A 'fat shard' finder. Cranks through the indices of a BAM file or list of
BAM files looking for outliers (outliers right now are defined naively as shards whose sizes are more than 5 stddevs away from the mean). Runs in 13 minutes per chromosome on 707 low pass whole genome BAMs -- not great, but much faster than running UG on the same region to discover anomalies. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5782 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna
parent
3ffc2ccd81
commit
f275be6968
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@ -47,6 +47,7 @@ import java.util.*;
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import net.sf.picard.filter.SamRecordFilter;
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import org.broadinstitute.sting.utils.exceptions.UserException;
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import org.broadinstitute.sting.utils.text.ListFileUtils;
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import org.broadinstitute.sting.utils.text.XReadLines;
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/**
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@ -72,11 +73,6 @@ public abstract class CommandLineExecutable extends CommandLineProgram {
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*/
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private final Collection<Object> argumentSources = new ArrayList<Object>();
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/**
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* Lines starting with this String in .list files are considered comments.
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*/
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public static final String LIST_FILE_COMMENT_START = "#";
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/**
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* this is the function that the inheriting class can expect to have called
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* when the command line system has initialized.
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@ -93,8 +89,8 @@ public abstract class CommandLineExecutable extends CommandLineProgram {
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engine.setArguments(getArgumentCollection());
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// File lists can require a bit of additional expansion. Set these explicitly by the engine.
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engine.setSAMFileIDs(unpackBAMFileList(getArgumentCollection()));
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engine.setReferenceMetaDataFiles(unpackRODBindings(getArgumentCollection()));
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engine.setSAMFileIDs(ListFileUtils.unpackBAMFileList(getArgumentCollection().samFiles,parser));
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engine.setReferenceMetaDataFiles(ListFileUtils.unpackRODBindings(getArgumentCollection().RODBindings,getArgumentCollection().DBSNPFile,parser));
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engine.setWalker(walker);
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walker.setToolkit(engine);
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@ -200,104 +196,4 @@ public abstract class CommandLineExecutable extends CommandLineProgram {
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return engine.getWalkerName((Class<Walker>)argumentSource);
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}
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/**
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* Unpack the bam files to be processed, given a list of files. That list of files can
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* itself contain entries which are lists of other files to be read (note: you cannot have lists
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* of lists of lists). Lines in .list files containing only whitespace or which begin with
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* LIST_FILE_COMMENT_START are ignored.
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*
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* @param argCollection the command-line arguments from which to extract the BAM file list.
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* @return a flattened list of the bam files provided
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*/
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protected List<SAMReaderID> unpackBAMFileList(GATKArgumentCollection argCollection) {
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List<SAMReaderID> unpackedReads = new ArrayList<SAMReaderID>();
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for( String inputFileName: argCollection.samFiles ) {
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Tags inputFileNameTags = parser.getTags(inputFileName);
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inputFileName = expandFileName(inputFileName);
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if (inputFileName.toLowerCase().endsWith(".list") ) {
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try {
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for ( String fileName : new XReadLines(new File(inputFileName), true) ) {
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if ( fileName.length() > 0 && ! fileName.startsWith(LIST_FILE_COMMENT_START) ) {
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unpackedReads.add(new SAMReaderID(fileName,parser.getTags(inputFileName)));
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}
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}
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}
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catch( FileNotFoundException ex ) {
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throw new UserException.CouldNotReadInputFile(new File(inputFileName), "Unable to find file while unpacking reads", ex);
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}
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}
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else if(inputFileName.toLowerCase().endsWith(".bam")) {
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unpackedReads.add(new SAMReaderID(inputFileName,inputFileNameTags));
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}
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else if(inputFileName.endsWith("stdin")) {
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unpackedReads.add(new SAMReaderID(inputFileName,inputFileNameTags));
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}
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else {
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throw new UserException.CommandLineException(String.format("The GATK reads argument (-I) supports only BAM files with the .bam extension and lists of BAM files " +
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"with the .list extension, but the file %s has neither extension. Please ensure that your BAM file or list " +
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"of BAM files is in the correct format, update the extension, and try again.",inputFileName));
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}
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}
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return unpackedReads;
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}
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/**
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* Convert command-line argument representation of ROD bindings to something more easily understandable by the engine.
