On path to SampleDB engine integration
-- PedReader tag parser -- Separation of SampleDBBuilder from SampleDB (now immutable) -- Removed old sample engine arguments
This commit is contained in:
Mark DePristo
parent
8ee0f91904
commit
dd71884b0c
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@ -32,6 +32,7 @@ import org.broadinstitute.sting.commandline.Input;
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import org.broadinstitute.sting.gatk.DownsampleType;
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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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@ -44,10 +45,7 @@ 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.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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import java.util.*;
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/**
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* @author aaron
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@ -72,11 +70,6 @@ public class GATKArgumentCollection {
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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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// parameters and their defaults
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@ElementList(required = false)
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@Argument(fullName = "sample_metadata", shortName = "SM", doc = "Sample file(s) in JSON format", required = false)
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public List<File> sampleFiles = new ArrayList<File>();
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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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@ -215,9 +208,25 @@ public class GATKArgumentCollection {
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// --------------------------------------------------------------------------------------------------------------
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//
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// distributed GATK arguments
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// PED (pedigree) support
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//
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// --------------------------------------------------------------------------------------------------------------
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/**
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* MARK: add documentation details
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*/
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@Argument(fullName="pedigree", shortName = "ped", doc="Pedigree file / string for samples",required=false)
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public List<String> pedigreeData = Collections.emptyList();
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@Argument(fullName="pedigreeValidationType", shortName = "pedValidationType", doc="How strict should we be in validating the pedigree information?",required=false)
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public PedigreeValidationType pedigreeValidationType = PedigreeValidationType.STRICT;
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// --------------------------------------------------------------------------------------------------------------
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//
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// BAM indexing and sharding arguments
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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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@ -114,10 +114,42 @@ public class PedReader {
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final static private Set<String> CATAGORICAL_TRAIT_VALUES = new HashSet<String>(Arrays.asList("-9", "0", "1", "2"));
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final static private String commentMarker = "#";
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/**
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* An enum that specifies which, if any, of the standard PED fields are
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* missing from the input records. For example, suppose we have the full record:
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*
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* "fam1 kid dad mom 1 2"
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*
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* indicating a male affected child. This can be parsed with the -ped x.ped argument
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* to the GATK. Suppose we only have:
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*
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* "fam1 kid 1"
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*
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* we can parse the reduced version of this record with -ped:NO_PARENTS,NO_PHENOTYPE x.ped
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*/
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public enum MissingPedField {
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/**
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* The PED records do not have the first (FAMILY_ID) argument. The family id
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* will be set to null / empty.
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*/
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NO_FAMILY_ID,
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/**
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* The PED records do not have either the paternal or maternal IDs, so
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* the corresponding IDs are set to null.
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*/
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NO_PARENTS,
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/**
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* The PED records do not have the GENDER field, so the sex of each
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* sample will be set to UNKNOWN.
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*/
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NO_SEX,
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/**
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* The PED records do not have the PHENOTYPE field, so the phenotype
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* of each sample will be set to UNKNOWN.
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*/
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NO_PHENOTYPE
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}
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@ -233,8 +265,6 @@ public class PedReader {
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if ( mom != null ) samples.add(mom);
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}
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sampleDB.validate(samples);
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return samples;
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}
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@ -253,4 +283,26 @@ public class PedReader {
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} else
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return null;
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}
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/**
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* Parses a list of tags from the command line, assuming it comes from the GATK Engine
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* tags, and returns the corresponding EnumSet.
