Rev'ing Picard, which includes the update to get all the reads in the query region (GSA-173). With it come a bunch of fixes, including retiring the FourBaseRecaller code, and updated md5 for some walker tests.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1751 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
aaron
parent
303972aa4b
commit
2e4949c4d6
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@ -1,13 +1,12 @@
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package org.broadinstitute.sting.gatk.refdata;
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import net.sf.samtools.util.SequenceUtil;
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import org.broadinstitute.sting.utils.GenomeLoc;
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import org.broadinstitute.sting.utils.Utils;
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import org.broadinstitute.sting.utils.GenomeLocParser;
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import org.broadinstitute.sting.utils.Utils;
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import java.util.List;
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import java.util.Arrays;
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import net.sf.picard.util.SequenceUtil;
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import java.util.List;
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/**
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* ReferenceOrderedDatum class to hold HapMap AlleleFrequency Data
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@ -1,8 +1,10 @@
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package org.broadinstitute.sting.gatk.refdata;
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import net.sf.picard.util.SequenceUtil;
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import net.sf.samtools.util.SequenceUtil;
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import org.broadinstitute.sting.utils.*;
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import org.broadinstitute.sting.utils.genotype.*;
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import org.broadinstitute.sting.utils.genotype.BasicGenotype;
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import org.broadinstitute.sting.utils.genotype.DiploidGenotype;
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import org.broadinstitute.sting.utils.genotype.VariantBackedByGenotype;
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import java.util.ArrayList;
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import java.util.Arrays;
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@ -163,9 +163,6 @@ public class IntervalCleanerWalker extends LocusWindowWalker<Integer, Integer>
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while ( iter.hasNext() )
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writer.addAlignment(iter.next().getRecord());
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}
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if ( writer != null ) {
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writer.close();
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}
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if ( OUT_INDELS != null ) {
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try {
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indelOutput.close();
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@ -25,21 +25,21 @@
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package org.broadinstitute.sting.gatk.walkers.recalibration;
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import net.sf.samtools.*;
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import org.broadinstitute.sting.gatk.walkers.WalkerName;
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import net.sf.samtools.SAMFileWriter;
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import net.sf.samtools.SAMRecord;
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import org.apache.log4j.Logger;
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import org.broadinstitute.sting.gatk.walkers.DataSource;
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import org.broadinstitute.sting.gatk.walkers.ReadWalker;
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import org.broadinstitute.sting.gatk.walkers.Requires;
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import org.broadinstitute.sting.gatk.walkers.DataSource;
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import org.broadinstitute.sting.utils.cmdLine.Argument;
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import org.broadinstitute.sting.gatk.walkers.WalkerName;
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import org.broadinstitute.sting.utils.*;
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import org.apache.log4j.Logger;
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import org.broadinstitute.sting.utils.cmdLine.Argument;
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import java.util.*;
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import java.util.regex.Pattern;
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import java.util.regex.Matcher;
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import java.io.File;
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import java.io.FileNotFoundException;
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import java.lang.reflect.Method;
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import java.util.*;
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import java.util.regex.Matcher;
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import java.util.regex.Pattern;
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@WalkerName("TableRecalibration")
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@Requires({DataSource.READS}) // , DataSource.REFERENCE})
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@ -320,17 +320,6 @@ public class TableRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWrite
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return recalQuals;
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}
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// --------------------------------------------------------------------------------------------------------------
