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.
This commit is contained in:
Eric Banks
parent
4a7e6fee3f
commit
8c4dbce6d8
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@ -29,13 +29,11 @@ package org.broadinstitute.sting.gatk.arguments;
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import org.broadinstitute.sting.commandline.Input;
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import org.broadinstitute.sting.commandline.RodBinding;
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import org.broadinstitute.sting.utils.variantcontext.VariantContext;
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import org.simpleframework.xml.*;
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/**
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* @author ebanks
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* @version 1.0
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*/
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@Root
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public class DbsnpArgumentCollection {
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/**
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@ -36,24 +36,16 @@ import org.broadinstitute.sting.gatk.DownsamplingMethod;
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import org.broadinstitute.sting.gatk.phonehome.GATKRunReport;
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import org.broadinstitute.sting.gatk.samples.PedigreeValidationType;
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import org.broadinstitute.sting.utils.baq.BAQ;
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import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
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import org.broadinstitute.sting.utils.interval.IntervalMergingRule;
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import org.broadinstitute.sting.utils.interval.IntervalSetRule;
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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.io.InputStream;
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import java.io.PrintStream;
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import java.util.*;
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/**
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* @author aaron
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* @version 1.0
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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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@ -64,23 +56,18 @@ public class GATKArgumentCollection {
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public GATKArgumentCollection() {
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}
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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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@Input(fullName = "input_file", shortName = "I", doc = "SAM or BAM file(s)", required = false)
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public List<String> samFiles = new ArrayList<String>();
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@Element(required = false)
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@Argument(fullName = "read_buffer_size", shortName = "rbs", doc="Number of reads per SAM file to buffer in memory", required = false)
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public Integer readBufferSize = null;
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@Element(required = false)
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@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)
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public GATKRunReport.PhoneHomeOption phoneHomeType = GATKRunReport.PhoneHomeOption.STANDARD;
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@ElementList(required = false)
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@Argument(fullName = "read_filter", shortName = "rf", doc = "Specify filtration criteria to apply to each read individually", required = false)
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public List<String> readFilters = new ArrayList<String>();
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@ -106,28 +93,23 @@ public class GATKArgumentCollection {
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* 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
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* for which there is a record in a VCF but just in chromosome 20 (-L chr20 -L file.vcf -isr INTERSECTION).
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*/
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@Element(required = false)
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@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)
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public IntervalSetRule intervalSetRule = IntervalSetRule.UNION;
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/**
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* Should abutting (but not overlapping) intervals be treated as separate intervals?
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*/
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@Element(required = false)
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@Argument(fullName = "interval_merging", shortName = "im", doc = "Indicates the interval merging rule we should use for abutting intervals", required = false)
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public IntervalMergingRule intervalMerging = IntervalMergingRule.ALL;
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@Element(required = false)
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@Input(fullName = "reference_sequence", shortName = "R", doc = "Reference sequence file", required = false)
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public File referenceFile = null;
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@Deprecated
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@Hidden
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@ElementList(required = false)
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@Input(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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@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)
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public boolean nonDeterministicRandomSeed = false;
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@ -140,15 +122,12 @@ public class GATKArgumentCollection {
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private static DownsampleType DEFAULT_DOWNSAMPLING_TYPE = DownsampleType.BY_SAMPLE;
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private static int DEFAULT_DOWNSAMPLING_COVERAGE = 1000;
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@Element(required = false)
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@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)
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public DownsampleType downsamplingType = 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 Double 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 at any given locus; note that downsampled reads are randomly selected from all possible reads at a locus", required = false)
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public Integer downsampleCoverage = null;
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@ -182,11 +161,9 @@ public class GATKArgumentCollection {
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// BAQ arguments
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//
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// --------------------------------------------------------------------------------------------------------------
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@Element(required = false)
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@Argument(fullName = "baq", shortName="baq", doc="Type of BAQ calculation to apply in the engine", required = false)
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public BAQ.CalculationMode BAQMode = BAQ.CalculationMode.OFF;
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@Element(required = false)
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@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)
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public double BAQGOP = BAQ.DEFAULT_GOP;
