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Moved secondary base stuff out of playground for the purpose of making it a core utility. Modified package names and imports such that things would build properly. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@680 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
kiran 2009-05-12 20:24:18 +00:00
parent 8079acb1d3
commit 688358190c
14 changed files with 491 additions and 24 deletions
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55
build.xml
View File

@ -102,44 +102,57 @@
</jar>
<jar jarfile="dist/FourBaseRecaller.jar" whenmanifestonly="skip">
<!--<fileset dir="build" includes="**/fourbasecaller/**/*.class" />-->
<fileset dir="build">
<include name="**/fourbasecaller/**/*.class" />
<include name="**/illumina/**/*.class" />
<include name="**/secondarybase/**/*.class" />
</fileset>
<manifest>
<attribute name="Main-Class" value="org.broadinstitute.sting.playground.fourbasecaller.FourBaseRecaller" />
<attribute name="Main-Class" value="org.broadinstitute.sting.secondarybase.FourBaseRecaller" />
</manifest>
</jar>
<jar jarfile="dist/CombineSamAndFourProbs.jar" whenmanifestonly="skip">
<!--<fileset dir="build" includes="**/fourbasecaller/**/*.class" />-->
<jar jarfile="dist/AnnotateSecondaryBase.jar" whenmanifestonly="skip">
<fileset dir="build">
<include name="**/fourbasecaller/**/*.class" />
<include name="**/illumina/**/*.class" />
<include name="**/secondarybase/**/*.class" />
</fileset>
<manifest>
<attribute name="Main-Class" value="org.broadinstitute.sting.playground.fourbasecaller.CombineSamAndFourProbs" />
<attribute name="Main-Class" value="org.broadinstitute.sting.secondarybase.AnnotateSecondaryBase" />
</manifest>
</jar>
<!--
<jar jarfile="dist/CombineSamAndFourProbs.jar" whenmanifestonly="skip">
<fileset dir="build">
<include name="**/secondarybase/**/*.class" />
</fileset>
<manifest>
<attribute name="Main-Class" value="org.broadinstitute.sting.secondarybase.CombineSamAndFourProbs" />
</manifest>
</jar>
<jar jarfile="dist/MatchSQTagToStrand.jar" whenmanifestonly="skip">
<!--<fileset dir="build" includes="**/fourbasecaller/**/*.class" />-->
<fileset dir="build">
<include name="**/fourbasecaller/**/*.class" />
<include name="**/illumina/**/*.class" />
<include name="**/secondarybase/**/*.class" />
</fileset>
<manifest>
<attribute name="Main-Class" value="org.broadinstitute.sting.playground.fourbasecaller.MatchSQTagToStrand" />
<attribute name="Main-Class" value="org.broadinstitute.sting.secondarybase.MatchSQTagToStrand" />
</manifest>
</jar>
<jar jarfile="dist/AddFourProbsToSAM.jar" whenmanifestonly="skip">
<fileset dir="build">
<include name="**/secondarybase/**/*.class" />
</fileset>
<manifest>
<attribute name="Main-Class" value="org.broadinstitute.sting.secondarybase.AddFourProbsToSAM" />
</manifest>
</jar>
-->
<jar jarfile="dist/Playground.jar" whenmanifestonly="skip">
<fileset dir="build">
<include name="**/*.class"/>
<exclude name="**/utils/**"/>
<exclude name="**/gatk/**"/>
<exclude name="**/fourbasecaller/**"/>
</fileset>
</jar>
@ -166,6 +179,13 @@
</manifest>
</jar>
<jar jarfile="dist/AnnotateSecondaryBase.jar" update="true" whenmanifestonly="skip">
<manifest>
<attribute name="Class-Path" value="${jar.classpath}" />
</manifest>
</jar>
<!--
<jar jarfile="dist/CombineSamAndFourProbs.jar" update="true" whenmanifestonly="skip">
<manifest>
<attribute name="Class-Path" value="${jar.classpath}" />
@ -178,6 +198,13 @@
</manifest>
</jar>
<jar jarfile="dist/AddFourProbsToSAM.jar" update="true" whenmanifestonly="skip">
<manifest>
<attribute name="Class-Path" value="${jar.classpath}" />
</manifest>
</jar>
-->
<jar jarfile="dist/Playground.jar" update="true" whenmanifestonly="skip">
<manifest>
<attribute name="Class-Path" value="${jar.classpath}"/>

