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my move ended up being a copy, so this is to delete dupplicate files. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@651 348d0f76-0448-11de-a6fe-93d51630548a
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aaron 2009-05-11 02:10:26 +00:00
parent 898f65547e
commit 4ce3feba4d
2 changed files with 0 additions and 397 deletions
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272
java/src/org/broadinstitute/sting/utils/cmdLine/GATKArgumentCollection.java
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package org.broadinstitute.sting.utils.cmdLine;
import org.broadinstitute.sting.utils.StingException;
import org.simpleframework.xml.*;
import org.simpleframework.xml.core.Persister;
import java.io.File;
import java.util.ArrayList;
import java.util.List;
import java.util.Map;
import java.util.HashMap;
/**
*
* User: aaron
* Date: May 7, 2009
* Time: 11:46:21 AM
*
* The Broad Institute
* SOFTWARE COPYRIGHT NOTICE AGREEMENT
* This software and its documentation are copyright 2009 by the
* Broad Institute/Massachusetts Institute of Technology. All rights are reserved.
*
* This software is supplied without any warranty or guaranteed support whatsoever. Neither
* the Broad Institute nor MIT can be responsible for its use, misuse, or functionality.
*
*/
/**
* @author aaron
* @version 1.0
* @date May 7, 2009
* <p/>
* Class ArgumentObject
* <p/>
* Encapsolute the massively large list of possible parameters we take in the Genome Analysis tool
*/
@Root
public class GATKArgumentCollection {
/* our version number */
private float versionNumber = 1;
private String description = "GATK Arguments";
/** the constructor */
public GATKArgumentCollection() {
}
// parameters and their defaults
@ElementList
@Argument(fullName = "input_file", shortName = "I", doc = "SAM or BAM file(s)", required = false)
public List<File> samFiles = new ArrayList<File>();
@Element
@Argument(fullName = "maximum_reads", shortName = "M", doc = "Maximum number of reads to process before exiting", required = false)
public String maximumReads = "-1";
@Element
@Argument(fullName = "validation_strictness", shortName = "S", doc = "How strict should we be with validation (LENIENT|SILENT|STRICT)", required = false)
public String strictnessLevel = "strict";
@Element
@Argument(fullName = "reference_sequence", shortName = "R", doc = "Reference sequence file", required = false)
public File referenceFile = null;
@Element
@Argument(fullName = "genome_region", shortName = "L", doc = "Genome region to operation on: from chr:start-end", required = false)
public String genomeRegion = null;
@Element
@Argument(fullName = "analysis_type", shortName = "T", doc = "Type of analysis to run")
public String analysisName = null;
// parameters and their defaults
@ElementMap(entry = "analysis_argument", key = "key", attribute = true, inline = true)
public Map<String, String> walkerArgs = new HashMap<String, String>();
@Element
@Argument(fullName = "DBSNP", shortName = "D", doc = "DBSNP file", required = false)
public String DBSNPFile = null;
@Element
@Argument(fullName = "hapmap", shortName = "H", doc = "Hapmap file", required = false)
public String HAPMAPFile = null;
@Element
@Argument(fullName = "hapmap_chip", shortName = "hc", doc = "Hapmap chip file", required = false)
public String HAPMAPChipFile = null;
@Element
@Argument(fullName = "threaded_IO", shortName = "P", doc = "If set, enables threaded I/O operations", required = false)
public Boolean EnabledThreadedIO = false;
@Element
@Argument(fullName = "unsafe", shortName = "U", doc = "If set, enables unsafe operations, nothing will be checked at runtime.", required = false)
public Boolean unsafe = false;
@Element
@Argument(fullName = "sort_on_the_fly", shortName = "sort", doc = "Maximum number of reads to sort on the fly", required = false)
public String maximumReadSorts = null;
@Element
@Argument(fullName = "downsample_to_fraction", shortName = "dfrac", doc = "Fraction [0.0-1.0] of reads to downsample to", required = false)
public String downsampleFraction = null;
@Element
@Argument(fullName = "downsample_to_coverage", shortName = "dcov", doc = "Coverage [integer] to downsample to", required = false)
public String downsampleCoverage = null;
@Element
@Argument(fullName = "intervals_file", shortName = "V", doc = "File containing list of genomic intervals to operate on. line := <contig> <start> <end>", required = false)
public String intervalsFile = null;
@Element
@Argument(fullName = "all_loci", shortName = "A", doc = "Should we process all loci, not just those covered by reads", required = false)
public Boolean walkAllLoci = false;
@Element
@Argument(fullName = "disablethreading", shortName = "dt", doc = "Disable experimental threading support.", required = false)
public Boolean disableThreading = false;
/** An output file presented to the walker. */
@Element
@Argument(fullName = "out", shortName = "o", doc = "An output file presented to the walker. Will overwrite contents if file exists.", required = false)
public String outFileName = null;
/** An error output file presented to the walker. */
@Element
@Argument(fullName = "err", shortName = "e", doc = "An error output file presented to the walker. Will overwrite contents if file exists.", required = false)
public String errFileName = null;
/** A joint file for both 'normal' and error output presented to the walker. */
@Element
@Argument(fullName = "outerr", shortName = "oe", doc = "A joint file for 'normal' and error output presented to the walker. Will overwrite contents if file exists.", required = false)
