checked in a sample xml file used to store the defaults for the SomaticCoverage tool, and added it to the SomaticCoverage.jar in build.sml. Also added a inputStream marshalling method to the GATKArgumentCollection.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@979 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
aaron
parent
8d25f1a105
commit
94b0e46d12
11
build.xml
11
build.xml
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@ -103,11 +103,14 @@
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<jar jarfile="dist/SomaticCoverage.jar" whenmanifestonly="skip">
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<fileset dir="build">
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<include name="**/*.class"/>
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<exclude name="**/utils/**"/>
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<exclude name="**/gatk/**"/>
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<include name="**/somaticcoverage/*.class"/>
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<include name="**/walkers/SomaticCoverageWalker.class"/>
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</fileset>
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<manifest>
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<fileset dir="java">
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<include name="**/somaticcoverage/*.xml"/>
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</fileset>
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<manifest>
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<attribute name="Main-Class" value="org.broadinstitute.sting.playground.somaticcoverage.SomaticCoverageTool" />
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</manifest>
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</jar>
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@ -8,6 +8,7 @@ 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.io.InputStream;
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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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@ -33,11 +34,6 @@ import java.util.Map;
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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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@ -50,102 +46,102 @@ public class GATKArgumentCollection {
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public GATKArgumentCollection() {
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}
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@Element(required=false)
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@Element(required = false)
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public String analysisName = null;
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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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@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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// parameters and their defaults
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@ElementList(required=false)
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@ElementList(required = false)
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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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@Element(required = false)
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@Argument(fullName = "intervals", shortName = "L", doc = "A list of genomic intervals over which to operate. Can be explicitly specified on the command line or in a file.", required = false)
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public String intervals = null;
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public String intervals = null;
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@Element(required=false)
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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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@ElementList(required=false)
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@ElementList(required = false)
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@Argument(fullName = "rodBind", shortName = "B", doc = "Bindings for reference-ordered data, in the form <name>,<type>,<file>", required = false)
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public ArrayList<String> RODBindings = new ArrayList<String>();
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@Element(required=false)
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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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@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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@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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/** An output file presented to the walker. */
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@Element(required=false)
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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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@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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@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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@Element(required=false)
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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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public Boolean walkAllLoci = false;
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@Element(required=false)
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@Element(required = false)
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@Argument(fullName = "maximum_reads", shortName = "M", doc = "Maximum number of iterations to process before exiting, the lower bound is zero. Intended only for testing", required = false)
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public Integer maximumEngineIterations = -1;
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@Element(required=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 Integer maximumReadSorts = null;
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@Element(required=false)
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@Element(required = false)
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@Argument(fullName = "bam_compression", shortName = "compress", doc = "Compression level to use for writing BAM files", required = false)
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public Integer BAMcompression = null;
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@Element(required=false)
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@Element(required = false)
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@Argument(fullName = "filterZeroMappingQualityReads", shortName = "fmq0", doc = "If true, mapping quality zero reads will be filtered at the lowest GATK level. Vastly improves performance at areas with abnormal depth due to mapping Q0 reads", required = false)
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public Boolean filterZeroMappingQualityReads = false;
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@Element(required=false)
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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 Double downsampleFraction = null;
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@Element(required=false)
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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 Integer downsampleCoverage = null;
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public Integer downsampleCoverage = null;
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@Element(required=false)
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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 = "silent";
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@Element(required=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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public Boolean unsafe = false;
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@Element(required=false)
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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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@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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/** How many threads should be allocated to this analysis. */
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@Element(required=false)
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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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@ -155,7 +151,7 @@ public class GATKArgumentCollection {
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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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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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@ -170,7 +166,7 @@ public class GATKArgumentCollection {
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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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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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@ -181,13 +177,31 @@ public class GATKArgumentCollection {
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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 file the inputstream to marshal from
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*/
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public static GATKArgumentCollection unmarshal( InputStream file ) {
