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refdata directory cleanup 

Removing unused files RODRecordIterator, ReferenceOrderedData, QueryableTrack, RMDTrackCreationException, GATKFeatureIterator, ReferenceOrderedDataUnitTest
Refactored dbSNP and refseq utilities to be closer to the other files implementing these features
This commit is contained in:
Mark DePristo 2011-07-25 13:21:52 -04:00
parent 90947ab359
commit f3049fba63
32 changed files with 28 additions and 604 deletions
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2
public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
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@ -43,7 +43,7 @@ import org.broadinstitute.sting.gatk.filters.ReadGroupBlackListFilter;
import org.broadinstitute.sting.gatk.io.OutputTracker;
import org.broadinstitute.sting.gatk.io.stubs.Stub;
import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrack;
import org.broadinstitute.sting.gatk.refdata.tracks.builders.RMDTrackBuilder;
import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrackBuilder;
import org.broadinstitute.sting.gatk.refdata.utils.RMDIntervalGenerator;
import org.broadinstitute.sting.gatk.refdata.utils.RMDTriplet;
import org.broadinstitute.sting.gatk.walkers.*;

2
public/java/src/org/broadinstitute/sting/gatk/datasources/rmd/ReferenceOrderedDataPool.java
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@ -27,7 +27,7 @@ package org.broadinstitute.sting.gatk.datasources.rmd;
import net.sf.samtools.SAMSequenceDictionary;
import org.broadinstitute.sting.gatk.refdata.SeekableRODIterator;
import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrack;
import org.broadinstitute.sting.gatk.refdata.tracks.builders.RMDTrackBuilder;
import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrackBuilder;
import org.broadinstitute.sting.gatk.refdata.utils.FlashBackIterator;
import org.broadinstitute.sting.gatk.refdata.utils.LocationAwareSeekableRODIterator;
import org.broadinstitute.sting.gatk.refdata.utils.RMDTriplet;

2
public/java/src/org/broadinstitute/sting/gatk/datasources/rmd/ReferenceOrderedDataSource.java
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@ -29,7 +29,7 @@ import org.broadinstitute.sting.commandline.Tags;
import org.broadinstitute.sting.gatk.datasources.reads.Shard;
import org.broadinstitute.sting.gatk.refdata.SeekableRODIterator;
import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrack;
import org.broadinstitute.sting.gatk.refdata.tracks.builders.RMDTrackBuilder;
import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrackBuilder;
import org.broadinstitute.sting.gatk.refdata.utils.LocationAwareSeekableRODIterator;
import org.broadinstitute.sting.gatk.refdata.utils.RMDTriplet;
import org.broadinstitute.sting.utils.GenomeLoc;