137
java/src/org/broadinstitute/sting/secondarybase/AbstractFirecrestFileParser.java 100644
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@ -0,0 +1,137 @@
/*
* 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.
*/
//package edu.mit.broad.picard.illumina;
package org.broadinstitute.sting.secondarybase;
import edu.mit.broad.picard.util.BasicTextFileParser;
import java.io.Closeable;
import java.io.File;
import java.io.FilenameFilter;
import java.util.*;
import net.sf.samtools.util.StringUtil;
import org.broadinstitute.sting.secondarybase.FirecrestReadData;
import org.broadinstitute.sting.secondarybase.FirecrestFilenameComparator;
/**
* Abstract base class for implementing parsers for various versions of Firecrest output
*/
public abstract class AbstractFirecrestFileParser implements Iterator<FirecrestReadData>, Iterable<FirecrestReadData>, Closeable {
protected final int lane;
protected final File firecrestDirectory;
private FirecrestReadData next = null;
private boolean iterating = false;
/**
* Examine the bustard directory to see if it is valid, and prepare for parsing
*/
public AbstractFirecrestFileParser(final File firecrestDirectory, final int lane) {
this.lane = lane;
this.firecrestDirectory = firecrestDirectory;
}
/**
* @return true if the given bustard directory contains the appropriate files, or at least enough
* of them so that it appears to be a Firecrest directory corresponding to the version of the concrete
* FirecrestFileParser implementation.
*/
public abstract boolean isValidFirecrestDirectory();
/**
* Called before iteration begins. If this method is called when isValidFirecrestDirectory() had
* return false, it will generate exceptions that may help the user diagnose the problem.
*/
protected abstract void prepareToIterate();
/**
* @return the next read
*/
protected abstract FirecrestReadData readNext();
/**
* @return an iterator over a set of elements of type FirecrestReadData
*/
public Iterator<FirecrestReadData> iterator() {
if (iterating) {
throw new IllegalStateException("iterator() method can only be called once, before the first call to hasNext()");
}
prepareToIterate();
next = readNext();
iterating = true;
return this;
}
/**
* @return true if the iteration has more elements. Otherwise returns false.
*/
public boolean hasNext() {
if (!iterating) {
iterator();
}
return next != null;
}
/**
* Returns the next element in the iteration.
*
* @return the next element in the iteration
* @throws java.util.NoSuchElementException
*/
public FirecrestReadData next() {
if (!hasNext()) {
throw new NoSuchElementException("Iteration has no more elements.");
}
final FirecrestReadData result = next;
next = readNext();
return result;
}
/**
* Required method for Iterator API.
*
* @throws UnsupportedOperationException
*/
public void remove() {
throw new UnsupportedOperationException("Remove() not supported.");
}
/**
* Override, e.g. to close parser
*/
public void close() {
}
public int getLane() { return this.lane; }
/**
* Convenience method to create a parser for a list of files of the same format that should
* be parsed in order defined by FirecrestFilenameComparator
* @param files to be iterated, in arbitrary order
* @return parser that iterates through the files in the appropriate order
*/
protected BasicTextFileParser makeParserForTextFiles(final boolean treatGroupedDelimitersAsOne, File[] files) {
final SortedSet<File> sortedRead1 = new TreeSet<File>(new FirecrestFilenameComparator());
sortedRead1.addAll(Arrays.asList(files));
files = sortedRead1.toArray(files);
return new BasicTextFileParser(treatGroupedDelimitersAsOne, files);
}
protected File[] getFilesMatchingRegexp(final String regexp) {
return firecrestDirectory.listFiles( new FilenameFilter() {
public boolean accept(final File dir, final String name) {
return name.matches(regexp);
}
});
}
}

0
java/src/org/broadinstitute/sting/playground/fourbasecaller/AddFourProbsToSAM.java → java/src/org/broadinstitute/sting/secondarybase/AddFourProbsToSAM.java
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3
java/src/org/broadinstitute/sting/playground/fourbasecaller/AnnotateSecondaryBase.java → java/src/org/broadinstitute/sting/secondarybase/AnnotateSecondaryBase.java
View File