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//
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// Standard I/O routines
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//
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// --------------------------------------------------------------------------------------------------------------
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public void onTraversalDone(SAMFileWriter output) {
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if ( output != null ) {
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output.close();
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}
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}
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public SAMFileWriter reduceInit() {
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return outputBam;
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}
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@ -1,242 +0,0 @@
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package org.broadinstitute.sting.secondarybase;
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import edu.mit.broad.picard.illumina.AbstractBustardFileParser;
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import edu.mit.broad.picard.illumina.BustardFileParser;
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import edu.mit.broad.picard.illumina.BustardFileParser_1_1;
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import edu.mit.broad.picard.illumina.BustardReadData;
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import net.sf.samtools.SAMFileHeader;
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import net.sf.samtools.SAMFileWriter;
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import net.sf.samtools.SAMFileWriterFactory;
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import net.sf.samtools.SAMRecord;
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import org.broadinstitute.sting.utils.BaseUtils;
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import org.broadinstitute.sting.utils.QualityUtils;
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import org.broadinstitute.sting.utils.cmdLine.Argument;
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import org.broadinstitute.sting.utils.cmdLine.CommandLineProgram;
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import java.io.File;
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import java.io.IOException;
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import java.io.PrintWriter;
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public class FourBaseRecaller extends CommandLineProgram {
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public static FourBaseRecaller Instance = null;
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@Argument(fullName="dir", shortName="D", doc="Illumina Bustard directory")
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public File DIR;
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@Argument(fullName="lane", shortName="L", doc="Illumina flowcell lane")
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public int LANE;
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@Argument(fullName="run_barcode", shortName="B", doc="Illumina Run Barcode (e.g. 305PJAAXX080716)")
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public String RUN_BARCODE;
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@Argument(fullName="out", shortName="O", doc="Output path for sam file")
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public File OUT;
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@Argument(fullName="end", shortName="E", doc="End of read to process (0 = whole read, i.e. unpaired; 1 = first end; 2 = second end)", required=false)
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public int END = 0;
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@Argument(fullName="tlim", shortName="T", doc="Number of reads to use for parameter initialization", required=false)
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public int TRAINING_LIMIT = 1000000000;
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@Argument(fullName="clim", shortName="C", doc="Number of reads to basecall", required=false)
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public int CALLING_LIMIT = 1000000000;
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@Argument(fullName="raw", shortName="R", doc="Use raw intensities?", required=false)
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public Boolean RAW = false;
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@Argument(fullName="old", shortName="1", doc="Old Bustard 1.1 mode?", required=false)
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public Boolean OLD = false;
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@Argument(fullName="parse_sig2", shortName="P", doc="Parse sig2 files for Bustard pre-1.1 files (pre-1.1 only)")
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public Boolean PARSE_SIG2_FILES = false;
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@Argument(fullName="barcode", shortName="BCODE", doc="Only process reads that match this barcode (pre-1.1 only)")
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public String BARCODE = null;
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@Argument(fullName="barcode_cycle", shortName="BCYCLE", doc="1-based cycle number where barcode starts (pre-1.1 only)")
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public Integer BARCODE_CYCLE = null;
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@Argument(fullName="first_read_length", shortName="F", doc="First read length (v1.1 only)")
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public Integer FIRST_READ_LENGTH;
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public static void main(String[] argv) {
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Instance = new FourBaseRecaller();
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start(Instance, argv);
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}
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protected int execute() {
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boolean isPaired = (END > 0);
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// Set up debugging paths