238
public/java/src/org/broadinstitute/sting/gatk/refdata/RODRecordIterator.java
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@ -1,238 +0,0 @@
/*
* Copyright (c) 2010 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.gatk.refdata;
import org.broadinstitute.sting.gatk.iterators.PushbackIterator;
import org.broadinstitute.sting.utils.exceptions.DynamicClassResolutionException;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.text.XReadLines;
import java.io.File;
import java.io.FileNotFoundException;
import java.lang.reflect.Constructor;
import java.util.Iterator;
import java.util.regex.Pattern;
/**
* This is a low-level iterator designed to provide system-wide generic support for reading record-oriented data
* files. The only assumption made is that every line in the file provides a complete and separate data record. The records
* can be associated with coordinates or coordinate intervals, there can be one or more records associated with a given
* position/interval, or intervals can overlap. The records must be comprised of delimited fields, but the format is
* otherwise free. For any specific line-based data format, an appropriate implementation of ReferenceOrderedDatum must be
* provided that is capable of parsing itself from a single line of data. This implementation will be used,
* through reflection mechanism, as a callback to do all the work.
*
* The model is, hence, as follows:
*
* String dataRecord <---> RodImplementation ( ::parseLine(dataRecord.split(delimiter)) is aware of the format and fills
* an instance of RodImplementation with data values from dataRecord line).
*
*
* instantiation of RODRecordIterator(dataFile, trackName, RodImplementation.class) will immediately provide an iterator
* that walks along the dataFile line by line, and on each call to next() returns a new RodImplementation object
* representing a single line (record) of data. The returned object will be initialized with "track name" trackName -
* track names (as returned by ROD.getName()) are often used in other parts of the code to distinguish between
* multiple streams of (possibly heterogeneous) annotation data bound to an application.
*
* This generic iterator skips and ignores a) empty lines, b) lines starting with '#' (comments): they are never sent back
* to the ROD implementation class for processing.
*
* This iterator does not actually check if the ROD records (lines) in the file are indeed ordedered by coordinate,
* and it does not depend on such an order as it still implements a low-level line-based traversal of the data. Higher-level
* iterators/wrappers will perform all the necessary checks.
*
* Note: some data formats/ROD implementations may require a header line in the file. In this case the current (ugly)
* mechanism is as follows:
* 1) rod implementation's ::initialize(file) method should be able to open the file, find and read the header line
* and return the header object (to be kept by the iterator)
* 2) rod implementation's ::parseLine(header,line) method should be capable of making use of that saved header object now served to it
* and
* 3) ::parseLine(header,line) should be able to recognize the original header line in the file and skip it (after ROD's initialize()
* method is called, the iterator will re-open the file and start reading it from the very beginning; there is no
* other way, except for "smart" ::parseLine(), to avoid reading in the header line as "data").
*
* Created by IntelliJ IDEA.
* User: asivache
* Date: Sep 10, 2009
* Time: 1:22:23 PM
* To change this template use File | Settings | File Templates.
*/
public class RODRecordIterator<ROD extends ReferenceOrderedDatum> implements Iterator<ROD> {
private PushbackIterator<String> reader;
// stores name of the track this iterator reads (will be also returned by getName() of ROD objects
// generated by this iterator)
private String name;
// we keep the file object, only to use file name in error reports
private File file;
// rod type; this is what we will instantiate for RODs at runtime
private Class<ROD> type;
private Object header = null; // Some RODs may use header
// field delimiter in the file. Should it be the job of the iterator to split the lines though? RODs can do that!
private String fieldDelimiter;
// constructor for the ROD objects we are going to return. Constructor that takes the track name as its single arg is required.
private Constructor<ROD> named_constructor;
// keep track of the lines we are reading. used for error messages only.
private long linenum = 0;
private boolean allow_empty = true;
private boolean allow_comments = true;
public static Pattern EMPTYLINE_PATTERN = Pattern.compile("^\\s*$");
public RODRecordIterator(File file, String name, Class<ROD> type) {
try {
reader = new PushbackIterator<String>(new XReadLines(file));
} catch (FileNotFoundException e) {
throw new UserException.CouldNotReadInputFile(file, e);
}
this.file = file;
this.name = name;
this.type = type;
try {
named_constructor = type.getConstructor(String.class);
}
catch (java.lang.NoSuchMethodException e) {
throw new ReviewedStingException("ROD class "+type.getName()+" does not have constructor that accepts a single String argument (track name)");
}
ROD rod = instantiateROD(name);
fieldDelimiter = rod.delimiterRegex(); // get delimiter from the ROD itself
try {
header = rod.initialize(file);
} catch (FileNotFoundException e) {
throw new UserException.CouldNotReadInputFile(file, "ROD "+type.getName() + " failed to initialize properly from file "+file);
}
}
/**
* Returns <tt>true</tt> if the iteration has more elements. (In other
* words, returns <tt>true</tt> if <tt>next</tt> would return an element
* rather than throwing an exception.)
*
* @return <tt>true</tt> if the iterator has more elements.
*/
public boolean hasNext() {
if ( allow_empty || allow_comments ) {
while ( reader.hasNext() ) {
String line = reader.next();
if ( allow_empty && EMPTYLINE_PATTERN.matcher(line).matches() ) continue; // skip empty line
if ( allow_comments && line.charAt(0) == '#' ) continue; // skip comment lines
// the line is not empty and not a comment line, so we have next after all
reader.pushback(line);
return true;
}
return false; // oops, we end up here if there's nothing left
} else {
return reader.hasNext();
}
}
/**
* Returns the next valid ROD record in the file, skipping empty and comment lines.
*
* @return the next element in the iteration.
* @throws java.util.NoSuchElementException
* iteration has no more elements.
*/
public ROD next() {
ROD n = null;
boolean parsed_ok = false;
String line ;
while ( ! parsed_ok && reader.hasNext() ) {
line = reader.next();
linenum++;
while ( allow_empty && EMPTYLINE_PATTERN.matcher(line).matches() ||
allow_comments && line.charAt(0) == '#' ) {
if ( reader.hasNext() ) {
line = reader.next();
linenum++;
} else {
line = null;
break;
}
}
if ( line == null ) break; // if we ran out of lines while skipping empty lines/comments, then we are done
String parts[] = line.split(fieldDelimiter);
try {
n = instantiateROD(name);
parsed_ok = n.parseLine(header,parts) ;
}
catch ( Exception e ) {
throw new UserException.MalformedFile(file, "Failed to parse ROD data ("+type.getName()+") from file "+ file + " at line #"+linenum+
"\nOffending line: "+line+
"\nReason ("+e.getClass().getName()+")", e);
}
}
return n;
}
/**
* Removes from the underlying collection the last element returned by the
* iterator (optional operation). This method can be called only once per
* call to <tt>next</tt>. The behavior of an iterator is unspecified if
* the underlying collection is modified while the iteration is in
* progress in any way other than by calling this method.
*
* @throws UnsupportedOperationException if the <tt>remove</tt>
* operation is not supported by this Iterator.
* @throws IllegalStateException if the <tt>next</tt> method has not
* yet been called, or the <tt>remove</tt> method has already
* been called after the last call to the <tt>next</tt>
* method.
*/
public void remove() {
throw new UnsupportedOperationException("remove() operation is not supported by RODRecordIterator");
}
/** Instantiates appropriate implementation of the ROD used by this iteratot. The 'name' argument is the name
* of the ROD track.
* @param name
* @return
*/
private ROD instantiateROD(final String name) {
try {
return (ROD) named_constructor.newInstance(name);
} catch (Exception e) {
throw new DynamicClassResolutionException(named_constructor.getDeclaringClass(), e);
}
}
}

