Interface check-in for Matt
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@300 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
aaron
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package org.broadinstitute.sting.gatk.dataSources.simpleDataSources;
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import org.broadinstitute.sting.gatk.iterators.ReferenceIterator;
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import org.broadinstitute.sting.utils.FastaSequenceFile2;
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import org.broadinstitute.sting.utils.GenomeLoc;
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import java.io.File;
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/**
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*
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* User: aaron
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* Date: Apr 6, 2009
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* Time: 3:55:21 PM
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*
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* The Broad Institute
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* SOFTWARE COPYRIGHT NOTICE AGREEMENT
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* This software and its documentation are copyright 2009 by the
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* Broad Institute/Massachusetts Institute of Technology. All rights are reserved.
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*
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* This software is supplied without any warranty or guaranteed support whatsoever. Neither
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* the Broad Institute nor MIT can be responsible for its use, misuse, or functionality.
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*
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*/
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/**
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* @author aaron
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* @version 1.0
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* @date Apr 6, 2009
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* <p/>
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* Class ReferenceDataSource
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* <p/>
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* A descriptions should go here. Blame aaron if it's missing.
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*/
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public class ReferenceDataSource implements SimpleDataSource {
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final protected FastaSequenceFile2 refFile;
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final protected ReferenceIterator refIter;
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/**
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* Query the data source for a region of interest, specified by the genome location.
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* The iterator will generate successive calls
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*
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* @param location the genome location to extract data for
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* @return an iterator of the appropriate type, that is limited by the region
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*/
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public ReferenceIterator seek(GenomeLoc location) {
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ReferenceIterator refSite = refIter.seekForward(location);
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return refSite;
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}
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/**
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* Constructor - ReferenceDataSource
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*
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* @param refFileName the reference file
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* @throws SimpleDataSourceLoadException
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*/
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public ReferenceDataSource(String refFileName) throws SimpleDataSourceLoadException {
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if (refFileName == null) {
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throw new SimpleDataSourceLoadException("ReferenceDataSource: refFileName passed in is null");
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}
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File infile = new File(refFileName);
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if (!infile.canRead()) {
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throw new SimpleDataSourceLoadException("ReferenceDataSource: Unable to load file: " + refFileName);
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}
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refFile = new FastaSequenceFile2(new File(refFileName));
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refIter = new ReferenceIterator(this.refFile);
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}
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}
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package org.broadinstitute.sting.gatk.dataSources.simpleDataSources;
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import org.broadinstitute.sting.gatk.refdata.HapMapAlleleFrequenciesROD;
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import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedData;
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import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
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import org.broadinstitute.sting.gatk.refdata.rodDbSNP;
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import org.broadinstitute.sting.utils.GenomeLoc;
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import java.io.File;
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import java.util.*;
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/**
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*
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* User: aaron
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* Date: Apr 6, 2009
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* Time: 4:33:10 PM
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*
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* The Broad Institute
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* SOFTWARE COPYRIGHT NOTICE AGREEMENT
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* This software and its documentation are copyright 2009 by the
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* Broad Institute/Massachusetts Institute of Technology. All rights are reserved.
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*
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* This software is supplied without any warranty or guaranteed support whatsoever. Neither
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* the Broad Institute nor MIT can be responsible for its use, misuse, or functionality.
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*
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*/
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/**
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* @author aaron
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* @version 1.0
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* @date Apr 6, 2009
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* <p/>
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* Class ReferenceMetaDataSource
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* <p/>
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* A descriptions should go here. Blame aaron if it's missing.
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*/
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public class ReferenceMetaDataSource implements SimpleDataSource {
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// our enumerated types
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public enum RODTYPE {
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DBSNP, HAPMAP
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}
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// these could go on the stack, but a heap copy isn't too bad
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private List<ReferenceOrderedDatum> myData = null;
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private List<ReferenceOrderedData<? extends ReferenceOrderedDatum>.RODIterator> rodIters = null;
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private List<ReferenceOrderedData<? extends ReferenceOrderedDatum>> rods = null;
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/**
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* Prepare the list of reference ordered data iterators for each of the rods
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*
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* @return A list of ROD iterators for getting data from each ROD
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*/
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protected List<ReferenceOrderedData<? extends ReferenceOrderedDatum>.RODIterator> initializeRODs() {
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// set up reference ordered data
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rodIters = new ArrayList<ReferenceOrderedData<? extends ReferenceOrderedDatum>.RODIterator>();
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for (ReferenceOrderedData<? extends ReferenceOrderedDatum> data : rods) {
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rodIters.add(data.iterator());
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}
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return rodIters;
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}
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/**
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* Builds a list of the reference ordered datum at loc from each of the iterators. This function
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* assumes you are accessing the data in order. You can't use this function for random access. Each
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* successive call moves you along the file, consuming all data before loc.