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File debugdir = new File(OUT.getPath() + ".debug/");
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debugdir.mkdir();
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PrintWriter debugout = null;
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try {
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debugout = new PrintWriter(debugdir.getPath() + "/debug.out");
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} catch (IOException e) {
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}
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AbstractBustardFileParser bfp;
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BustardReadData bread;
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FirecrestFileParser ffp;
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FirecrestReadData fread;
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bfp = OLD ? new BustardFileParser_1_1(DIR, LANE, isPaired, RUN_BARCODE, FIRST_READ_LENGTH) : new BustardFileParser(DIR, LANE, isPaired, RUN_BARCODE, PARSE_SIG2_FILES, BARCODE, BARCODE_CYCLE);
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bread = bfp.next();
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ffp = new FirecrestFileParser(DIR.getParentFile(), LANE);
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fread = ffp.next();
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int cycle_offset = (END <= 1) ? 0 : bread.getIntensities().length/2;
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BasecallingReadModel model = new BasecallingReadModel(bread.getFirstReadSequence().length());
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int queryid;
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// learn mean parameters
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System.err.println("Computing mean parameters...");
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queryid = 0;
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do {
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assert(bread.getXCoordinate() == fread.getXCoordinate() && bread.getYCoordinate() == fread.getYCoordinate());
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String bases = (END <= 1) ? bread.getFirstReadSequence() : bread.getSecondReadSequence();
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byte[] quals = (END <= 1) ? bread.getFirstReadPhredBinaryQualities() : bread.getSecondReadPhredBinaryQualities();
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double[][] intensities = bread.getIntensities();
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double[][] rawintensities = fread.getIntensities();
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for (int cycle = 0; cycle < bases.length(); cycle++) {
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char baseCur = bases.charAt(cycle);
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byte qualCur = quals[cycle];
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//double[] fourprob = getBaseProbabilityDistribution(bases.charAt(cycle), quals[cycle]);
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double[] fourintensity = (RAW || OLD) ? rawintensities[cycle + cycle_offset] : intensities[cycle + cycle_offset];
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//model.addMeanPoint(cycle, cycle == 0 ? '.' : bases.charAt(cycle - 1), baseCur, qualCur, fourintensity);
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model.addMeanPoint(cycle,
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model.getBaseProbabilityMatrix(cycle, cycle == 0 ? '.' : bases.charAt(cycle - 1),
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baseCur,
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QualityUtils.qualToProb(qualCur)),
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fourintensity);
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}
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queryid++;
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} while (queryid < TRAINING_LIMIT && bfp.hasNext() && (bread = bfp.next()) != null && (fread = ffp.next()) != null);
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// learn covariance parameters
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System.err.println("Computing covariance parameters...");
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bfp = OLD ? new BustardFileParser_1_1(DIR, LANE, isPaired, RUN_BARCODE, FIRST_READ_LENGTH) : new BustardFileParser(DIR, LANE, isPaired, RUN_BARCODE, PARSE_SIG2_FILES, BARCODE, BARCODE_CYCLE);
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bread = bfp.next();
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ffp = new FirecrestFileParser(DIR.getParentFile(), LANE);
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fread = ffp.next();
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queryid = 0;
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do {
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assert(bread.getXCoordinate() == fread.getXCoordinate() && bread.getYCoordinate() == fread.getYCoordinate());
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String bases = (END <= 1) ? bread.getFirstReadSequence() : bread.getSecondReadSequence();
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byte[] quals = (END <= 1) ? bread.getFirstReadPhredBinaryQualities() : bread.getSecondReadPhredBinaryQualities();
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double[][] intensities = bread.getIntensities();
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double[][] rawintensities = fread.getIntensities();
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for (int cycle = 0; cycle < bases.length(); cycle++) {
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char baseCur = bases.charAt(cycle);
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byte qualCur = quals[cycle];
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double[] fourintensity = (RAW || OLD) ? rawintensities[cycle + cycle_offset] : intensities[cycle + cycle_offset];
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model.addCovariancePoint(cycle,
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model.getBaseProbabilityMatrix(cycle, cycle == 0 ? '.' : bases.charAt(cycle - 1),
