    @Element(required = false)
     @Argument(fullName = "baq", shortName="baq", doc="Type of BAQ calculation to apply in the engine", required = false)
     public BAQ.CalculationMode BAQMode = BAQ.CalculationMode.OFF;
 
-    @Element(required = false)
     @Argument(fullName = "baqGapOpenPenalty", shortName="baqGOP", doc="BAQ gap open penalty (Phred Scaled).  Default value is 40.  30 is perhaps better for whole genome call sets", required = false)
     public double BAQGOP = BAQ.DEFAULT_GOP;
 
@@ -195,7 +172,6 @@ public class GATKArgumentCollection {
     // performance log arguments
     //
     // --------------------------------------------------------------------------------------------------------------
-    @Element(required = false)
     @Argument(fullName = "performanceLog", shortName="PF", doc="If provided, a GATK runtime performance log will be written to this file", required = false)
     public File performanceLog = null;
 
@@ -208,26 +184,21 @@ public class GATKArgumentCollection {
         return new DownsamplingMethod(DEFAULT_DOWNSAMPLING_TYPE,DEFAULT_DOWNSAMPLING_COVERAGE,null);
     }
 
-    @Element(required = false)
     @Argument(fullName="useOriginalQualities", shortName = "OQ", doc = "If set, use the original base quality scores from the OQ tag when present instead of the standard scores", required=false)
     public Boolean useOriginalBaseQualities = false;
 
     @Argument(fullName="defaultBaseQualities", shortName = "DBQ", doc = "If reads are missing some or all base quality scores, this value will be used for all base quality scores", required=false)
     public byte defaultBaseQualities = -1;
 
-    @Element(required = false)
     @Argument(fullName = "validation_strictness", shortName = "S", doc = "How strict should we be with validation", required = false)
     public SAMFileReader.ValidationStringency strictnessLevel = SAMFileReader.ValidationStringency.SILENT;
 
-    @Element(required = false)
     @Argument(fullName = "unsafe", shortName = "U", doc = "If set, enables unsafe operations: nothing will be checked at runtime.  For expert users only who know what they are doing.  We do not support usage of this argument.", required = false)
     public ValidationExclusion.TYPE unsafe;
 
-    @Element(required = false)
     @Argument(fullName = "num_threads", shortName = "nt", doc = "How many threads should be allocated to running this analysis", required = false)
     public int numberOfThreads = 1;
 
-    @ElementList(required = false)
     @Input(fullName = "read_group_black_list", shortName="rgbl", doc="Filters out read groups matching <TAG>:<STRING> or a .txt file containing the filter strings one per line", required = false)
     public List<String> readGroupBlackList = null;
 
@@ -319,12 +290,10 @@ public class GATKArgumentCollection {
     //
     // --------------------------------------------------------------------------------------------------------------
 
-    @Element(required = false)
     @Argument(fullName="allow_intervals_with_unindexed_bam",doc="Allow interval processing with an unsupported BAM.  NO INTEGRATION TESTS are available.  Use at your own risk.",required=false)
     @Hidden
     public boolean allowIntervalsWithUnindexedBAM = false;
 
-    @Element(required = false)
     @Argument(fullName="disable_experimental_low_memory_sharding",doc="Disable experimental low-memory sharding functionality",required=false)
     public boolean disableLowMemorySharding = false;
 
@@ -334,69 +303,6 @@ public class GATKArgumentCollection {
     //
     // --------------------------------------------------------------------------------------------------------------
 