130
public/java/src/org/broadinstitute/sting/gatk/refdata/ReferenceOrderedData.java
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@ -1,130 +0,0 @@
package org.broadinstitute.sting.gatk.refdata;
import org.apache.log4j.Logger;
import org.broadinstitute.sting.utils.exceptions.UserException;
import java.io.*;
import java.lang.reflect.Method;
import java.util.ArrayList;
import java.util.Iterator;
import java.util.List;
/**
* Class for representing arbitrary reference ordered data sets
* <p/>
* User: mdepristo
* Date: Feb 27, 2009
* Time: 10:47:14 AM
* To change this template use File | Settings | File Templates.
*/
public class ReferenceOrderedData<ROD extends ReferenceOrderedDatum> implements Iterable<ReferenceOrderedDatum> {
private String name;
private File file = null;
// private String fieldDelimiter;
/** Header object returned from the datum */
// private Object header = null;
private Class<ROD> type = null; // runtime type information for object construction
/** our log, which we want to capture anything from this class */
private static Logger logger = Logger.getLogger(ReferenceOrderedData.class);
/**
* given an existing file, open it and append all the valid triplet lines to an existing list
*
* @param rodTripletList the list of existing triplets
* @param filename the file to attempt to extract ROD triplets from
*/
protected static void extractRodsFromFile(List<String> rodTripletList, String filename) {
BufferedReader str;
try {
str = new BufferedReader(new FileReader(new File(filename)));
} catch (FileNotFoundException e) {
throw new UserException.CouldNotReadInputFile(new File(filename), "Unable to load the ROD input file", e);
}
String line = "NO LINES READ IN";
try {
while ((line = str.readLine()) != null) {
if (line.matches(".+,.+,.+")) rodTripletList.add(line.trim());
else logger.warn("the following file line didn't parsing into a triplet -> " + line);
}
} catch (IOException e) {
throw new UserException.CouldNotReadInputFile(new File(filename), "Failed reading the input rod file; last line read was " + line, e);
}
}
// ----------------------------------------------------------------------
//
// Constructors
//
// ----------------------------------------------------------------------
public ReferenceOrderedData(final String name, File file, Class<ROD> type ) {
this.name = name;
this.file = file;
this.type = type;
// this.header = initializeROD(name, file, type);
// this.fieldDelimiter = newROD(name, type).delimiterRegex();
}
public String getName() { return name; }
public File getFile() { return file; }
public Class<ROD> getType() { return type; }
/**
* Special equals override to see if this ROD is compatible with the given
* name and type. 'Compatible' means that this ROD has the name that's passed
* in and its data can fit into the container specified by type.
*
* @param name Name to check.
* @param type Type to check.
*
* @return True if these parameters imply this rod. False otherwise.
*/
public boolean matches(String name, Class<? extends ReferenceOrderedDatum> type) {
return this.name.equals(name) && type.isAssignableFrom(this.type);
}
public Iterator<ReferenceOrderedDatum> iterator() {
Iterator<ReferenceOrderedDatum> it;
try {
Method m = type.getDeclaredMethod("createIterator", String.class, java.io.File.class);
it = (Iterator<ReferenceOrderedDatum>) m.invoke(null, name, file);
} catch (java.lang.NoSuchMethodException e) {
it = new RODRecordIterator(file,name,type);
} catch (java.lang.NullPointerException e) {
throw new RuntimeException(e);
} catch (java.lang.SecurityException e) {
throw new RuntimeException(e);
} catch (java.lang.IllegalAccessException e) {
throw new RuntimeException(e);
} catch (java.lang.IllegalArgumentException e) {
throw new RuntimeException(e);
} catch (java.lang.reflect.InvocationTargetException e) {
throw new RuntimeException(e);
}
// return new RODIterator<ROD>(it);
return it;
}
// ----------------------------------------------------------------------
//
// Manipulations of all of the data
//
// ----------------------------------------------------------------------
public static void write(ArrayList<ReferenceOrderedDatum> data, File output) throws IOException {
final FileWriter out = new FileWriter(output);
for (ReferenceOrderedDatum rec : data) {
out.write(rec.repl() + "\n");
}
out.close();
}
}