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baseCur,
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QualityUtils.qualToProb(qualCur)),
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fourintensity);
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}
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queryid++;
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} while (queryid < TRAINING_LIMIT && bfp.hasNext() && (bread = bfp.next()) != null && (fread = ffp.next()) != null);
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// write model parameters
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model.write(debugdir);
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// call bases
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System.err.println("Calling bases...");
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SAMFileHeader sfh = new SAMFileHeader();
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SAMFileWriter sfw = new SAMFileWriterFactory().makeSAMOrBAMWriter(sfh, false, OUT);
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bfp = OLD ? new BustardFileParser_1_1(DIR, LANE, isPaired, RUN_BARCODE, FIRST_READ_LENGTH) : new BustardFileParser(DIR, LANE, isPaired, RUN_BARCODE, PARSE_SIG2_FILES, BARCODE, BARCODE_CYCLE);
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bread = bfp.next();
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ffp = new FirecrestFileParser(DIR.getParentFile(), LANE);
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fread = ffp.next();
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int[][] base_counts = new int[4][bread.getFirstReadSequence().length()];
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int bases_incorrect = 0, bases_total = 0;
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if (debugout != null) { debugout.println("cycle int_a int_c int_g int_t bustard_base kiran_base bustard_prob kiran_prob kiran_base_prev"); }
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queryid = 0;
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do {
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assert(bread.getXCoordinate() == fread.getXCoordinate() && bread.getYCoordinate() == fread.getYCoordinate());
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String bases = (END <= 1) ? bread.getFirstReadSequence() : bread.getSecondReadSequence();
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byte[] quals = (END <= 1) ? bread.getFirstReadPhredBinaryQualities() : bread.getSecondReadPhredBinaryQualities();
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double[][] intensities = bread.getIntensities();
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double[][] rawintensities = fread.getIntensities();
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byte[] asciiseq = new byte[bases.length()];
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byte[] bestqual = new byte[bases.length()];
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byte[] nextbestqual = new byte[bases.length()];
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for (int cycle = 0; cycle < bases.length(); cycle++) {
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double[] fourintensity = (RAW || OLD) ? rawintensities[cycle + cycle_offset] : intensities[cycle + cycle_offset];
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char basePrev = (cycle == 0 ? '.' : (char) asciiseq[cycle - 1]);
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byte qualPrev = (cycle == 0 ? 40 : bestqual[cycle - 1]);
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FourProb fp = model.computeProbabilities(cycle, basePrev, qualPrev, fourintensity);
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asciiseq[cycle] = (byte) fp.baseAtRank(0);
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bestqual[cycle] = fp.qualAtRank(0);
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nextbestqual[cycle] = QualityUtils.baseAndProbToCompressedQuality(fp.indexAtRank(1), fp.probAtRank(1));
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if (debugout != null && bases.charAt(cycle) != '.' && base_counts[BaseUtils.simpleBaseToBaseIndex(bases.charAt(cycle))][cycle] < 1000) {
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debugout.println(cycle + " " + fourintensity[0] + " " + fourintensity[1] + " " + fourintensity[2] + " " + fourintensity[3] + " " + (bases.charAt(cycle)) + " " + ((char) asciiseq[cycle]) + " " + bestqual[cycle] + " " + quals[cycle] + " " + basePrev);
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base_counts[BaseUtils.simpleBaseToBaseIndex(bases.charAt(cycle))][cycle]++;
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}
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bases_incorrect += (bases.charAt(cycle) == (char) asciiseq[cycle]) ? 0 : 1;
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bases_total++;
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}
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sfw.addAlignment(constructSAMRecord("KIR_", new String(asciiseq), bestqual, nextbestqual, bread, sfh));
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sfw.addAlignment(constructSAMRecord("BUS_", bases, quals, null, bread, sfh));
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queryid++;
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} while (queryid < CALLING_LIMIT && bfp.hasNext() && (bread = bfp.next()) != null && (fread = ffp.next()) != null);
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if (debugout != null) {
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debugout.close();
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}
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sfw.close();
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System.out.println("Disagreement rate: " + ((double) bases_incorrect)/((double) bases_total));
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return 0;
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}
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private double[] getBaseProbabilityDistribution(char base, byte qual) {
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double[] dist = new double[4];
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int baseIndex = BaseUtils.simpleBaseToBaseIndex(base);