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@ -195,7 +172,6 @@ public class GATKArgumentCollection {
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// performance log arguments
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//
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// --------------------------------------------------------------------------------------------------------------
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@Element(required = false)
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@Argument(fullName = "performanceLog", shortName="PF", doc="If provided, a GATK runtime performance log will be written to this file", required = false)
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public File performanceLog = null;
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@ -208,26 +184,21 @@ public class GATKArgumentCollection {
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return new DownsamplingMethod(DEFAULT_DOWNSAMPLING_TYPE,DEFAULT_DOWNSAMPLING_COVERAGE,null);
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}
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@Element(required = false)
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@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)
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public Boolean useOriginalBaseQualities = false;
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@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)
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public byte defaultBaseQualities = -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", required = false)
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public SAMFileReader.ValidationStringency strictnessLevel = SAMFileReader.ValidationStringency.SILENT;
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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. For expert users only who know what they are doing. We do not support usage of this argument.", required = false)
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public ValidationExclusion.TYPE unsafe;
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@Element(required = false)
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@Argument(fullName = "num_threads", 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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@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)
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public List<String> readGroupBlackList = null;
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@ -319,12 +290,10 @@ public class GATKArgumentCollection {
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//
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// --------------------------------------------------------------------------------------------------------------
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@Element(required = false)
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@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)
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@Hidden
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public boolean allowIntervalsWithUnindexedBAM = false;
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@Element(required = false)
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@Argument(fullName="disable_experimental_low_memory_sharding",doc="Disable experimental low-memory sharding functionality",required=false)
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public boolean disableLowMemorySharding = false;
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@ -334,69 +303,6 @@ public class GATKArgumentCollection {
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//
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// --------------------------------------------------------------------------------------------------------------
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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 ReviewedStingException("Failed to marshal the data to the file " + outputFile, e);
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}
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}
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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 stream to write to
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*/
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public static void marshal(GATKArgumentCollection collection, PrintStream outputFile) {
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Serializer serializer = new Persister(new Format(new HyphenStyle()));
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try {
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serializer.write(collection, outputFile);
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} catch (Exception e) {
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throw new ReviewedStingException("Failed to marshal the data to 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 ReviewedStingException("Failed to marshal the data from file " + filename, 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 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 ReviewedStingException("Failed to marshal the data from 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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@ -28,13 +28,11 @@ package org.broadinstitute.sting.gatk.arguments;
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import org.broadinstitute.sting.commandline.Input;
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import org.broadinstitute.sting.commandline.RodBinding;
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import org.broadinstitute.sting.utils.variantcontext.VariantContext;
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import org.simpleframework.xml.Root;
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/**
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* @author ebanks
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* @version 1.0
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*/
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@Root
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public class StandardVariantContextInputArgumentCollection {
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/**
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@ -28,7 +28,6 @@ import org.apache.log4j.Level;
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import org.apache.log4j.Logger;
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import org.broadinstitute.sting.gatk.CommandLineGATK;
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import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
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import org.broadinstitute.sting.gatk.arguments.GATKArgumentCollection;
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import org.broadinstitute.sting.gatk.walkers.Walker;
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import org.broadinstitute.sting.utils.Utils;
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import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
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@ -101,9 +100,6 @@ public class GATKRunReport {
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@Element(required = false, name = "exception")
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private final ExceptionToXML mException;
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@Element(required = false, name = "argument_collection")
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private final GATKArgumentCollection mCollection;
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@Element(required = true, name = "working_directory")
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private String currentPath;
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@ -187,7 +183,6 @@ public class GATKRunReport {
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cmdLine = engine.createApproximateCommandLineArgumentString(engine, walker);
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} catch (Exception ignore) { }
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this.mCollection = engine.getArguments();
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walkerName = engine.getWalkerName(walker.getClass());
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svnVersion = CommandLineGATK.getVersionNumber();