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*
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* @param rodIters Iterators to access the RODs
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* @param loc The location to get the rods at
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* @return A list of ReferenceOrderDatum at loc. ROD without a datum at loc will be null in the list
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*/
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protected List<ReferenceOrderedDatum> getReferenceOrderedDataAtLocus(List<ReferenceOrderedData<? extends ReferenceOrderedDatum>.RODIterator> rodIters,
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final GenomeLoc loc) {
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List<ReferenceOrderedDatum> data = new ArrayList<ReferenceOrderedDatum>();
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for (ReferenceOrderedData<? extends ReferenceOrderedDatum>.RODIterator iter : rodIters) {
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data.add(iter.seekForward(loc));
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}
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return data;
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}
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/**
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* Query the data source for a region of interest, specified by the genome location.
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* The iterator will generate successive calls
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*
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* @param location the genome location to extract data for
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* @return an iterator of the appropriate type, that is limited by the region
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*/
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public Iterator<ReferenceOrderedDatum> seek(GenomeLoc location) {
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myData = getReferenceOrderedDataAtLocus(rodIters, location);
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return myData.iterator();
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}
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public ReferenceMetaDataSource(HashMap<String, RODTYPE> files) {
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// setup a rod list
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List<ReferenceOrderedData<? extends ReferenceOrderedDatum>> rods = new ArrayList<ReferenceOrderedData<? extends ReferenceOrderedDatum>>();
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// cycle through the passed in rod's
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Set<String> fileNames = files.keySet();
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for (String file : fileNames) {
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switch (files.get(file)) {
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case DBSNP: {
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ReferenceOrderedData<rodDbSNP> dbsnp = new ReferenceOrderedData<rodDbSNP>(new File(file), rodDbSNP.class);
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//dbsnp.testMe();
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rods.add(dbsnp); // { gff, dbsnp };
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}
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case HAPMAP: {
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ReferenceOrderedData<HapMapAlleleFrequenciesROD> hapmap = new ReferenceOrderedData<HapMapAlleleFrequenciesROD>(new File(file), HapMapAlleleFrequenciesROD.class);
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//dbsnp.testMe();
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rods.add(hapmap); // { gff, dbsnp };
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}
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}
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}
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}
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}
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@ -0,0 +1,114 @@
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package org.broadinstitute.sting.gatk.dataSources.simpleDataSources;
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import edu.mit.broad.picard.sam.SamFileHeaderMerger;
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import net.sf.samtools.SAMFileHeader;
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import net.sf.samtools.SAMFileReader;
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import org.apache.log4j.Logger;
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import org.broadinstitute.sting.gatk.iterators.MergingSamRecordIterator2;
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import org.broadinstitute.sting.utils.GenomeLoc;
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import java.io.File;
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import java.util.ArrayList;
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import java.util.List;
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/**
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* User: aaron
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* Date: Mar 26, 2009
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* Time: 2:36:16 PM
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* <p/>
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* The Broad Institute
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* SOFTWARE COPYRIGHT NOTICE AGREEMENT
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* This software and its documentation are copyright 2009 by the
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* Broad Institute/Massachusetts Institute of Technology. All rights are reserved.
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* <p/>
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* This software is supplied without any warranty or guaranteed support whatsoever. Neither
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* the Broad Institute nor MIT can be responsible for its use, misuse, or functionality.
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*/
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public class SAMBAMDataSource implements SimpleDataSource {
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/** our SAM data files */
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private final SAMFileHeader.SortOrder SORT_ORDER = SAMFileHeader.SortOrder.coordinate;
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/** our log, which we want to capture anything from this class */
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protected static Logger logger = Logger.getLogger(SAMBAMDataSource.class);
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// our sam file readers
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private final ArrayList<SAMFileReader> readers = new ArrayList<SAMFileReader>();
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// do we care that the SAM files respect the sort order.