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dist[baseIndex] = QualityUtils.qualToProb(qual);
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double residualprob = (1.0 - dist[baseIndex])/3.0;
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for (int i = 0; i < 4; i++) {
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if (i != baseIndex) {
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dist[i] = residualprob;
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}
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}
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return dist;
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}
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private SAMRecord constructSAMRecord(String readNamePrefix, String bases, byte[] bestqual, byte[] nextbestqual, BustardReadData bread, SAMFileHeader sfh) {
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SAMRecord sr = new SAMRecord(sfh);
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sr.setReadName(readNamePrefix + bread.getReadName());
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sr.setReadUmappedFlag(true);
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sr.setReadString(bases);
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sr.setBaseQualities(bestqual);
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if (nextbestqual != null) { sr.setAttribute("SQ", nextbestqual); }
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sr.setReadFailsVendorQualityCheckFlag(!bread.isPf());
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return sr;
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}
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}
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@ -1,28 +1,27 @@
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package org.broadinstitute.sting.utils.fasta;
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import net.sf.picard.reference.ReferenceSequenceFile;
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import net.sf.picard.reference.ReferenceSequence;
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import net.sf.picard.PicardException;
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import net.sf.picard.io.IoUtil;
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import net.sf.picard.reference.ReferenceSequence;
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import net.sf.picard.reference.ReferenceSequenceFile;
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import net.sf.samtools.SAMFileHeader;
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import net.sf.samtools.SAMSequenceDictionary;
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import net.sf.samtools.SAMSequenceRecord;
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import net.sf.samtools.SAMTextHeaderCodec;
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import net.sf.samtools.util.AsciiLineReader;
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import org.broadinstitute.sting.utils.StingException;
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|
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import java.io.File;
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import java.io.FileInputStream;
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import java.io.FileNotFoundException;
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import java.io.IOException;
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import java.nio.channels.FileChannel;
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import java.nio.ByteBuffer;
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import java.nio.charset.CharsetDecoder;
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import java.nio.charset.Charset;
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import java.nio.channels.FileChannel;
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import java.nio.charset.CharacterCodingException;
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import java.util.Scanner;
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import java.nio.charset.Charset;
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import java.nio.charset.CharsetDecoder;
|
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import java.util.Iterator;
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|
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import net.sf.samtools.SAMSequenceDictionary;
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import net.sf.samtools.SAMTextHeaderCodec;
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import net.sf.samtools.SAMFileHeader;
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import net.sf.samtools.SAMSequenceRecord;
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import net.sf.samtools.util.AsciiLineReader;
|
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import org.broadinstitute.sting.utils.StingException;
|
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import java.util.Scanner;
|
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|
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/**
|
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* Created by IntelliJ IDEA.
|
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|
@ -255,6 +254,11 @@ public class IndexedFastaSequenceFile implements ReferenceSequenceFile {
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return getSequence( indexIterator.next().getContig() );
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}
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||||
|
||||
@Override
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public void reset() {
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||||
// TODO: FOR MATT TO IMPL.
|
||||
}
|
||||
|
||||
public String toString() {
|
||||
return this.file.getAbsolutePath();
|
||||
}
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|
|
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|
|
@ -29,9 +29,7 @@ import java.util.*;
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* functionality.
|
||||
*/
|
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|
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/**
|
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* Base support for testing variants of the LocusView family of classes.
