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