@ -1,4 +1,4 @@
package org.broadinstitute.sting.playground.fourbasecaller;
package org.broadinstitute.sting.secondarybase;
import org.broadinstitute.sting.utils.cmdLine.CommandLineProgram;
import org.broadinstitute.sting.utils.cmdLine.Argument;
@ -6,6 +6,7 @@ import org.broadinstitute.sting.utils.fasta.FastaSequenceFile2;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.StingException;
import org.broadinstitute.sting.utils.QualityUtils;
import org.broadinstitute.sting.playground.fourbasecaller.BasecallingReadModel;
import java.io.File;
import java.util.HashMap;

3
java/src/org/broadinstitute/sting/playground/fourbasecaller/BasecallingBaseModel.java → java/src/org/broadinstitute/sting/secondarybase/BasecallingBaseModel.java
View File

@ -1,4 +1,4 @@
package org.broadinstitute.sting.playground.fourbasecaller;
package org.broadinstitute.sting.secondarybase;
import cern.colt.matrix.DoubleMatrix1D;
import cern.colt.matrix.DoubleFactory1D;
@ -6,7 +6,6 @@ import cern.colt.matrix.DoubleMatrix2D;
import cern.colt.matrix.DoubleFactory2D;
import cern.colt.matrix.linalg.Algebra;
import org.broadinstitute.sting.utils.QualityUtils;
import org.broadinstitute.sting.utils.BaseUtils;
import java.io.*;

4
java/src/org/broadinstitute/sting/playground/fourbasecaller/BasecallingReadModel.java → java/src/org/broadinstitute/sting/secondarybase/BasecallingReadModel.java
View File

@ -1,7 +1,9 @@
package org.broadinstitute.sting.playground.fourbasecaller;
package org.broadinstitute.sting.secondarybase;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.QualityUtils;
import org.broadinstitute.sting.secondarybase.BasecallingBaseModel;
import org.broadinstitute.sting.secondarybase.FourProb;
import java.io.File;

2
java/src/org/broadinstitute/sting/playground/fourbasecaller/CombineSamAndFourProbs.java → java/src/org/broadinstitute/sting/secondarybase/CombineSamAndFourProbs.java
View File

@ -1,4 +1,4 @@
package org.broadinstitute.sting.playground.fourbasecaller;
package org.broadinstitute.sting.secondarybase;
import org.broadinstitute.sting.utils.cmdLine.CommandLineProgram;
import org.broadinstitute.sting.utils.cmdLine.Argument;

105
java/src/org/broadinstitute/sting/secondarybase/FirecrestFileParser.java 100644
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@ -0,0 +1,105 @@
/*
* 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.
*/
package org.broadinstitute.sting.secondarybase;
import edu.mit.broad.picard.util.PasteParser;
import edu.mit.broad.picard.util.FormatUtil;
import edu.mit.broad.picard.util.BasicTextFileParser;
import edu.mit.broad.picard.PicardException;
import java.io.File;
import org.broadinstitute.sting.secondarybase.FirecrestReadData;
/**
* Class to parse the data in an Illumina Firecrest directory and return an iterator over that data, in order
* by tile.
*
* @author Kiran Garimella
*/
public class FirecrestFileParser extends AbstractFirecrestFileParser {
private BasicTextFileParser parser;
private final FormatUtil formatter = new FormatUtil();
private final File[] intensityFiles;
/**
* Constructor
*
* @param firecrestDirectory directory where the Firecrest files can be located
* @param lane the lane to parse
*/
public FirecrestFileParser(final File firecrestDirectory, final int lane) {
super(firecrestDirectory, lane);
intensityFiles = getFilesMatchingRegexp("s_" + lane + "_\\d{4}_int.txt(.gz)?");
}
@Override
public boolean isValidFirecrestDirectory() {
return (intensityFiles.length > 0);
}
/**
* Sorts the relevant files in the firecrestDirectory. Does some basic sanity checking to ensure that some files
* are found and that they are the expected multiple for paired-end or not.
*/
@Override
protected void prepareToIterate() {
// Some basic sanity checking on file counts
if (intensityFiles.length == 0) {
throw new PicardException("No Firecrest 1.3 intensity files found in " + firecrestDirectory.getAbsolutePath() + " for lane " + lane);
}
// Sort each set of reads and create a text parser for it
parser = makeParserForTextFiles(true, intensityFiles);
}
/**
* Parses the next line from the parser and constructs a FirecrestReadData object from it
* The first 4 fields are position information for the read, and the remaining value are
* the intensities data.
*
* @return a fully populated FirecrestReadData object
*/
protected FirecrestReadData readNext() {
if (!parser.hasNext()) {
return null;
}
final String[] data = parser.next();
final int lane = formatter.parseInt(data[0]);
final int tile = formatter.parseInt(data[1]);
final int x = formatter.parseInt(data[2]);
final int y = formatter.parseInt(data[3]);
int intensityOffset = 4;
int numIntensities = (data.length - 4)/4;
double[][] intensities = new double[numIntensities][4];
for (int cycle = 0, index = intensityOffset; cycle < numIntensities; cycle++) {
for (int channel = 0; channel < 4; channel++, index++) {
intensities[cycle][channel] = formatter.parseFloat(data[index]);
}
}
return new FirecrestReadData(lane, tile, x, y, intensities);
}
/**
* Closes the underlying PasteParser
*/
@Override
public void close() {
if (parser != null) {
parser.close();
}
}
}