|
||||
*/
|
||||
/** Base support for testing variants of the LocusView family of classes. */
|
||||
|
||||
public abstract class LocusViewTemplate extends BaseTest {
|
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protected static ReferenceSequenceFile sequenceSourceFile = null;
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|
|
@ -46,200 +44,203 @@ public abstract class LocusViewTemplate extends BaseTest {
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public void emptyAlignmentContextTest() {
|
||||
SAMRecordIterator iterator = new SAMRecordIterator();
|
||||
|
||||
GenomeLoc shardBounds = GenomeLocParser.createGenomeLoc("chr1",1,5);
|
||||
GenomeLoc shardBounds = GenomeLocParser.createGenomeLoc("chr1", 1, 5);
|
||||
Shard shard = new LocusShard(shardBounds);
|
||||
ShardDataProvider dataProvider = new ShardDataProvider( shard, iterator );
|
||||
ShardDataProvider dataProvider = new ShardDataProvider(shard, iterator);
|
||||
|
||||
LocusView view = createView( dataProvider );
|
||||
LocusView view = createView(dataProvider);
|
||||
|
||||
testReadsInContext( view, shard.getGenomeLoc(), Collections.<SAMRecord>emptyList() );
|
||||
testReadsInContext(view, shard.getGenomeLoc(), Collections.<SAMRecord>emptyList());
|
||||
}
|
||||
|
||||
@Test
|
||||
public void singleReadTest() {
|
||||
SAMRecord read = buildSAMRecord("chr1",1,5);
|
||||
SAMRecord read = buildSAMRecord("chr1", 1, 5);
|
||||
SAMRecordIterator iterator = new SAMRecordIterator(read);
|
||||
|
||||
GenomeLoc shardBounds = GenomeLocParser.createGenomeLoc("chr1",1,5);
|
||||
GenomeLoc shardBounds = GenomeLocParser.createGenomeLoc("chr1", 1, 5);
|
||||
Shard shard = new LocusShard(shardBounds);
|
||||
ShardDataProvider dataProvider = new ShardDataProvider( shard, iterator );
|
||||
ShardDataProvider dataProvider = new ShardDataProvider(shard, iterator);
|
||||
|
||||
LocusView view = createView( dataProvider );
|
||||
LocusView view = createView(dataProvider);
|
||||
|
||||
testReadsInContext( view, shard.getGenomeLoc(), Collections.singletonList(read) );
|
||||
testReadsInContext(view, shard.getGenomeLoc(), Collections.singletonList(read));
|
||||
}
|
||||
|
||||
@Test
|
||||
public void readCoveringFirstPartTest() {
|
||||
SAMRecord read = buildSAMRecord("chr1",1,5);
|
||||
SAMRecord read = buildSAMRecord("chr1", 1, 5);
|
||||
SAMRecordIterator iterator = new SAMRecordIterator(read);
|
||||
|
||||
Shard shard = new LocusShard(GenomeLocParser.createGenomeLoc("chr1",1,10));
|
||||
ShardDataProvider dataProvider = new ShardDataProvider( shard, iterator );
|
||||
LocusView view = createView( dataProvider );
|
||||
Shard shard = new LocusShard(GenomeLocParser.createGenomeLoc("chr1", 1, 10));
|
||||
ShardDataProvider dataProvider = new ShardDataProvider(shard, iterator);
|
||||
LocusView view = createView(dataProvider);
|
||||
|
||||
testReadsInContext( view, shard.getGenomeLoc(), Collections.singletonList(read) );
|
||||
testReadsInContext(view, shard.getGenomeLoc(), Collections.singletonList(read));
|
||||
}
|
||||
|
||||
@Test
|
||||
public void readCoveringLastPartTest() {
|
||||
SAMRecord read = buildSAMRecord("chr1",6,10);
|
||||
SAMRecord read = buildSAMRecord("chr1", 6, 10);
|
||||
SAMRecordIterator iterator = new SAMRecordIterator(read);
|
||||
|
||||