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* @param argCollection input arguments to the GATK.
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* @return a list of expanded, bound RODs.
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*/
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private Collection<RMDTriplet> unpackRODBindings(GATKArgumentCollection argCollection) {
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Collection<RMDTriplet> rodBindings = new ArrayList<RMDTriplet>();
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for (String fileName: argCollection.RODBindings) {
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final Tags tags = parser.getTags(fileName);
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fileName = expandFileName(fileName);
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List<String> positionalTags = tags.getPositionalTags();
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if(positionalTags.size() != 2)
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throw new UserException("Invalid syntax for -B (reference-ordered data) input flag. " +
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"Please use the following syntax when providing reference-ordered " +
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"data: -B:<name>,<type> <filename>.");
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// Assume that if tags are present, those tags are name and type.
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// Name is always first, followed by type.
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String name = positionalTags.get(0);
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String type = positionalTags.get(1);
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RMDStorageType storageType = null;
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if(tags.getValue("storage") != null)
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storageType = Enum.valueOf(RMDStorageType.class,tags.getValue("storage"));
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else if(fileName.toLowerCase().endsWith("stdin"))
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storageType = RMDStorageType.STREAM;
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else
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storageType = RMDStorageType.FILE;
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rodBindings.add(new RMDTriplet(name,type,fileName,storageType,tags));
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}
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if (argCollection.DBSNPFile != null) {
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if(argCollection.DBSNPFile.toLowerCase().contains("vcf"))
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throw new UserException("--DBSNP (-D) argument currently does not support VCF. To use dbSNP in VCF format, please use -B:dbsnp,vcf <filename>.");
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final Tags tags = parser.getTags(argCollection.DBSNPFile);
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String fileName = expandFileName(argCollection.DBSNPFile);
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RMDStorageType storageType = fileName.toLowerCase().endsWith("stdin") ? RMDStorageType.STREAM : RMDStorageType.FILE;
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rodBindings.add(new RMDTriplet(DbSNPHelper.STANDARD_DBSNP_TRACK_NAME,"dbsnp",fileName,storageType,tags));
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}
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return rodBindings;
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}
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/**
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* Expand any special characters that appear in the filename. Right now, '-' is expanded to
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* '/dev/stdin' only, but in the future, special characters like '~' and '*' that are passed
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* directly to the command line in some circumstances could be expanded as well. Be careful
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* when adding UNIX-isms.
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* @param argument the text appearing on the command-line.
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* @return An expanded string suitable for opening by Java/UNIX file handling utilities.
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*/
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private String expandFileName(String argument) {
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if(argument.trim().equals("-"))
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return "/dev/stdin";
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return argument;
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}
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}
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@ -46,7 +46,7 @@ import java.util.TreeMap;
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/**
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* Represents a small section of a BAM file, and every associated interval.
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*/
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class FilePointer {
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public class FilePointer {
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protected final SortedMap<SAMReaderID,SAMFileSpan> fileSpans = new TreeMap<SAMReaderID,SAMFileSpan>();
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protected final BAMOverlap overlap;
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protected final List<GenomeLoc> locations;
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@ -72,6 +72,14 @@ class FilePointer {
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this.isRegionUnmapped = false;
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}
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/**
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* Returns an immutable variant of the list of locations.
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* @return
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*/
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public List<GenomeLoc> getLocations() {
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return Collections.unmodifiableList(locations);
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}
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@Override
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public boolean equals(final Object other) {
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if(!(other instanceof FilePointer))
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@ -150,7 +150,7 @@ public class SAMDataSource {
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new ArrayList<ReadFilter>(),
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false,
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false,
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false);
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true);
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}
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/**
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@ -0,0 +1,187 @@
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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.datasources.reads.utilities;
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import net.sf.picard.reference.IndexedFastaSequenceFile;
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import net.sf.samtools.SAMSequenceRecord;
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import org.apache.log4j.Logger;
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import org.broadinstitute.sting.commandline.CommandLineProgram;
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import org.broadinstitute.sting.commandline.Input;
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import org.broadinstitute.sting.gatk.datasources.reads.FilePointer;
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import org.broadinstitute.sting.gatk.datasources.reads.LowMemoryIntervalSharder;
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import org.broadinstitute.sting.gatk.datasources.reads.SAMDataSource;
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import org.broadinstitute.sting.gatk.datasources.reads.SAMReaderID;
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import org.broadinstitute.sting.utils.GenomeLoc;
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import org.broadinstitute.sting.utils.GenomeLocParser;
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import org.broadinstitute.sting.utils.GenomeLocSortedSet;
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import org.broadinstitute.sting.utils.interval.IntervalMergingRule;
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import org.broadinstitute.sting.utils.interval.IntervalUtils;
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import org.broadinstitute.sting.utils.text.ListFileUtils;
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import java.io.File;
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import java.io.IOException;
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import java.math.BigInteger;
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import java.util.ArrayList;
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import java.util.List;
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/**
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* Traverses a region in a dataset looking for outliers.