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@ -1,115 +0,0 @@
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package org.broadinstitute.sting.gatk.arguments;
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import org.broad.tribble.Feature;
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import org.broadinstitute.sting.BaseTest;
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import org.broadinstitute.sting.commandline.IntervalBinding;
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import org.testng.annotations.AfterMethod;
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import org.testng.annotations.BeforeMethod;
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import org.testng.annotations.Test;
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import static org.testng.Assert.fail;
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import java.io.File;
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import java.util.*;
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import net.sf.samtools.SAMFileReader;
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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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/**
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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 GATKArgumentCollection
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* <p/>
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* Test out the argument collection class
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*/
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public class GATKArgumentCollectionUnitTest extends BaseTest {
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// our collection of arguments
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private GATKArgumentCollection collect;
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// where to write our xml file
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private String xmlFileLoc = "testfile.xml";
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/** setup our test */
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@BeforeMethod
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public void setup() {
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collect = new GATKArgumentCollection();
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}
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/** destroy the temp file */
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@AfterMethod
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public void takedown() {
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File f = new File(xmlFileLoc);
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if (f.exists()) {
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f.delete();
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}
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}
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private void setupCollection() {
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// parameters and their defaults
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Map<String, String> wArgs = new HashMap<String, String>();
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wArgs.put("wArgType1", "Arg1");
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wArgs.put("wArgType2", "Arg2");
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wArgs.put("wArgType3", "Arg3");
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collect.walkerArgs = wArgs;
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List<String> input = new ArrayList<String>();
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input.add("test.file");
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collect.samFiles = input;
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collect.strictnessLevel = SAMFileReader.ValidationStringency.STRICT;
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collect.referenceFile = new File("referenceFile".toLowerCase());
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collect.unsafe = ValidationExclusion.TYPE.ALL;
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collect.downsampleFraction = null;
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collect.downsampleCoverage = null;
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collect.intervals = new ArrayList<IntervalBinding<Feature>>();
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//collect.intervals.add(new IntervalBinding<Feature>("intervals".toLowerCase()));
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collect.excludeIntervals = new ArrayList<IntervalBinding<Feature>>();
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collect.numberOfThreads = 1;
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}
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/** test the output of an XML file in the arg collection */
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@Test
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public void testOutput() {
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setupCollection();
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GATKArgumentCollection.marshal(collect, xmlFileLoc);
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GATKArgumentCollection collection = GATKArgumentCollection.unmarshal(xmlFileLoc);
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if (!collect.equals(collection)) {
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fail("Collections not equal");
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}
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}
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/** test the output of an XML file in the arg collection */
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@Test
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public void testInput() {
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setupCollection();
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GATKArgumentCollection.marshal(collect, xmlFileLoc);
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}
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}
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@ -51,7 +51,6 @@ public class IntervalFileMergingIteratorUnitTest extends BaseTest {
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private static File refFile = new File(validationDataLocation + "Homo_sapiens_assembly17.fasta");
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private static String intervalFileNameGATK = validationDataLocation+"test.gatk.intervals";
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private static String intervalFileNameBED = validationDataLocation+"test.bed";
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private static List<GenomeLoc> results1 = null;
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private static List<GenomeLoc> results2 = null;
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@ -122,18 +121,4 @@ public class IntervalFileMergingIteratorUnitTest extends BaseTest {
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}
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}
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@Test
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public void testBEDIntervalFileIterator_Overlap() {
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logger.warn("Executing testBEDIntervalFileIterator_Overlap");
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Iterator<GenomeLoc> it = new IntervalFileMergingIterator(genomeLocParser,new File(intervalFileNameBED),IntervalMergingRule.OVERLAPPING_ONLY);
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Iterator<GenomeLoc> check_it = results1.iterator();
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while(it.hasNext()) {
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GenomeLoc l = it.next();
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GenomeLoc l_expected = check_it.next();
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// System.out.println("int: "+l+" expected: "+l_expected) ;
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Assert.assertEquals(l_expected, l, "Unexpected location returned by the iterator: "+l);
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}
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}
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}
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Reference in New Issue