Shard shard = new LocusShard(GenomeLocParser.createGenomeLoc("chr1",1,10));
|
||||
ShardDataProvider dataProvider = new ShardDataProvider( shard, iterator );
|
||||
LocusView view = createView( dataProvider );
|
||||
Shard shard = new LocusShard(GenomeLocParser.createGenomeLoc("chr1", 1, 10));
|
||||
ShardDataProvider dataProvider = new ShardDataProvider(shard, iterator);
|
||||
LocusView view = createView(dataProvider);
|
||||
|
||||
testReadsInContext( view, shard.getGenomeLoc(), Collections.singletonList(read) );
|
||||
testReadsInContext(view, shard.getGenomeLoc(), Collections.singletonList(read));
|
||||
}
|
||||
|
||||
@Test
|
||||
public void readCoveringMiddleTest() {
|
||||
SAMRecord read = buildSAMRecord("chr1",3,7);
|
||||
SAMRecord read = buildSAMRecord("chr1", 3, 7);
|
||||
SAMRecordIterator iterator = new SAMRecordIterator(read);
|
||||
|
||||
Shard shard = new LocusShard(GenomeLocParser.createGenomeLoc("chr1",1,10));
|
||||
ShardDataProvider dataProvider = new ShardDataProvider( shard, iterator );
|
||||
LocusView view = createView( dataProvider );
|
||||
Shard shard = new LocusShard(GenomeLocParser.createGenomeLoc("chr1", 1, 10));
|
||||
ShardDataProvider dataProvider = new ShardDataProvider(shard, iterator);
|
||||
LocusView view = createView(dataProvider);
|
||||
|
||||
testReadsInContext( view, shard.getGenomeLoc(), Collections.singletonList(read) );
|
||||
testReadsInContext(view, shard.getGenomeLoc(), Collections.singletonList(read));
|
||||
}
|
||||
|
||||
@Test
|
||||
public void readOverlappingStartTest() {
|
||||
SAMRecord read = buildSAMRecord("chr1",1,10);
|
||||
SAMRecord read = buildSAMRecord("chr1", 1, 10);
|
||||
SAMRecordIterator iterator = new SAMRecordIterator(read);
|
||||
|
||||
Shard shard = new LocusShard(GenomeLocParser.createGenomeLoc("chr1",6,15));
|
||||
ShardDataProvider dataProvider = new ShardDataProvider( shard, iterator );
|
||||
LocusView view = createView( dataProvider );
|
||||
Shard shard = new LocusShard(GenomeLocParser.createGenomeLoc("chr1", 6, 15));
|
||||
ShardDataProvider dataProvider = new ShardDataProvider(shard, iterator);
|
||||
LocusView view = createView(dataProvider);
|
||||
|
||||
testReadsInContext( view, shard.getGenomeLoc(), Collections.singletonList(read) );
|
||||
testReadsInContext(view, shard.getGenomeLoc(), Collections.singletonList(read));
|
||||
}
|
||||
|
||||
@Test
|
||||
public void readOverlappingEndTest() {
|
||||
SAMRecord read = buildSAMRecord("chr1",6,15);
|
||||
SAMRecord read = buildSAMRecord("chr1", 6, 15);
|
||||
SAMRecordIterator iterator = new SAMRecordIterator(read);
|
||||
|
||||
Shard shard = new LocusShard(GenomeLocParser.createGenomeLoc("chr1",1,10));
|
||||
ShardDataProvider dataProvider = new ShardDataProvider( shard, iterator );
|
||||
LocusView view = createView( dataProvider );
|
||||
Shard shard = new LocusShard(GenomeLocParser.createGenomeLoc("chr1", 1, 10));
|
||||
ShardDataProvider dataProvider = new ShardDataProvider(shard, iterator);
|
||||
LocusView view = createView(dataProvider);
|
||||
|
||||
testReadsInContext( view, shard.getGenomeLoc(), Collections.singletonList(read) );
|
||||
testReadsInContext(view, shard.getGenomeLoc(), Collections.singletonList(read));
|
||||
}
|
||||
|
||||
@Test
|
||||
public void readsSpanningTest() {
|
||||
SAMRecord read1 = buildSAMRecord("chr1",1,5);
|
||||