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*/
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public class FindLargeShards extends CommandLineProgram {
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private static Logger logger = Logger.getLogger(FindLargeShards.class);
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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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@Input(fullName = "reference_sequence", shortName = "R", doc = "Reference sequence file", required = false)
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public File referenceFile = null;
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@Input(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 List<String> intervals = null;
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/**
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* The square of the sum of all uncompressed data. Based on the BAM spec, the size of this could be
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* up to (2^64)^2.
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*/
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private BigInteger sumOfSquares = BigInteger.valueOf(0);
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/**
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* The running sum of all uncompressed data. Based on the BAM spec, the BAM must be less than Long.MAX_LONG
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* when compressed -- in other words, the sum of the sizes of all BGZF blocks must be < 2^64.
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*/
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private BigInteger sum = BigInteger.valueOf(0);
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/**
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* The number of shards viewed.
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*/
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private long numberOfShards;
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@Override
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public int execute() throws IOException {
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// initialize reference
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IndexedFastaSequenceFile refReader = new IndexedFastaSequenceFile(referenceFile);
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GenomeLocParser genomeLocParser = new GenomeLocParser(refReader);
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// initialize reads
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List<SAMReaderID> bamReaders = ListFileUtils.unpackBAMFileList(samFiles,parser);
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SAMDataSource dataSource = new SAMDataSource(bamReaders,genomeLocParser);
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// intervals
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GenomeLocSortedSet intervalSortedSet = null;
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if(intervals != null)
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intervalSortedSet = IntervalUtils.sortAndMergeIntervals(genomeLocParser, IntervalUtils.parseIntervalArguments(genomeLocParser, intervals, true), IntervalMergingRule.ALL);
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else {
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intervalSortedSet = new GenomeLocSortedSet(genomeLocParser);
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for(SAMSequenceRecord entry: refReader.getSequenceDictionary().getSequences())
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intervalSortedSet.add(genomeLocParser.createGenomeLoc(entry.getSequenceName(),1,entry.getSequenceLength()));
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}
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logger.info(String.format("Calculating mean and variance: Contig\tRegion.Start\tRegion.Stop\tSize"));
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LowMemoryIntervalSharder sharder = new LowMemoryIntervalSharder(dataSource,intervalSortedSet);
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while(sharder.hasNext()) {
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FilePointer filePointer = sharder.next();
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// Size of the file pointer.
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final long size = filePointer.size();
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BigInteger bigSize = BigInteger.valueOf(size);
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sumOfSquares = sumOfSquares.add(bigSize.pow(2));
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sum = sum.add(bigSize);
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numberOfShards++;
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if(numberOfShards % 1000 == 0) {
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GenomeLoc boundingRegion = getBoundingRegion(filePointer,genomeLocParser);
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logger.info(String.format("Calculating mean and variance: %s\t%d\t%d\t%d",boundingRegion.getContig(),boundingRegion.getStart(),boundingRegion.getStop(),size));
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}
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}
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// Print out the stddev: (sum(x^2) - (1/N)*sum(x)^2)/N
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long mean = sum.divide(BigInteger.valueOf(numberOfShards)).longValue();
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long stddev = (long)(Math.sqrt(sumOfSquares.subtract(sum.pow(2).divide(BigInteger.valueOf(numberOfShards))).divide(BigInteger.valueOf(numberOfShards)).doubleValue()));
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logger.info(String.format("Number of shards: %d; mean uncompressed size = %d; stddev uncompressed size = %d%n",numberOfShards,mean,stddev));
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// Crank through the shards again, this time reporting on the shards significantly larger than the mean.