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private boolean matchedSortOrders = true;
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// our merged sam iterator for spliting up the files
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MergingSamRecordIterator2 mergeIterator;
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// are we set to locus mode or read mode for dividing
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private boolean locusMode = true;
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// How strict should we be with SAM/BAM parsing?
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protected SAMFileReader.ValidationStringency strictness = SAMFileReader.ValidationStringency.STRICT;
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/**
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* constructor, given a single sam file
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*
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* @param samFiles the list of sam files
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*/
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public SAMBAMDataSource(List<String> samFiles) throws SimpleDataSourceLoadException {
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List<SAMFileReader> readers = new ArrayList<SAMFileReader>();
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for (String fileName : samFiles) {
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File smFile = new File(fileName);
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if (!smFile.canRead()) {
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throw new SimpleDataSourceLoadException("SAMBAMDataSource: Unable to load file: " + fileName);
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}
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SAMFileReader reader = initializeSAMFile(smFile);
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if (reader != null) {
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readers.add(reader);
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}
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}
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SamFileHeaderMerger headerMerger = new SamFileHeaderMerger(readers, SORT_ORDER);
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this.mergeIterator = new MergingSamRecordIterator2(headerMerger);
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}
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protected SAMFileReader initializeSAMFile(final File samFile) {
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if (samFile.toString().endsWith(".list")) {
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return null;
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} else {
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SAMFileReader samReader = new SAMFileReader(samFile, true);
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samReader.setValidationStringency(strictness);
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final SAMFileHeader header = samReader.getFileHeader();
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logger.info(String.format("Sort order is: " + header.getSortOrder()));
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return samReader;
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}
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}
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/**
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* set the mode to by loci, which let's you duplicate reads, but never at a single
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* locus, or false for read mode where no read is seen twice.
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*
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* @param tr true if by loci, false if by read
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*/
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public void setToByLociMode(boolean tr) {
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locusMode = tr;
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}
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/**
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* <p>
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* getQueryRegionIterator
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* </p>
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*
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* @param location the genome location to extract data for
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* @return an iterator for that region
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*/
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public MergingSamRecordIterator2 seek(GenomeLoc location) {
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MergingSamRecordIterator2 iter = new MergingSamRecordIterator2(this.mergeIterator);
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if (locusMode) {
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iter.query(location.getContig(), (int) location.getStart(), (int) location.getStop(), true);
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} else {
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iter.queryContained(location.getContig(), (int) location.getStart(), (int) location.getStop());
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}
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return iter; //To change body of implemented methods use File | Settings | File Templates.
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}
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}
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@ -1,117 +0,0 @@
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package org.broadinstitute.sting.gatk.dataSources.simpleDataSources;
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import edu.mit.broad.picard.io.IoUtil;
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import edu.mit.broad.picard.sam.MergingSamRecordIterator;
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import edu.mit.broad.picard.sam.SamFileHeaderMerger;
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import net.sf.samtools.SAMFileHeader;
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import net.sf.samtools.SAMFileReader;
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import net.sf.samtools.SAMFileWriter;
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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.List;
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/**
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* User: aaron
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* Date: Mar 26, 2009
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* Time: 2:36:16 PM
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* <p/>
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|
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* The Broad Institute
|
|
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* SOFTWARE COPYRIGHT NOTICE AGREEMENT
|
|
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* This software and its documentation are copyright 2009 by the
|
|
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* Broad Institute/Massachusetts Institute of Technology. All rights are reserved.
|
|
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* <p/>
|
|
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* This software is supplied without any warranty or guaranteed support whatsoever. Neither
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|
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* the Broad Institute nor MIT can be responsible for its use, misuse, or functionality.
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|
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*/
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public class SAMDataSource implements SimpleDataSource {
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/** our SAM data files */
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private final SAMFileHeader.SortOrder SORT_ORDER = SAMFileHeader.SortOrder.coordinate;
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// our sam file readers
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private final ArrayList<SAMFileReader> readers = new ArrayList<SAMFileReader>();
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// do we care that the SAM files respect the sort order.