75
java/src/org/broadinstitute/sting/secondarybase/FirecrestFilenameComparator.java 100644
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@ -0,0 +1,75 @@
/*
* 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.
*/
//package edu.mit.broad.picard.illumina;
package org.broadinstitute.sting.secondarybase;
import java.io.File;
import java.util.Comparator;
/**
* Comparator for getting Firecrest files in "sorted" order for use by the FirecrestFileParser. Expected order is
* by lane in ascending order, then by tile in ascending order.
*
* IMPORTANT: Currently this class expects to receive ONLY int files.
*
* @author Kiran Garimella
*/
public class FirecrestFilenameComparator implements Comparator<File> {
/**
* Compares its two arguments for order. Returns a negative integer, zero, or a positive integer as
* the first argument is less than, equal to, or greater than the second.
*
* @param file1
* @param file2
* @return a negative integer, zero, or a positive integer as
* the first argument is less than, equal to, or greater than the second.
*/
public int compare(File file1, File file2)
{
Integer parts1[] = parseFileNameParts(file1.getName());
Integer parts2[] = parseFileNameParts(file2.getName());
for (int i = 1; i < parts1.length; i++)
{
if (!parts1[i].equals(parts2[i])) {
return parts1[i].compareTo(parts2[i]);
}
}
return 0;
}
/**
* Utility method that returns an array of integers that represent, in order,
* the lane, tile, type (0 for qseq files, 1 for sig2 files), and read (if any)
* represented by the given file name
*
* @param name
* @return an array of integers that represent, in order,
* the lane, tile, type (0 for qseq files, 1 for sig2 files), and read (if any)
* represented by the given file name
*/
private Integer[] parseFileNameParts(String name)
{
Integer parts[] = new Integer[3]; // Lane, tile, read
String src[] = name.split("_");
parts[0] = new Integer(src[1]); // Lane is always the second part
if (src[2].length() == 4) { // Tile is 3rd or fourth
parts[1] = new Integer(src[2]);
}
else {
parts[1] = new Integer(src[3]);
}
if (src[2].length() == 1) { // read is last
parts[2] = new Integer(src[2]);
}
return parts;
}
}

57
java/src/org/broadinstitute/sting/secondarybase/FirecrestReadData.java 100644
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@ -0,0 +1,57 @@
/*
* 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.
*/
package org.broadinstitute.sting.secondarybase;
/**
* Holds all the Firecrest-level data we need (so far) about an individual read.
*
* @author Kiran Garimella
*/
public class FirecrestReadData {
final private int laneNumber;
final private int tileNumber;
final private int xCoordinate;
final private int yCoordinate;
final private double[][] intensities;
/**
* Constructor that takes everything to populate this object
*
* @param laneNumber
* @param tileNumber
* @param xCoordinate
* @param yCoordinate
* @param intensities
*/
public FirecrestReadData(int laneNumber, int tileNumber, int xCoordinate, int yCoordinate, double[][] intensities) {
this.laneNumber = laneNumber;
this.tileNumber = tileNumber;
this.xCoordinate = xCoordinate;
this.yCoordinate = yCoordinate;
this.intensities = intensities;
}
/**
* Composes a name for this read from its values.
*
* @return the read name
*/
public String getReadName() {
return this.laneNumber + ":" + this.tileNumber + ":" + this.xCoordinate + ":" + this.yCoordinate + "#0";
}
public int getLaneNumber() { return laneNumber; }
public int getTileNumber() { return tileNumber; }
public int getXCoordinate() { return xCoordinate; }
public int getYCoordinate() { return yCoordinate; }
public double[][] getIntensities() { return intensities; }
}