public String outErrFileName = null;
/** How many threads should be allocated to this analysis. */
@Element
@Argument(fullName = "numthreads", shortName = "nt", doc = "How many threads should be allocated to running this analysis.", required = false)
public int numberOfThreads = 1;
@ElementList
@Argument(fullName = "rodBind", shortName = "B", doc = "", required = false)
public ArrayList<String> RODBindings = new ArrayList<String>();
/**
* 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();
File result = new File(outputFile);
try {
serializer.write(collection, result);
} catch (Exception e) {
throw new StingException("Failed to marshal the data from 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();
File source = new File(filename);
try {
GATKArgumentCollection example = serializer.read(GATKArgumentCollection.class, source);
return example;
} catch (Exception e) {
throw new StingException("Failed to marshal the data to file " + filename, e);
}
}
/**
* test equality between two arg collections. This functions defines the statement:
* "not fun to write"
* @param other the other collection
* @return true if they're equal
*/
public boolean equals(GATKArgumentCollection other) {
if (other.samFiles.size() != samFiles.size()) {
return false;
}
for (int x = 0; x < samFiles.size(); x++) {
if (!samFiles.get(x).equals(other.samFiles.get(x))) {
return false;
}
}
if (other.walkerArgs.size() != walkerArgs.size()) {
return false;
}
for (String s : walkerArgs.keySet()) {
if (!other.walkerArgs.containsKey(s)) {
return false;
}
}
if (other.RODBindings.size() != RODBindings.size()) {
return false;
}
for (int x = 0; x < RODBindings.size(); x++) {
if (!RODBindings.get(x).equals(other.RODBindings.get(x))) {
return false;
}
}
if (!other.samFiles.equals(this.samFiles)) {
return false;
}
if (!other.maximumReads.equals(this.maximumReads)) {
return false;
}
if (!other.strictnessLevel.equals(this.strictnessLevel)) {
return false;
}
if (!other.referenceFile.equals(this.referenceFile)) {
return false;
}
if (!other.genomeRegion.equals(this.genomeRegion)) {
return false;
}
if (!other.analysisName.equals(this.analysisName)) {
return false;
}
if (!other.DBSNPFile.equals(this.DBSNPFile)) {
return false;
}
if (!other.HAPMAPFile.equals(this.HAPMAPFile)) {
return false;
}
if (!other.HAPMAPChipFile.equals(this.HAPMAPChipFile)) {
return false;
}
if (!other.EnabledThreadedIO.equals(this.EnabledThreadedIO)) {
return false;
}
if (!other.unsafe.equals(this.unsafe)) {
return false;
}
if (!other.maximumReadSorts.equals(this.maximumReadSorts)) {
return false;
}
if (!other.downsampleFraction.equals(this.downsampleFraction)) {
return false;
}
if (!other.downsampleCoverage.equals(this.downsampleCoverage)) {
return false;
}
if (!other.intervalsFile.equals(this.intervalsFile)) {
return false;
}
if (!other.walkAllLoci.equals(this.walkAllLoci)) {
return false;
}
if (!other.outFileName.equals(this.outFileName)) {
return false;
}
if (!other.errFileName.equals(this.errFileName)) {
return false;
}
if (!other.outErrFileName.equals(this.outErrFileName)) {
return false;
}
if (other.numberOfThreads != this.numberOfThreads) {
return false;
}
return true;
}
}

125
java/test/org/broadinstitute/sting/utils/cmdLine/GATKArgumentCollectionTest.java
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package org.broadinstitute.sting.utils.cmdLine;
import org.broadinstitute.sting.BaseTest;
import org.junit.After;
import static org.junit.Assert.fail;
import org.junit.Before;
import org.junit.Test;
import java.io.File;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
/**
*
* User: aaron
* Date: May 7, 2009
* Time: 1:12:58 PM
*
* The Broad Institute
* SOFTWARE COPYRIGHT NOTICE AGREEMENT
* This software and its documentation are copyright 2009 by the
* Broad Institute/Massachusetts Institute of Technology. All rights are reserved.
*
* This software is supplied without any warranty or guaranteed support whatsoever. Neither
* the Broad Institute nor MIT can be responsible for its use, misuse, or functionality.
*
*/
/**
* @author aaron
* @version 1.0
* @date May 7, 2009
* <p/>
* Class GATKArgumentCollection
* <p/>
* A descriptions should go here. Blame aaron if it's missing.
*/
public class GATKArgumentCollectionTest extends BaseTest {
// our collection of arguments
private GATKArgumentCollection collect;
// where to write our xml file
private String xmlFileLoc = "testfile.xml";
/** setup our test */
@Before
public void setup() {
collect = new GATKArgumentCollection();
}
/** destroy the temp file */
@After
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<File> input = new ArrayList<File>();
input.add(new File("test.file"));
collect.samFiles = input;
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();
collect.HAPMAPChipFile = "HAPMAPChipFile".toLowerCase();
collect.EnabledThreadedIO = true;
collect.unsafe = false;
collect.maximumReadSorts = "maximumReadSorts".toLowerCase();
collect.downsampleFraction = "downsampleFraction".toLowerCase();
collect.downsampleCoverage = "downsampleCoverage".toLowerCase();
collect.intervalsFile = "intervalsFile".toLowerCase();
collect.walkAllLoci = true;
collect.disableThreading = false;
collect.outFileName = "outFileName".toLowerCase();
collect.errFileName = "errFileName".toLowerCase();
collect.outErrFileName = "outErrFileName".toLowerCase();
collect.numberOfThreads = 1;
// make some rod bindings up
ArrayList<String> fakeBindings = new ArrayList<String>();
fakeBindings.add("Bind1");
fakeBindings.add("Bind2");
fakeBindings.add("Bind3");
collect.RODBindings = fakeBindings;
}
/** 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);
}
}