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long threshold = mean + stddev*5;
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logger.warn(String.format("Searching for large shards: Contig\tRegion.Start\tRegion.Stop\tSize"));
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sharder = new LowMemoryIntervalSharder(dataSource,intervalSortedSet);
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while(sharder.hasNext()) {
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FilePointer filePointer = sharder.next();
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// Bounding region.
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GenomeLoc boundingRegion = getBoundingRegion(filePointer,genomeLocParser);
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// Size of the file pointer.
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final long size = filePointer.size();
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numberOfShards++;
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if(filePointer.size() <= threshold) {
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if(numberOfShards % 1000 == 0)
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logger.info(String.format("%s\t%d\t%d\t%d",boundingRegion.getContig(),boundingRegion.getStart(),boundingRegion.getStop(),size));
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continue;
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}
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logger.warn(String.format("FOUND LARGE SHARD: %s\t%d\t%d\t%d",boundingRegion.getContig(),boundingRegion.getStart(),boundingRegion.getStop(),size));
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}
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return 0;
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}
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private GenomeLoc getBoundingRegion(final FilePointer filePointer, final GenomeLocParser genomeLocParser) {
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List<GenomeLoc> regions = filePointer.getLocations();
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// The region contained by this FilePointer.
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final String contig = regions.get(0).getContig();
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final int start = regions.get(0).getStart();
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final int stop = regions.get(regions.size()-1).getStop();
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return genomeLocParser.createGenomeLoc(contig,start,stop);
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}
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/**
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* Required main method implementation.
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* @param argv Command-line argument text.
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* @throws Exception on error.
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*/
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public static void main(String[] argv) throws Exception {
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int returnCode = 0;
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try {
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FindLargeShards instance = new FindLargeShards();
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start(instance, argv);
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returnCode = 0;
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}
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catch(Exception ex) {
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returnCode = 1;
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ex.printStackTrace();
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throw ex;
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}
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finally {
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System.exit(returnCode);
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}
|
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}
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}
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|
|
@ -0,0 +1,152 @@
|
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/*
|
||||
* Copyright (c) 2011, The Broad Institute
|
||||
*
|
||||
* Permission is hereby granted, free of charge, to any person
|
||||
* obtaining a copy of this software and associated documentation
|
||||
* files (the "Software"), to deal in the Software without
|
||||
* restriction, including without limitation the rights to use,
|
||||
* copy, modify, merge, publish, distribute, sublicense, and/or sell
|
||||
* copies of the Software, and to permit persons to whom the
|
||||
* Software is furnished to do so, subject to the following
|
||||
* conditions:
|
||||
*
|
||||
* The above copyright notice and this permission notice shall be
|
||||
* included in all copies or substantial portions of the Software.
|
||||
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
|
||||
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
|
||||
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
|
||||
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
|
||||
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
|
||||
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
|
||||
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
|
||||
* OTHER DEALINGS IN THE SOFTWARE.
|
||||
*/
|
||||
|
||||
package org.broadinstitute.sting.utils.text;
|
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|
||||
import org.broadinstitute.sting.commandline.ParsingEngine;
|
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import org.broadinstitute.sting.commandline.Tags;
|
||||
import org.broadinstitute.sting.gatk.arguments.GATKArgumentCollection;
|
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import org.broadinstitute.sting.gatk.datasources.reads.SAMReaderID;
|
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import org.broadinstitute.sting.gatk.refdata.utils.RMDTriplet;
|
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import org.broadinstitute.sting.gatk.refdata.utils.helpers.DbSNPHelper;
|
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import org.broadinstitute.sting.utils.exceptions.UserException;
|
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|
||||
import java.io.File;
|
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import java.io.FileNotFoundException;
|
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import java.util.ArrayList;
|
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import java.util.Collection;
|
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import java.util.List;
|
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|
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/**
|
||||
* A collection of convenience methods for working with list files.
|
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*/
|
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public class ListFileUtils {
|
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/**
|
||||
* Lines starting with this String in .list files are considered comments.