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*
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* @param arg the actual engine arg, used for the UserException if there's an error
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* @param tags a list of string tags that should be converted to the MissingPedField value
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* @return
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*/
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public static final EnumSet<MissingPedField> parseMissingFieldTags(final Object arg, final List<String> tags) {
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final EnumSet<MissingPedField> missingFields = EnumSet.noneOf(MissingPedField.class);
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for ( final String tag : tags ) {
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try {
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missingFields.add(MissingPedField.valueOf(tag));
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} catch ( IllegalArgumentException e ) {
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throw new UserException.BadArgumentValue(arg.toString(), "Unknown tag " + tag + " allowed values are " + MissingPedField.values());
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}
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}
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return missingFields;
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}
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}
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@ -0,0 +1,34 @@
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/*
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* Copyright (c) 2011, 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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* 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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package org.broadinstitute.sting.gatk.samples;
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/**
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*
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*/
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public enum PedigreeValidationType {
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STRICT,
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LINIENT,
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SILENT,
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}
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@ -38,51 +38,9 @@ public class SampleDB {
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}
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public SampleDB(final SAMFileHeader header, final List<File> sampleFiles) {
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this();
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addSamples(header);
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addSamples(sampleFiles);
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}
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// --------------------------------------------------------------------------------
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//
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// Functions for adding samples to the DB
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//
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// TODO: these should be protected, really
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//
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// --------------------------------------------------------------------------------
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/**
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* Hallucinates sample objects for all the samples in the SAM file and stores them
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*/
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protected SampleDB addSamples(SAMFileHeader header) {
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for (String sampleName : SampleUtils.getSAMFileSamples(header)) {
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if (getSample(sampleName) == null) {
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Sample newSample = new Sample(sampleName, this);
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samples.put(sampleName, newSample);
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}
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}
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return this;
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}
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protected SampleDB addSamples(final List<File> sampleFiles) {
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// add files consecutively
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for (File file : sampleFiles) {
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addSamples(file);
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}
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return this;
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}
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/**
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* Parse one sample file and integrate it with samples that are already there
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* Fail quickly if we find any errors in the file
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*/
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protected SampleDB addSamples(File sampleFile) {
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return this;
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}
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/**
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* Add a sample to the collection
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* Protected function to add a single sample to the database
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*
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* @param sample to be added
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*/
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protected SampleDB addSample(Sample sample) {
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@ -215,10 +173,14 @@ public class SampleDB {
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// --------------------------------------------------------------------------------
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public final void validate() {
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validate(getSamples());
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validate(getSamples(), PedigreeValidationType.STRICT);
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}
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public final void validate(Collection<Sample> samplesToCheck) {
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public final void validate(PedigreeValidationType validationType) {
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validate(getSamples(), validationType);
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}
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public final void validate(Collection<Sample> samplesToCheck, PedigreeValidationType validationType) {
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// todo -- actually do an implementation
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}
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}
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@ -0,0 +1,121 @@
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/*
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* Copyright (c) 2011, 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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* 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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package org.broadinstitute.sting.gatk.samples;
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import net.sf.samtools.SAMFileHeader;
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import net.sf.samtools.SAMReadGroupRecord;
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import net.sf.samtools.SAMRecord;
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import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
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import org.broadinstitute.sting.utils.SampleUtils;
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import org.broadinstitute.sting.utils.exceptions.StingException;
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import org.broadinstitute.sting.utils.exceptions.UserException;
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import org.broadinstitute.sting.utils.variantcontext.Genotype;
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import java.io.File;
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import java.io.FileNotFoundException;
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import java.util.*;
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/**
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*
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*/
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public class SampleDBBuilder {
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PedigreeValidationType validationStrictness;
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final SampleDB sampleDB = new SampleDB();
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final GenomeAnalysisEngine engine;
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/**
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* Constructor takes both a SAM header and sample files because the two must be integrated.
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*/
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public SampleDBBuilder(GenomeAnalysisEngine engine, PedigreeValidationType validationStrictness) {
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this.engine = engine;
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this.validationStrictness = validationStrictness;
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}
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/**
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* Hallucinates sample objects for all the samples in the SAM file and stores them
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*/
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public SampleDBBuilder addSamples(SAMFileHeader header) {
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for (String sampleName : SampleUtils.getSAMFileSamples(header)) {
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if (sampleDB.getSample(sampleName) == null) {
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final Sample newSample = new Sample(sampleName, sampleDB);
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addSample(newSample);
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}
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}
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return this;
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}