-    /**
-     * marshal the data out to a object
-     *
-     * @param collection the GATKArgumentCollection to load into
-     * @param outputFile the file to write to
-     */
-    public static void marshal(GATKArgumentCollection collection, String outputFile) {
-        Serializer serializer = new Persister(new Format(new HyphenStyle()));
-        File result = new File(outputFile);
-        try {
-            serializer.write(collection, result);
-        } catch (Exception e) {
-            throw new ReviewedStingException("Failed to marshal the data to the file " + outputFile, e);
-        }
-    }
-
-    /**
-     * marshal the data out to a object
-     *
-     * @param collection the GATKArgumentCollection to load into
-     * @param outputFile the stream to write to
-     */
-    public static void marshal(GATKArgumentCollection collection, PrintStream outputFile) {
-        Serializer serializer = new Persister(new Format(new HyphenStyle()));
-        try {
-            serializer.write(collection, outputFile);
-        } catch (Exception e) {
-            throw new ReviewedStingException("Failed to marshal the data to the file " + outputFile, e);
-        }
-    }
-
-    /**
-     * unmashall the object from a configuration file
-     *
-     * @param filename the filename to marshal from
-     */
-    public static GATKArgumentCollection unmarshal(String filename) {
-        Serializer serializer = new Persister(new Format(new HyphenStyle()));
-        File source = new File(filename);
-        try {
-            GATKArgumentCollection example = serializer.read(GATKArgumentCollection.class, source);
-            return example;
-        } catch (Exception e) {
-            throw new ReviewedStingException("Failed to marshal the data from file " + filename, e);
-        }
-    }
-
-    /**
-     * unmashall the object from a configuration file
-     *
-     * @param file the inputstream to marshal from
-     */
-    public static GATKArgumentCollection unmarshal(InputStream file) {
-        Serializer serializer = new Persister(new Format(new HyphenStyle()));
-        try {
-            GATKArgumentCollection example = serializer.read(GATKArgumentCollection.class, file);
-            return example;
-        } catch (Exception e) {
-            throw new ReviewedStingException("Failed to marshal the data from file " + file.toString(), e);
-        }
-    }
-
-
     /**
      * test equality between two arg collections.  This function defines the statement:
      * "not fun to write"

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

@@ -28,13 +28,11 @@ package org.broadinstitute.sting.gatk.arguments;
 import org.broadinstitute.sting.commandline.Input;
 import org.broadinstitute.sting.commandline.RodBinding;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.simpleframework.xml.Root;
 
 /**
  * @author ebanks
  * @version 1.0
  */
-@Root
 public class StandardVariantContextInputArgumentCollection {
 
     /**

public/java/src/org/broadinstitute/sting/gatk/phonehome/GATKRunReport.java

@@ -28,7 +28,6 @@ import org.apache.log4j.Level;
 import org.apache.log4j.Logger;
 import org.broadinstitute.sting.gatk.CommandLineGATK;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
-import org.broadinstitute.sting.gatk.arguments.GATKArgumentCollection;
 import org.broadinstitute.sting.gatk.walkers.Walker;
 import org.broadinstitute.sting.utils.Utils;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
@@ -101,9 +100,6 @@ public class GATKRunReport {
     @Element(required = false, name = "exception")
     private final ExceptionToXML mException;
 
-    @Element(required = false, name = "argument_collection")
-    private final GATKArgumentCollection mCollection;
-
     @Element(required = true, name = "working_directory")
     private String currentPath;
 
@@ -187,7 +183,6 @@ public class GATKRunReport {
             cmdLine = engine.createApproximateCommandLineArgumentString(engine, walker);
         } catch (Exception ignore) { }
 
-        this.mCollection = engine.getArguments();
         walkerName = engine.getWalkerName(walker.getClass());
         svnVersion = CommandLineGATK.getVersionNumber();
 