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private boolean matchedSortOrders = true;
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// our record iterator, we use it to iterate over all the reads
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private MergingSamRecordIterator iterator = null;
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// we may want to write out the file
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private SAMFileWriter out = null;
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// are we set to locus mode or read mode for dividing
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private boolean locusMode = true;
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/**
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* constructor for multiple sam files
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*
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* @param samfiles
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*/
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public SAMDataSource(ArrayList<String> samfiles) throws FileNotFoundException {
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loadFiles(samfiles);
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}
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private void loadFiles(ArrayList<String> samfiles) throws FileNotFoundException {
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// verify the list passed to the class
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ArrayList<File> INPUT = new ArrayList<File>();
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for (String check : samfiles) {
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File nf = new File(check);
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if (!nf.exists()) {
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throw new FileNotFoundException(check + " doesn't exist");
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}
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}
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// Open the files for reading and writing
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List<SAMFileReader> readers = new ArrayList<SAMFileReader>();
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for (File inFile : INPUT) {
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IoUtil.assertFileIsReadable(inFile);
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SAMFileReader in = new SAMFileReader(inFile);
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readers.add(in);
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matchedSortOrders = matchedSortOrders && in.getFileHeader().getSortOrder() == SORT_ORDER;
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}
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// If all the input sort orders match the output sort order then just merge them and
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// write on the fly, otherwise setup to merge and sort before writing out the final file
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if (matchedSortOrders || SORT_ORDER == SAMFileHeader.SortOrder.unsorted) {
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|
||||||
SamFileHeaderMerger headerMerger = new SamFileHeaderMerger(readers, SORT_ORDER);
|
|
||||||
iterator = new MergingSamRecordIterator(headerMerger);
|
|
||||||
|
|
||||||
} else {
|
|
||||||
SamFileHeaderMerger headerMerger = new SamFileHeaderMerger(readers, SAMFileHeader.SortOrder.unsorted);
|
|
||||||
iterator = new MergingSamRecordIterator(headerMerger);
|
|
||||||
SAMFileHeader header = headerMerger.getMergedHeader();
|
|
||||||
header.setSortOrder(SORT_ORDER);
|
|
||||||
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
/**
|
|
||||||
* constructor, given a single sam file
|
|
||||||
*
|
|
||||||
* @param samFile
|
|
||||||
*/
|
|
||||||
public SAMDataSource(String samFile) throws FileNotFoundException {
|
|
||||||
ArrayList<String> samfiles = new ArrayList<String>();
|
|
||||||
samfiles.add(samFile);
|
|
||||||
loadFiles(samfiles);
|
|
||||||
}
|
|
||||||
|
|
||||||
/**
|
|
||||||
* Chunk the sam file at appropriate locations, given the chunk count
|
|
||||||
*
|
|
||||||
* @param chunkCount
|
|
||||||
* @return
|
|
||||||
*/
|
|
||||||
public void chunk(int chunkCount) {
|
|
||||||
|
|
||||||
}
|
|
||||||
|
|
||||||
/** set this source to divide on reads */
|
|
||||||
public void setToReadMode() {
|
|
||||||
locusMode = true;
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
@ -1,6 +1,10 @@
|
||||||
package org.broadinstitute.sting.gatk.dataSources.simpleDataSources;
|
package org.broadinstitute.sting.gatk.dataSources.simpleDataSources;
|
||||||
|
|
||||||
|
import org.broadinstitute.sting.utils.GenomeLoc;
|
||||||
|
|
||||||
import java.io.Serializable;
|
import java.io.Serializable;
|
||||||
|
import java.util.Iterator;
|
||||||
|
|
||||||
|
|
||||||
/**
|
/**
|
||||||
* User: aaron
|
* User: aaron
|
||||||
|
|
@ -14,17 +18,20 @@ import java.io.Serializable;
|
||||||
* <p/>
|
* <p/>
|
||||||
* This software is supplied without any warranty or guaranteed support whatsoever. Neither
|
* This software is supplied without any warranty or guaranteed support whatsoever. Neither
|
||||||
* the Broad Institute nor MIT can be responsible for its use, misuse, or functionality.
|
* the Broad Institute nor MIT can be responsible for its use, misuse, or functionality.