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public SampleDBBuilder addSamples(final List<String> pedigreeArguments) {
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for (final String ped : pedigreeArguments) {
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final File pedFile = new File(ped);
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if ( pedFile.exists() )
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addSamples(pedFile);
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else
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addSamples(ped);
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}
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return this;
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}
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/**
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* Parse one sample file and integrate it with samples that are already there
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* Fail quickly if we find any errors in the file
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*/
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protected SampleDBBuilder addSamples(File sampleFile) {
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final PedReader reader = new PedReader();
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try {
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reader.parse(sampleFile, getMissingFields(sampleFile), sampleDB);
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} catch ( FileNotFoundException e ) {
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throw new UserException.CouldNotReadInputFile(sampleFile, e);
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}
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return this;
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}
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protected SampleDBBuilder addSamples(final String string) {
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final PedReader reader = new PedReader();
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reader.parse(string, getMissingFields(string), sampleDB);
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return this;
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}
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/**
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* Add a sample to the collection
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* @param sample to be added
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*/
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protected SampleDBBuilder addSample(Sample sample) {
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sampleDB.addSample(sample);
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return this;
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}
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public SampleDB getFinalSampleDB() {
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sampleDB.validate(validationStrictness);
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return sampleDB;
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}
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public EnumSet<PedReader.MissingPedField> getMissingFields(final Object engineArg) {
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final List<String> posTags = engine.getTags(engineArg).getPositionalTags();
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return PedReader.parseMissingFieldTags(engineArg, posTags);
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}
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}
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@ -27,6 +27,7 @@ package org.broadinstitute.sting.gatk.samples;
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import org.apache.log4j.Logger;
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import org.broadinstitute.sting.BaseTest;
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import org.broadinstitute.sting.utils.Utils;
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import org.broadinstitute.sting.utils.exceptions.UserException;
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import org.testng.Assert;
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import org.testng.annotations.DataProvider;
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import org.testng.annotations.Test;
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@ -285,4 +286,69 @@ public class PedReaderUnitTest extends BaseTest {
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parts.remove(field.ordinal());
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return Utils.join("\t", parts);
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}
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// -----------------------------------------------------------------
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// parsing tags
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// -----------------------------------------------------------------
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private class PedReaderTestTagParsing extends TestDataProvider {
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public EnumSet<PedReader.MissingPedField> expected;
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public final List<String> tags;
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private PedReaderTestTagParsing(final List<String> tags, EnumSet<PedReader.MissingPedField> missingDesc) {
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super(PedReaderTestTagParsing.class);
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this.tags = tags;
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this.expected = missingDesc;
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}
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}
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@DataProvider(name = "readerTestTagParsing")
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public Object[][] createReaderTestTagParsing() {
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new PedReaderTestTagParsing(
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Collections.<String>emptyList(),
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EnumSet.noneOf(PedReader.MissingPedField.class));
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new PedReaderTestTagParsing(
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Arrays.asList("NO_FAMILY_ID"),
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EnumSet.of(PedReader.MissingPedField.NO_FAMILY_ID));
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new PedReaderTestTagParsing(
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Arrays.asList("NO_PARENTS"),
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EnumSet.of(PedReader.MissingPedField.NO_PARENTS));
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new PedReaderTestTagParsing(
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Arrays.asList("NO_PHENOTYPE"),
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EnumSet.of(PedReader.MissingPedField.NO_PHENOTYPE));
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new PedReaderTestTagParsing(
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Arrays.asList("NO_SEX"),
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EnumSet.of(PedReader.MissingPedField.NO_SEX));
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new PedReaderTestTagParsing(
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Arrays.asList("NO_SEX", "NO_PHENOTYPE"),
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EnumSet.of(PedReader.MissingPedField.NO_SEX, PedReader.MissingPedField.NO_PHENOTYPE));
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new PedReaderTestTagParsing(
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Arrays.asList("NO_SEX", "NO_PHENOTYPE", "NO_PARENTS"),
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EnumSet.of(PedReader.MissingPedField.NO_SEX, PedReader.MissingPedField.NO_PHENOTYPE, PedReader.MissingPedField.NO_PARENTS));
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return PedReaderTestTagParsing.getTests(PedReaderTestTagParsing.class);
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}
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@Test(enabled = true, dataProvider = "readerTestTagParsing")
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public void testPedReaderTagParsing(PedReaderTestTagParsing test) {
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EnumSet<PedReader.MissingPedField> parsed = PedReader.parseMissingFieldTags("test", test.tags);
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Assert.assertEquals(test.expected, parsed, "Failed to properly parse tags " + test.tags);
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}
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@Test(enabled = true, expectedExceptions = UserException.class)
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public void testPedReaderTagParsing1() {
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EnumSet<PedReader.MissingPedField> parsed = PedReader.parseMissingFieldTags("test", Arrays.asList("XXX"));
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}
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@Test(enabled = true, expectedExceptions = UserException.class)
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public void testPedReaderTagParsing2() {
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EnumSet<PedReader.MissingPedField> parsed = PedReader.parseMissingFieldTags("test", Arrays.asList("NO_SEX", "XXX"));
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}
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}
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@ -14,7 +14,7 @@ import java.util.*;
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* Date: Sep 9, 2010
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* Time: 8:21:00 AM
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*/
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public class SampleDataSourceUnitTest extends BaseTest {
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public class SampleDBUnitTest extends BaseTest {
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// this empty header used to instantiate sampledatasource objects
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private static SAMFileHeader header = new SAMFileHeader();
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@ -24,6 +24,6 @@ public class SampleDataSourceUnitTest extends BaseTest {
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// make sure samples are created from the SAM file correctly
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@Test()
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public void loadSAMSamplesTest() {
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SampleDB s = new SampleDB(header, Collections.<File>emptyList());
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//SampleDB s = new SampleDB(header);
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}
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}
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