2
public/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java
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@ -4,7 +4,7 @@ import org.broad.tribble.Feature;
import org.broad.tribble.dbsnp.DbSNPFeature;
import org.broad.tribble.gelitext.GeliTextFeature;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.utils.helpers.DbSNPHelper;
import org.broadinstitute.sting.gatk.refdata.features.DbSNPHelper;
import org.broadinstitute.sting.utils.classloader.PluginManager;
import org.broadinstitute.sting.utils.codecs.hapmap.HapMapFeature;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;

2
public/java/src/org/broadinstitute/sting/gatk/refdata/utils/helpers/DbSNPHelper.java → public/java/src/org/broadinstitute/sting/gatk/refdata/features/DbSNPHelper.java
View File

@ -1,4 +1,4 @@
package org.broadinstitute.sting.gatk.refdata.utils.helpers;
package org.broadinstitute.sting.gatk.refdata.features;
import net.sf.samtools.util.SequenceUtil;
import org.broad.tribble.annotation.Strand;

1
public/java/src/org/broadinstitute/sting/gatk/refdata/features/refseq/RefSeqFeature.java
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@ -1,7 +1,6 @@
package org.broadinstitute.sting.gatk.refdata.features.refseq;
import org.broad.tribble.Feature;
import org.broadinstitute.sting.gatk.refdata.Transcript;
import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
import org.broadinstitute.sting.gatk.refdata.utils.RODRecordList;
import org.broadinstitute.sting.utils.GenomeLoc;

2
public/java/src/org/broadinstitute/sting/gatk/refdata/Transcript.java → public/java/src/org/broadinstitute/sting/gatk/refdata/features/refseq/Transcript.java
View File

@ -1,4 +1,4 @@
package org.broadinstitute.sting.gatk.refdata;
package org.broadinstitute.sting.gatk.refdata.features.refseq;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.HasGenomeLocation;

2
public/java/src/org/broadinstitute/sting/gatk/refdata/indexer/RMDIndexer.java
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@ -12,7 +12,7 @@ import org.broadinstitute.sting.commandline.CommandLineProgram;
import org.broadinstitute.sting.commandline.Input;
import org.broadinstitute.sting.gatk.arguments.ValidationExclusion;
import org.broadinstitute.sting.gatk.refdata.ReferenceDependentFeatureCodec;
import org.broadinstitute.sting.gatk.refdata.tracks.builders.RMDTrackBuilder;
import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrackBuilder;
import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile;