|
||||
*/
|
||||
public static final String LIST_FILE_COMMENT_START = "#";
|
||||
|
||||
/**
|
||||
* Unpack the bam files to be processed, given a list of files. That list of files can
|
||||
* itself contain entries which are lists of other files to be read (note: you cannot have lists
|
||||
* of lists of lists). Lines in .list files containing only whitespace or which begin with
|
||||
* LIST_FILE_COMMENT_START are ignored.
|
||||
*
|
||||
* @param samFiles The sam files, in string format.
|
||||
* @return a flattened list of the bam files provided
|
||||
*/
|
||||
public static List<SAMReaderID> unpackBAMFileList(final List<String> samFiles, final ParsingEngine parser) {
|
||||
List<SAMReaderID> unpackedReads = new ArrayList<SAMReaderID>();
|
||||
for( String inputFileName: samFiles ) {
|
||||
Tags inputFileNameTags = parser.getTags(inputFileName);
|
||||
inputFileName = expandFileName(inputFileName);
|
||||
if (inputFileName.toLowerCase().endsWith(".list") ) {
|
||||
try {
|
||||
for ( String fileName : new XReadLines(new File(inputFileName), true) ) {
|
||||
if ( fileName.length() > 0 && ! fileName.startsWith(LIST_FILE_COMMENT_START) ) {
|
||||
unpackedReads.add(new SAMReaderID(fileName,parser.getTags(inputFileName)));
|
||||
}
|
||||
}
|
||||
}
|
||||
catch( FileNotFoundException ex ) {
|
||||
throw new UserException.CouldNotReadInputFile(new File(inputFileName), "Unable to find file while unpacking reads", ex);
|
||||
}
|
||||
}
|
||||
else if(inputFileName.toLowerCase().endsWith(".bam")) {
|
||||
unpackedReads.add(new SAMReaderID(inputFileName,inputFileNameTags));
|
||||
}
|
||||
else if(inputFileName.endsWith("stdin")) {
|
||||
unpackedReads.add(new SAMReaderID(inputFileName,inputFileNameTags));
|
||||
}
|
||||
else {
|
||||
throw new UserException.CommandLineException(String.format("The GATK reads argument (-I) supports only BAM files with the .bam extension and lists of BAM files " +
|
||||
"with the .list extension, but the file %s has neither extension. Please ensure that your BAM file or list " +
|
||||
"of BAM files is in the correct format, update the extension, and try again.",inputFileName));
|
||||
}
|
||||
}
|
||||
return unpackedReads;
|
||||
}
|
||||
|
||||
/**
|
||||
* Convert command-line argument representation of ROD bindings to something more easily understandable by the engine.
|
||||
* @param RODBindings a text equivale
|
||||
* @return a list of expanded, bound RODs.
|
||||
*/
|
||||
public static Collection<RMDTriplet> unpackRODBindings(final List<String> RODBindings, final String dbSNPFile, final ParsingEngine parser) {
|
||||
Collection<RMDTriplet> rodBindings = new ArrayList<RMDTriplet>();
|
||||
|
||||
for (String fileName: RODBindings) {
|
||||
final Tags tags = parser.getTags(fileName);
|
||||
fileName = expandFileName(fileName);
|
||||
|
||||
List<String> positionalTags = tags.getPositionalTags();
|
||||
if(positionalTags.size() != 2)
|
||||
throw new UserException("Invalid syntax for -B (reference-ordered data) input flag. " +
|
||||
"Please use the following syntax when providing reference-ordered " +
|
||||
"data: -B:<name>,<type> <filename>.");
|
||||
// Assume that if tags are present, those tags are name and type.
|
||||
// Name is always first, followed by type.