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

@@ -1,115 +0,0 @@
-package org.broadinstitute.sting.gatk.arguments;
-
-import org.broad.tribble.Feature;
-import org.broadinstitute.sting.BaseTest;
-import org.broadinstitute.sting.commandline.IntervalBinding;
-import org.testng.annotations.AfterMethod;
-import org.testng.annotations.BeforeMethod;
-import org.testng.annotations.Test;
-import static org.testng.Assert.fail;
-
-import java.io.File;
-import java.util.*;
-
-import net.sf.samtools.SAMFileReader;
-
-/*
- * Copyright (c) 2009 The Broad Institute
- *
- * Permission is hereby granted, free of charge, to any person
- * obtaining a copy of this software and associated documentation
- * files (the "Software"), to deal in the Software without
- * restriction, including without limitation the rights to use,
- * copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the
- * Software is furnished to do so, subject to the following
- * conditions:
- *
- * The above copyright notice and this permission notice shall be
- * included in all copies or substantial portions of the Software.
- *
- * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
- * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
- * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
- * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
- * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
- * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
- * OTHER DEALINGS IN THE SOFTWARE.
- */
-
-/**
- * @author aaron
- * @version 1.0
- * @date May 7, 2009
- * <p/>
- * Class GATKArgumentCollection
- * <p/>
- * Test out the argument collection class
- */
-public class GATKArgumentCollectionUnitTest extends BaseTest {
-
-    // our collection of arguments
-    private GATKArgumentCollection collect;
-
-    // where to write our xml file
-    private String xmlFileLoc = "testfile.xml";
-
-    /** setup our test */
-    @BeforeMethod
-    public void setup() {
-        collect = new GATKArgumentCollection();
-    }
-
-    /** destroy the temp file */
-    @AfterMethod
-    public void takedown() {
-        File f = new File(xmlFileLoc);
-        if (f.exists()) {
-            f.delete();
-        }
-    }
-
-    private void setupCollection() {
-        // parameters and their defaults
-        Map<String, String> wArgs = new HashMap<String, String>();
-        wArgs.put("wArgType1", "Arg1");
-        wArgs.put("wArgType2", "Arg2");
-        wArgs.put("wArgType3", "Arg3");
-        collect.walkerArgs = wArgs;
-
-        List<String> input = new ArrayList<String>();
-        input.add("test.file");
-        collect.samFiles = input;
-        collect.strictnessLevel = SAMFileReader.ValidationStringency.STRICT;
-        collect.referenceFile = new File("referenceFile".toLowerCase());
-        collect.unsafe = ValidationExclusion.TYPE.ALL;
-        collect.downsampleFraction = null;
-        collect.downsampleCoverage = null;
-        collect.intervals = new ArrayList<IntervalBinding<Feature>>();
-        //collect.intervals.add(new IntervalBinding<Feature>("intervals".toLowerCase()));
-        collect.excludeIntervals = new ArrayList<IntervalBinding<Feature>>();
-        collect.numberOfThreads = 1;
-    }
-
-
-    /** test the output of an XML file in the arg collection */
-    @Test
-    public void testOutput() {
-        setupCollection();
-
-        GATKArgumentCollection.marshal(collect, xmlFileLoc);
-        GATKArgumentCollection collection = GATKArgumentCollection.unmarshal(xmlFileLoc);
-        if (!collect.equals(collection)) {
-            fail("Collections not equal");
-        }
-    }
-
-
-    /** test the output of an XML file in the arg collection */
-    @Test
-    public void testInput() {
-        setupCollection();
-        GATKArgumentCollection.marshal(collect, xmlFileLoc);
-    }
-}

public/java/test/org/broadinstitute/sting/utils/interval/IntervalFileMergingIteratorUnitTest.java

@@ -51,7 +51,6 @@ public class IntervalFileMergingIteratorUnitTest extends BaseTest {
 
         private static File refFile =  new File(validationDataLocation + "Homo_sapiens_assembly17.fasta");
         private static String intervalFileNameGATK = validationDataLocation+"test.gatk.intervals";
-        private static String intervalFileNameBED = validationDataLocation+"test.bed";
         private static List<GenomeLoc> results1 = null;
         private static List<GenomeLoc> results2 = null;
 
@@ -122,18 +121,4 @@ public class IntervalFileMergingIteratorUnitTest extends BaseTest {
         }
    }
 
-    @Test
-    public void testBEDIntervalFileIterator_Overlap() {
-        logger.warn("Executing testBEDIntervalFileIterator_Overlap");
-
-        Iterator<GenomeLoc> it = new IntervalFileMergingIterator(genomeLocParser,new File(intervalFileNameBED),IntervalMergingRule.OVERLAPPING_ONLY);
-        Iterator<GenomeLoc> check_it = results1.iterator();
-        while(it.hasNext()) {
-                GenomeLoc l = it.next();
-                GenomeLoc l_expected = check_it.next();
-//                System.out.println("int: "+l+" expected: "+l_expected) ;
-                Assert.assertEquals(l_expected, l, "Unexpected location returned by the iterator: "+l);
-        }
-   }
-
 }