45
public/java/src/org/broadinstitute/sting/gatk/refdata/tracks/QueryableTrack.java
View File

@ -1,45 +0,0 @@
/*
* Copyright (c) 2010. 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.gatk.refdata.tracks;
import net.sf.samtools.util.CloseableIterator;
import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
import org.broadinstitute.sting.utils.GenomeLoc;
import java.io.IOException;
/**
* @author aaron
* <p/>
* Interface QueryableTrack
* <p/>
* a decorator interface for tracks that are queryable
*/
public interface QueryableTrack {
public CloseableIterator<GATKFeature> query(final GenomeLoc interval) throws IOException;
public CloseableIterator<GATKFeature> query(final GenomeLoc interval, final boolean contained) throws IOException;
public CloseableIterator<GATKFeature> query(final String contig, final int start, final int stop) throws IOException;
public CloseableIterator<GATKFeature> query(final String contig, final int start, final int stop, final boolean contained) throws IOException;
public void close();
}

8
public/java/src/org/broadinstitute/sting/gatk/refdata/tracks/builders/RMDTrackBuilder.java → public/java/src/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrackBuilder.java
View File

@ -23,7 +23,7 @@
* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.gatk.refdata.tracks.builders;
package org.broadinstitute.sting.gatk.refdata.tracks;
import net.sf.samtools.SAMSequenceDictionary;
import net.sf.samtools.SAMSequenceRecord;
@ -36,8 +36,6 @@ import org.broad.tribble.util.LittleEndianOutputStream;
import org.broadinstitute.sting.commandline.Tags;
import org.broadinstitute.sting.gatk.arguments.ValidationExclusion;
import org.broadinstitute.sting.gatk.refdata.ReferenceDependentFeatureCodec;
import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrack;
import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrackCreationException;
import org.broadinstitute.sting.gatk.refdata.utils.RMDTriplet;
import org.broadinstitute.sting.gatk.refdata.utils.RMDTriplet.RMDStorageType;
import org.broadinstitute.sting.utils.GenomeLocParser;
@ -133,10 +131,8 @@ public class RMDTrackBuilder extends PluginManager<FeatureCodec> {
* @param fileDescriptor a description of the type of track to build.
*
* @return an instance of the track
* @throws RMDTrackCreationException
* if we don't know of the target class or we couldn't create it
*/
public RMDTrack createInstanceOfTrack(RMDTriplet fileDescriptor) throws RMDTrackCreationException {
public RMDTrack createInstanceOfTrack(RMDTriplet fileDescriptor) {
String name = fileDescriptor.getName();
File inputFile = new File(fileDescriptor.getFile());

45
public/java/src/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrackCreationException.java
View File

@ -1,45 +0,0 @@
/*
* Copyright (c) 2010. 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.gatk.refdata.tracks;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
/**
*
* @author aaron
*
* Class RMDTrackCreationException
*
* if we fail for some reason to make a track, throw this exception
*/
public class RMDTrackCreationException extends ReviewedStingException {
public RMDTrackCreationException(String msg) {
super(msg);
}
public RMDTrackCreationException(String message, Throwable throwable) {
super(message, throwable);
}
}

65
public/java/src/org/broadinstitute/sting/gatk/refdata/utils/GATKFeatureIterator.java
View File

@ -1,65 +0,0 @@
/*
* Copyright (c) 2010. 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.gatk.refdata.utils;
import net.sf.samtools.util.CloseableIterator;
import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
import java.util.Iterator;
/**
*
* @author aaron
*
* Class GATKFeatureIterator
*
* Takes a RODatum iterator and makes it an iterator of GATKFeatures. Shazam!
*/
public class GATKFeatureIterator implements CloseableIterator<GATKFeature> {
private final Iterator<ReferenceOrderedDatum> iter;
public GATKFeatureIterator(Iterator<ReferenceOrderedDatum> iter) {
this.iter = iter;
}
@Override
public boolean hasNext() {
return iter.hasNext();
}
@Override
public GATKFeature next() {
return new GATKFeature.RODGATKFeature(iter.next());
}
@Override
public void remove() {
throw new UnsupportedOperationException("Remove not supported");
}
@Override
public void close() {
// do nothing, our underlying iterator doesn't support this
}
}