|
||||
String name = positionalTags.get(0);
|
||||
String type = positionalTags.get(1);
|
||||
|
||||
RMDTriplet.RMDStorageType storageType = null;
|
||||
if(tags.getValue("storage") != null)
|
||||
storageType = Enum.valueOf(RMDTriplet.RMDStorageType.class,tags.getValue("storage"));
|
||||
else if(fileName.toLowerCase().endsWith("stdin"))
|
||||
storageType = RMDTriplet.RMDStorageType.STREAM;
|
||||
else
|
||||
storageType = RMDTriplet.RMDStorageType.FILE;
|
||||
|
||||
rodBindings.add(new RMDTriplet(name,type,fileName,storageType,tags));
|
||||
}
|
||||
|
||||
if (dbSNPFile != null) {
|
||||
if(dbSNPFile.toLowerCase().contains("vcf"))
|
||||
throw new UserException("--DBSNP (-D) argument currently does not support VCF. To use dbSNP in VCF format, please use -B:dbsnp,vcf <filename>.");
|
||||
|
||||
final Tags tags = parser.getTags(dbSNPFile);
|
||||
String fileName = expandFileName(dbSNPFile);
|
||||
RMDTriplet.RMDStorageType storageType = fileName.toLowerCase().endsWith("stdin") ? RMDTriplet.RMDStorageType.STREAM : RMDTriplet.RMDStorageType.FILE;
|
||||
|
||||
rodBindings.add(new RMDTriplet(DbSNPHelper.STANDARD_DBSNP_TRACK_NAME,"dbsnp",fileName,storageType,tags));
|
||||
}
|
||||
|
||||
return rodBindings;
|
||||
}
|
||||
|
||||
|
||||
/**
|
||||
* Expand any special characters that appear in the filename. Right now, '-' is expanded to
|
||||
* '/dev/stdin' only, but in the future, special characters like '~' and '*' that are passed
|
||||
* directly to the command line in some circumstances could be expanded as well. Be careful
|
||||
* when adding UNIX-isms.
|
||||
* @param argument the text appearing on the command-line.
|
||||
* @return An expanded string suitable for opening by Java/UNIX file handling utilities.
|
||||
*/
|
||||
private static String expandFileName(String argument) {
|
||||
if(argument.trim().equals("-"))
|
||||
return "/dev/stdin";
|
||||
return argument;
|
||||
}
|
||||
}
|
||||
|
|
@ -22,11 +22,12 @@
|
|||
* OTHER DEALINGS IN THE SOFTWARE.
|
||||
*/
|
||||
|
||||
package org.broadinstitute.sting.gatk;
|
||||
package org.broadinstitute.sting.utils.text;
|
||||
|
||||
import org.broadinstitute.sting.BaseTest;
|
||||
import org.broadinstitute.sting.commandline.ParsingEngine;
|
||||
import org.broadinstitute.sting.commandline.Tags;
|
||||
import org.broadinstitute.sting.gatk.CommandLineGATK;
|
||||
import org.broadinstitute.sting.gatk.arguments.GATKArgumentCollection;
|
||||
import org.broadinstitute.sting.gatk.datasources.reads.SAMReaderID;
|
||||
import org.testng.Assert;
|
||||
|
|
@ -42,7 +43,7 @@ import java.util.List;
|
|||
/**
|
||||
* Tests selected functionality in the CommandLineExecutable class
|
||||
*/
|
||||
public class CommandLineExecutableUnitTest extends BaseTest {
|
||||
public class ListFileUtilsUnitTest extends BaseTest {
|
||||
|
||||
@Test
|
||||
public void testIgnoreBlankLinesInBAMListFiles() throws Exception {
|
||||
|
|
@ -90,13 +91,10 @@ public class CommandLineExecutableUnitTest extends BaseTest {
|
|||
List<String> bamFiles = new ArrayList<String>();
|
||||
bamFiles.add(tempListFile.getAbsolutePath());
|
||||
|
||||
GATKArgumentCollection argCollection = new GATKArgumentCollection();
|
||||
argCollection.samFiles = bamFiles;
|
||||
|
||||
CommandLineGATK testInstance = new CommandLineGATK();
|
||||
testInstance.setParser(new ParsingEngine(testInstance));
|
||||
|
||||
List<SAMReaderID> unpackedBAMFileList = testInstance.unpackBAMFileList(argCollection);
|
||||
List<SAMReaderID> unpackedBAMFileList = ListFileUtils.unpackBAMFileList(bamFiles,new ParsingEngine(testInstance));
|
||||
|
||||
Assert.assertEquals(unpackedBAMFileList.size(), expectedUnpackedFileList.size(),
|
||||
"Unpacked BAM file list contains extraneous lines");
|
||||
Loading…
Reference in New Issue