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Serializer serializer = new Persister(new Format(new HyphenStyle()));
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try {
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GATKArgumentCollection example = serializer.read(GATKArgumentCollection.class, file);
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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 " + file.toString(), 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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*
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* @param other the other collection
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*
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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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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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@ -245,24 +259,24 @@ public class GATKArgumentCollection {
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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 == null && this.maximumReadSorts != null) ||
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(other.maximumReadSorts != null && !other.maximumReadSorts.equals(this.maximumReadSorts))) {
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if (( other.maximumReadSorts == null && this.maximumReadSorts != null ) ||
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( other.maximumReadSorts != null && !other.maximumReadSorts.equals(this.maximumReadSorts) )) {
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return false;
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}
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if ((other.BAMcompression == null && this.BAMcompression != null) ||
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(other.BAMcompression != null && !other.BAMcompression.equals(this.BAMcompression))) {
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if (( other.BAMcompression == null && this.BAMcompression != null ) ||
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( other.BAMcompression != null && !other.BAMcompression.equals(this.BAMcompression) )) {
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return false;
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}
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if ((other.filterZeroMappingQualityReads == null && this.filterZeroMappingQualityReads != null) ||
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(other.filterZeroMappingQualityReads != null && !other.filterZeroMappingQualityReads.equals(this.filterZeroMappingQualityReads))) {
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if (( other.filterZeroMappingQualityReads == null && this.filterZeroMappingQualityReads != null ) ||
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( other.filterZeroMappingQualityReads != null && !other.filterZeroMappingQualityReads.equals(this.filterZeroMappingQualityReads) )) {
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return false;
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}
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if ((other.downsampleFraction == null && this.downsampleFraction != null) ||
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(other.downsampleFraction != null && !other.downsampleFraction.equals(this.downsampleFraction))) {
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if (( other.downsampleFraction == null && this.downsampleFraction != null ) ||
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( other.downsampleFraction != null && !other.downsampleFraction.equals(this.downsampleFraction) )) {
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return false;
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}
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if ((other.downsampleCoverage == null && this.downsampleCoverage != null) ||
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(other.downsampleCoverage != null && !other.downsampleCoverage.equals(this.downsampleCoverage))) {
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if (( other.downsampleCoverage == null && this.downsampleCoverage != null ) ||
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( other.downsampleCoverage != null && !other.downsampleCoverage.equals(this.downsampleCoverage) )) {
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return false;
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}
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if (!other.walkAllLoci.equals(this.walkAllLoci)) {
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@ -0,0 +1,34 @@
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<!--
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~ Copyright (c) 2009 The Broad Institute
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~
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~ Permission is hereby granted, free of charge, to any person
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~ obtaining a copy of this software and associated documentation
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~ files (the "Software"), to deal in the Software without
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~ restriction, including without limitation the rights to use,
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~ copy, modify, merge, publish, distribute, sublicense, and/or sell
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~ copies of the Software, and to permit persons to whom the
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~ Software is furnished to do so, subject to the following
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~ conditions:
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~
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~ The above copyright notice and this permission notice shall be
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~ included in all copies or substantial portions of the Software.
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~
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~ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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~ EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
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~ OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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~ NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
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~ HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
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~ WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
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~ FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
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~ OTHER DEALINGS IN THE SOFTWARE.
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-->
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<GATK-argument-collection>
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<strictness-level>strict</strictness-level>
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<intervals>/seq/references/HybSelOligos/whole_exome_refseq_coding/whole_exome_refseq_coding.targets.interval_list</intervals>
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<reference-file>/seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta</reference-file>
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<enabled-threaded-IO>true</enabled-threaded-IO>
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<unsafe>false</unsafe>
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<disable-threading>false</disable-threading>
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<number-of-threads>1</number-of-threads>
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</GATK-argument-collection>
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@ -5,6 +5,7 @@ import org.broadinstitute.sting.gatk.GATKArgumentCollection;
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import org.broadinstitute.sting.utils.cmdLine.Argument;
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import java.io.File;
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import java.io.IOException;
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import java.util.List;
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import java.util.ArrayList;
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@ -69,8 +70,11 @@ public class SomaticCoverageTool extends CommandLineExecutable {
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/** override any arguments we see fit. */
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protected void overrideArguments() {
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this.argCollection = GATKArgumentCollection.unmarshal("SomaticCoverage.xml");
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this.argCollection.intervals = "CancerIntervals.list";
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try {
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this.argCollection = GATKArgumentCollection.unmarshal(this.getClass().getResource("/src/org/broadinstitute/sting/playground/somaticcoverage/SomaticCoverage.xml").openStream());
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} catch (IOException e) {
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throw new RuntimeException(e);
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}
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this.argCollection.samFiles = samFiles;
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}
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}
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