7
java/src/org/broadinstitute/sting/playground/fourbasecaller/FourBaseRecaller.java → java/src/org/broadinstitute/sting/secondarybase/FourBaseRecaller.java
View File

@ -1,4 +1,4 @@
package org.broadinstitute.sting.playground.fourbasecaller;
package org.broadinstitute.sting.secondarybase;
import edu.mit.broad.picard.illumina.BustardFileParser;
import edu.mit.broad.picard.illumina.BustardReadData;
@ -8,8 +8,9 @@ import net.sf.samtools.SAMFileHeader;
import net.sf.samtools.SAMFileWriter;
import net.sf.samtools.SAMFileWriterFactory;
import net.sf.samtools.SAMRecord;
import org.broadinstitute.sting.playground.illumina.FirecrestFileParser;
import org.broadinstitute.sting.playground.illumina.FirecrestReadData;
import org.broadinstitute.sting.secondarybase.FirecrestFileParser;
import org.broadinstitute.sting.secondarybase.FirecrestReadData;
import org.broadinstitute.sting.secondarybase.FourProb;
import org.broadinstitute.sting.utils.QualityUtils;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.cmdLine.CommandLineProgram;

63
java/src/org/broadinstitute/sting/secondarybase/FourIntensity.java 100755
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@ -0,0 +1,63 @@
package org.broadinstitute.sting.secondarybase;
import java.util.StringTokenizer;
public class FourIntensity {
private float[] fIntensities;
public FourIntensity() {
fIntensities = new float[4];
}
public FourIntensity(float[] fIntensities) {
this.fIntensities = fIntensities;
}
public FourIntensity(FourIntensity intensity) {
fIntensities = new float[4];
for (int channel = 0; channel < 4; channel++) {
fIntensities[channel] = intensity.getChannelIntensity(channel);
}
}
public void add(FourIntensity intensity) {
for (int channel = 0; channel < 4; channel++) {
fIntensities[channel] += intensity.getChannelIntensity(channel);
}
}
public void subtract(FourIntensity intensity) {
for (int channel = 0; channel < 4; channel++) {
fIntensities[channel] -= intensity.getChannelIntensity(channel);
}
}
public void divide(float divisor) {
for (int channel = 0; channel < 4; channel++) {
fIntensities[channel] /= divisor;
}
}
public float getChannelIntensity(int channel) { return fIntensities[channel]; }
public int brightestChannel() {
int brightest = 0;
for (int channel = 1; channel < 4; channel++) {
if (fIntensities[channel] > fIntensities[brightest]) {
brightest = channel;
}
}
return brightest;
}
public String toString() {
return "(" + getChannelIntensity(0) +
", " + getChannelIntensity(1) +
", " + getChannelIntensity(2) +
", " + getChannelIntensity(3) +
")";
}
}

2
java/src/org/broadinstitute/sting/playground/fourbasecaller/FourProb.java → java/src/org/broadinstitute/sting/secondarybase/FourProb.java
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@ -1,4 +1,4 @@
package org.broadinstitute.sting.playground.fourbasecaller;
package org.broadinstitute.sting.secondarybase;
import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.QualityUtils;

2
java/src/org/broadinstitute/sting/playground/fourbasecaller/MatchSQTagToStrand.java → java/src/org/broadinstitute/sting/secondarybase/MatchSQTagToStrand.java
View File

@ -1,4 +1,4 @@
package org.broadinstitute.sting.playground.fourbasecaller;
package org.broadinstitute.sting.secondarybase;
import org.broadinstitute.sting.utils.cmdLine.CommandLineProgram;
import org.broadinstitute.sting.utils.cmdLine.Argument;