2
public/java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java
View File

@ -32,8 +32,8 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
import org.broadinstitute.sting.gatk.refdata.features.DbSNPHelper;
import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
import org.broadinstitute.sting.gatk.refdata.utils.helpers.DbSNPHelper;
import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.collections.Pair;
import org.broadinstitute.sting.utils.pileup.ReadBackedExtendedEventPileup;

2
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java
View File

@ -30,7 +30,7 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.refdata.utils.helpers.DbSNPHelper;
import org.broadinstitute.sting.gatk.refdata.features.DbSNPHelper;
import org.broadinstitute.sting.gatk.walkers.annotator.genomicannotator.GenomicAnnotation;
import org.broadinstitute.sting.gatk.walkers.annotator.genomicannotator.JoinTable;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotationInterfaceManager;

2
public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageWalker.java
View File

@ -35,7 +35,7 @@ import org.broadinstitute.sting.gatk.refdata.SeekableRODIterator;
import org.broadinstitute.sting.gatk.refdata.features.refseq.RefSeqCodec;
import org.broadinstitute.sting.gatk.refdata.features.refseq.RefSeqFeature;
import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrack;
import org.broadinstitute.sting.gatk.refdata.tracks.builders.RMDTrackBuilder;
import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrackBuilder;
import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
import org.broadinstitute.sting.gatk.refdata.utils.LocationAwareSeekableRODIterator;
import org.broadinstitute.sting.gatk.refdata.utils.RODRecordList;

2
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
View File

@ -35,7 +35,7 @@ import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
import org.broadinstitute.sting.gatk.filters.BadMateFilter;
import org.broadinstitute.sting.gatk.filters.MappingQualityUnavailableReadFilter;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.refdata.utils.helpers.DbSNPHelper;
import org.broadinstitute.sting.gatk.refdata.features.DbSNPHelper;
import org.broadinstitute.sting.gatk.walkers.*;
import org.broadinstitute.sting.gatk.walkers.annotator.VariantAnnotatorEngine;
import org.broadinstitute.sting.utils.SampleUtils;

4
public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SomaticIndelDetectorWalker.java
View File

@ -39,11 +39,11 @@ import org.broadinstitute.sting.gatk.filters.PlatformUnitFilter;
import org.broadinstitute.sting.gatk.filters.PlatformUnitFilterHelper;
import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
import org.broadinstitute.sting.gatk.refdata.SeekableRODIterator;
import org.broadinstitute.sting.gatk.refdata.Transcript;
import org.broadinstitute.sting.gatk.refdata.features.refseq.Transcript;
import org.broadinstitute.sting.gatk.refdata.features.refseq.RefSeqCodec;
import org.broadinstitute.sting.gatk.refdata.features.refseq.RefSeqFeature;
import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrack;
import org.broadinstitute.sting.gatk.refdata.tracks.builders.RMDTrackBuilder;
import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrackBuilder;
import org.broadinstitute.sting.gatk.refdata.utils.LocationAwareSeekableRODIterator;
import org.broadinstitute.sting.gatk.refdata.utils.RODRecordList;
import org.broadinstitute.sting.gatk.walkers.ReadFilters;

2
public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java
View File

@ -32,7 +32,7 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
import org.broadinstitute.sting.gatk.io.StingSAMFileWriter;
import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
import org.broadinstitute.sting.gatk.refdata.utils.helpers.DbSNPHelper;
import org.broadinstitute.sting.gatk.refdata.features.DbSNPHelper;
import org.broadinstitute.sting.gatk.walkers.*;
import org.broadinstitute.sting.utils.QualityUtils;
import org.broadinstitute.sting.utils.Utils;

2
public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java
View File

@ -9,7 +9,7 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.refdata.utils.helpers.DbSNPHelper;
import org.broadinstitute.sting.gatk.refdata.features.DbSNPHelper;
import org.broadinstitute.sting.gatk.report.GATKReport;
import org.broadinstitute.sting.gatk.report.GATKReportTable;
import org.broadinstitute.sting.gatk.walkers.Reference;