|
||||||
|
*
|
||||||
*/
|
*/
|
||||||
|
|
||||||
|
/** This class is the interface for all data sources */
|
||||||
public interface SimpleDataSource extends Serializable {
|
public interface SimpleDataSource extends Serializable {
|
||||||
|
|
||||||
/**
|
|
||||||
* recommend how many data chunks we should be breaking the file into,
|
|
||||||
* as a recommendated number. If not specified (and even if specified)
|
|
||||||
* the chunking data source can make decisions to chunk differently.
|
|
||||||
*
|
|
||||||
* @param chunkCount
|
|
||||||
*/
|
|
||||||
public void chunk(int chunkCount);
|
|
||||||
|
|
||||||
|
/**
|
||||||
|
* Query the data source for a region of interest, specified by the genome location.
|
||||||
|
* The iterator will generate successive calls
|
||||||
|
*
|
||||||
|
* @param location the genome location to extract data for
|
||||||
|
* @return an iterator of the appropriate type, that is limited by the region
|
||||||
|
*/
|
||||||
|
public Iterator seek(GenomeLoc location);
|
||||||
|
|
||||||
}
|
}
|
||||||
|
|
|
||||||
|
|
@ -0,0 +1,33 @@
|
||||||
|
package org.broadinstitute.sting.gatk.dataSources.simpleDataSources;
|
||||||
|
|
||||||
|
/**
|
||||||
|
*
|
||||||
|
* User: aaron
|
||||||
|
* Date: Apr 6, 2009
|
||||||
|
* Time: 4:21:58 PM
|
||||||
|
*
|
||||||
|
* The Broad Institute
|
||||||
|
* SOFTWARE COPYRIGHT NOTICE AGREEMENT
|
||||||
|
* This software and its documentation are copyright 2009 by the
|
||||||
|
* Broad Institute/Massachusetts Institute of Technology. All rights are reserved.
|
||||||
|
*
|
||||||
|
* This software is supplied without any warranty or guaranteed support whatsoever. Neither
|
||||||
|
* the Broad Institute nor MIT can be responsible for its use, misuse, or functionality.
|
||||||
|
*
|
||||||
|
*/
|
||||||
|
|
||||||
|
|
||||||
|
/**
|
||||||
|
* @author aaron
|
||||||
|
* @version 1.0
|
||||||
|
* @date Apr 6, 2009
|
||||||
|
* <p/>
|
||||||
|
* Class SimpleDataSourceLoadException
|
||||||
|
* <p/>
|
||||||
|
* Generate this on a simple data source load exception
|
||||||
|
*/
|
||||||
|
public class SimpleDataSourceLoadException extends Exception {
|
||||||
|
public SimpleDataSourceLoadException(String msg) {
|
||||||
|
super(msg);
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
@ -0,0 +1,34 @@
|
||||||
|
package org.broadinstitute.sting.gatk.dataSources.simpleDataSources;
|
||||||
|
|
||||||
|
/**
|
||||||
|
*
|
||||||
|
* User: aaron
|
||||||
|
* Date: Apr 1, 2009
|
||||||
|
* Time: 11:08:06 AM
|
||||||
|
*
|
||||||
|
* The Broad Institute
|
||||||
|
* SOFTWARE COPYRIGHT NOTICE AGREEMENT
|
||||||
|
* This software and its documentation are copyright 2009 by the
|
||||||
|
* Broad Institute/Massachusetts Institute of Technology. All rights are reserved.
|
||||||
|
*
|
||||||
|
* This software is supplied without any warranty or guaranteed support whatsoever. Neither
|
||||||
|
* the Broad Institute nor MIT can be responsible for its use, misuse, or functionality.
|
||||||
|
*
|
||||||
|
*/
|
||||||
|
|
||||||
|
|
||||||
|
/**
|
||||||
|
* @author aaron
|
||||||
|
* @version 1.0
|
||||||
|
* @date Apr 1, 2009
|
||||||
|
* <p/>
|
||||||
|
* Class SimpleDataSourceSplitFailure
|
||||||
|
* <p/>
|
||||||
|
* A descriptions should go here. Blame aaron if it's missing.
|
||||||
|
*/
|
||||||
|
public class SimpleDataSourceSplitException extends Exception {
|
||||||
|
public SimpleDataSourceSplitException(String msg) {
|
||||||
|
super(msg);
|
||||||
|
}
|
||||||
|
|
||||||
|
}
|
||||||
Loading…
Reference in New Issue