2
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariants.java
View File

@ -33,7 +33,7 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.refdata.utils.helpers.DbSNPHelper;
import org.broadinstitute.sting.gatk.refdata.features.DbSNPHelper;
import org.broadinstitute.sting.gatk.walkers.*;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.variantcontext.Allele;

4
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCF.java
View File

@ -35,9 +35,9 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.refdata.VariantContextAdaptors;
import org.broadinstitute.sting.gatk.refdata.tracks.builders.RMDTrackBuilder;
import org.broadinstitute.sting.gatk.refdata.features.DbSNPHelper;
import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrackBuilder;
import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
import org.broadinstitute.sting.gatk.refdata.utils.helpers.DbSNPHelper;
import org.broadinstitute.sting.gatk.walkers.*;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.SampleUtils;

2
public/java/src/org/broadinstitute/sting/queue/extensions/gatk/GATKExtensionsGenerator.java
View File

@ -41,7 +41,7 @@ import org.broadinstitute.sting.gatk.io.stubs.OutputStreamArgumentTypeDescriptor
import org.broadinstitute.sting.gatk.io.stubs.SAMFileReaderArgumentTypeDescriptor;
import org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterArgumentTypeDescriptor;
import org.broadinstitute.sting.gatk.io.stubs.VCFWriterArgumentTypeDescriptor;
import org.broadinstitute.sting.gatk.refdata.tracks.builders.RMDTrackBuilder;
import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrackBuilder;
import org.broadinstitute.sting.gatk.walkers.PartitionBy;
import org.broadinstitute.sting.gatk.walkers.PartitionType;
import org.broadinstitute.sting.gatk.walkers.Walker;

2
public/java/src/org/broadinstitute/sting/queue/extensions/gatk/RodBindField.java
View File

@ -26,7 +26,7 @@ package org.broadinstitute.sting.queue.extensions.gatk;
import org.broadinstitute.sting.commandline.Input;
import org.broadinstitute.sting.gatk.WalkerManager;
import org.broadinstitute.sting.gatk.refdata.tracks.builders.RMDTrackBuilder;
import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrackBuilder;
import org.broadinstitute.sting.gatk.walkers.RMD;
import org.broadinstitute.sting.gatk.walkers.Walker;

1
public/java/src/org/broadinstitute/sting/utils/interval/IntervalFileMergingIterator.java
View File

@ -26,7 +26,6 @@
package org.broadinstitute.sting.utils.interval;
import org.broadinstitute.sting.gatk.iterators.PushbackIterator;
import org.broadinstitute.sting.gatk.refdata.utils.StringToGenomeLocIteratorAdapter;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.exceptions.UserException;

2
public/java/src/org/broadinstitute/sting/gatk/refdata/utils/StringToGenomeLocIteratorAdapter.java → public/java/src/org/broadinstitute/sting/utils/interval/StringToGenomeLocIteratorAdapter.java
View File

@ -23,7 +23,7 @@
* OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.gatk.refdata.utils;
package org.broadinstitute.sting.utils.interval;
import org.broadinstitute.sting.gatk.iterators.PushbackIterator;
import org.broadinstitute.sting.utils.GenomeLoc;

2
public/java/src/org/broadinstitute/sting/utils/text/ListFileUtils.java
View File

@ -27,8 +27,8 @@ package org.broadinstitute.sting.utils.text;
import org.broadinstitute.sting.commandline.ParsingEngine;
import org.broadinstitute.sting.commandline.Tags;
import org.broadinstitute.sting.gatk.datasources.reads.SAMReaderID;
import org.broadinstitute.sting.gatk.refdata.features.DbSNPHelper;
import org.broadinstitute.sting.gatk.refdata.utils.RMDTriplet;
import org.broadinstitute.sting.gatk.refdata.utils.helpers.DbSNPHelper;
import org.broadinstitute.sting.utils.exceptions.UserException;
import java.io.File;

2
public/java/test/org/broadinstitute/sting/gatk/datasources/providers/ReferenceOrderedViewUnitTest.java
View File

@ -3,13 +3,13 @@ package org.broadinstitute.sting.gatk.datasources.providers;
import org.broadinstitute.sting.commandline.Tags;
import org.broadinstitute.sting.gatk.datasources.reads.MockLocusShard;
import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrackBuilder;
import org.broadinstitute.sting.gatk.refdata.utils.RMDTriplet;
import org.testng.Assert;
import org.broadinstitute.sting.BaseTest;
import org.broadinstitute.sting.gatk.datasources.reads.Shard;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.refdata.features.table.TableFeature;
import org.broadinstitute.sting.gatk.refdata.tracks.builders.RMDTrackBuilder;
import org.broadinstitute.sting.gatk.refdata.utils.RMDTriplet.RMDStorageType;
import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile;

2
public/java/test/org/broadinstitute/sting/gatk/datasources/rmd/ReferenceOrderedDataPoolUnitTest.java
View File

@ -1,10 +1,10 @@
package org.broadinstitute.sting.gatk.datasources.rmd;
import org.broadinstitute.sting.commandline.Tags;
import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrackBuilder;
import org.testng.Assert;
import org.broadinstitute.sting.BaseTest;
import org.broadinstitute.sting.gatk.refdata.features.table.TableFeature;
import org.broadinstitute.sting.gatk.refdata.tracks.builders.RMDTrackBuilder;
import org.broadinstitute.sting.gatk.refdata.utils.LocationAwareSeekableRODIterator;
import org.broadinstitute.sting.gatk.refdata.utils.RMDTriplet;
import org.broadinstitute.sting.gatk.refdata.utils.RMDTriplet.RMDStorageType;

48
public/java/test/org/broadinstitute/sting/gatk/refdata/ReferenceOrderedDataUnitTest.java
View File

@ -1,48 +0,0 @@
package org.broadinstitute.sting.gatk.refdata;
import org.testng.Assert;
import org.broadinstitute.sting.BaseTest;
import org.testng.annotations.Test;
import java.util.ArrayList;
import java.util.List;
/**
*
* @author aaron
*
* Class ReferenceOrderedDataUnitTest
*
* some functionality to test parts of the reference ordered data system that I've added. This is by NO MEANS
* a complete test suite, but additions would be extremely welcome
*/
public class ReferenceOrderedDataUnitTest extends BaseTest {
@Test
public void extractRodsFromFileTest() {
String file = validationDataLocation + "testRODFileImpl.csv";
List<String> lst = new ArrayList<String>();
ReferenceOrderedData.extractRodsFromFile(lst,file);
Assert.assertEquals(lst.size(), 6);
int index = 0;
for (String entry: lst) {
String first = entry.subSequence(0,entry.indexOf(",")).toString();
Assert.assertTrue(first.equals("rod" + String.valueOf(++index)));
}
}
@Test
public void extractRodsFromMultiFileTest() {
String file = validationDataLocation + "testRODFileImpl.csv";
String file2 = validationDataLocation + "testRODFileImpl2.csv";
List<String> lst = new ArrayList<String>();
ReferenceOrderedData.extractRodsFromFile(lst,file);
ReferenceOrderedData.extractRodsFromFile(lst,file2);
Assert.assertEquals(lst.size(), 12);
int index = 0;
for (String entry: lst) {
String first = entry.subSequence(0,entry.indexOf(",")).toString();
Assert.assertTrue(first.equals("rod" + String.valueOf(++index)));
}
}
}

3
public/java/test/org/broadinstitute/sting/gatk/refdata/tracks/builders/RMDTrackBuilderUnitTest.java → public/java/test/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrackBuilderUnitTest.java
View File

@ -21,13 +21,14 @@
* OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.gatk.refdata.tracks.builders;
package org.broadinstitute.sting.gatk.refdata.tracks;
import net.sf.picard.reference.IndexedFastaSequenceFile;
import net.sf.samtools.SAMSequenceDictionary;
import org.broad.tribble.Tribble;
import org.broad.tribble.index.Index;
import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrackBuilder;
import org.broadinstitute.sting.utils.codecs.vcf.VCF3Codec;
import org.broadinstitute.sting.utils.codecs.vcf.VCFCodec;
import org.broadinstitute.sting.utils.exceptions.UserException;