SAMRecord read2 = buildSAMRecord("chr1",6,10);
|
||||
SAMRecordIterator iterator = new SAMRecordIterator(read1,read2);
|
||||
SAMRecord read1 = buildSAMRecord("chr1", 1, 5);
|
||||
SAMRecord read2 = buildSAMRecord("chr1", 6, 10);
|
||||
SAMRecordIterator iterator = new SAMRecordIterator(read1, read2);
|
||||
|
||||
Shard shard = new LocusShard(GenomeLocParser.createGenomeLoc("chr1",1,10));
|
||||
ShardDataProvider dataProvider = new ShardDataProvider( shard, iterator );
|
||||
LocusView view = createView( dataProvider );
|
||||
Shard shard = new LocusShard(GenomeLocParser.createGenomeLoc("chr1", 1, 10));
|
||||
ShardDataProvider dataProvider = new ShardDataProvider(shard, iterator);
|
||||
LocusView view = createView(dataProvider);
|
||||
|
||||
List<SAMRecord> expectedReads = new ArrayList<SAMRecord>();
|
||||
Collections.addAll(expectedReads,read1,read2);
|
||||
testReadsInContext( view, shard.getGenomeLoc(), expectedReads );
|
||||
Collections.addAll(expectedReads, read1, read2);
|
||||
testReadsInContext(view, shard.getGenomeLoc(), expectedReads);
|
||||
}
|
||||
|
||||
@Test
|
||||
public void duplicateReadsTest() {
|
||||
SAMRecord read1 = buildSAMRecord("chr1",1,5);
|
||||
SAMRecord read2 = buildSAMRecord("chr1",1,5);
|
||||
SAMRecord read3 = buildSAMRecord("chr1",6,10);
|
||||
SAMRecord read4 = buildSAMRecord("chr1",6,10);
|
||||
SAMRecordIterator iterator = new SAMRecordIterator(read1,read2,read3,read4);
|
||||
SAMRecord read1 = buildSAMRecord("chr1", 1, 5);
|
||||
SAMRecord read2 = buildSAMRecord("chr1", 1, 5);
|
||||
SAMRecord read3 = buildSAMRecord("chr1", 6, 10);
|
||||
SAMRecord read4 = buildSAMRecord("chr1", 6, 10);
|
||||
SAMRecordIterator iterator = new SAMRecordIterator(read1, read2, read3, read4);
|
||||
|
||||
Shard shard = new LocusShard(GenomeLocParser.createGenomeLoc("chr1",1,10));
|
||||
ShardDataProvider dataProvider = new ShardDataProvider( shard, iterator );
|
||||
LocusView view = createView( dataProvider );
|
||||
Shard shard = new LocusShard(GenomeLocParser.createGenomeLoc("chr1", 1, 10));
|
||||
ShardDataProvider dataProvider = new ShardDataProvider(shard, iterator);
|
||||
LocusView view = createView(dataProvider);
|
||||
|
||||
List<SAMRecord> expectedReads = new ArrayList<SAMRecord>();
|
||||
Collections.addAll(expectedReads,read1,read2,read3,read4);
|
||||
testReadsInContext( view, shard.getGenomeLoc(), expectedReads );
|
||||
Collections.addAll(expectedReads, read1, read2, read3, read4);
|
||||
testReadsInContext(view, shard.getGenomeLoc(), expectedReads);
|
||||
}
|
||||
|
||||
@Test
|
||||
public void cascadingReadsWithinBoundsTest() {
|
||||
SAMRecord read1 = buildSAMRecord("chr1",2,6);
|
||||
SAMRecord read2 = buildSAMRecord("chr1",3,7);
|
||||
SAMRecord read3 = buildSAMRecord("chr1",4,8);
|
||||
SAMRecord read4 = buildSAMRecord("chr1",5,9);
|
||||
SAMRecordIterator iterator = new SAMRecordIterator(read1,read2,read3,read4);
|
||||
SAMRecord read1 = buildSAMRecord("chr1", 2, 6);
|
||||
SAMRecord read2 = buildSAMRecord("chr1", 3, 7);
|
||||
SAMRecord read3 = buildSAMRecord("chr1", 4, 8);
|
||||
SAMRecord read4 = buildSAMRecord("chr1", 5, 9);
|
||||
SAMRecordIterator iterator = new SAMRecordIterator(read1, read2, read3, read4);
|
||||
|
||||
Shard shard = new LocusShard(GenomeLocParser.createGenomeLoc("chr1",1,10));
|
||||
ShardDataProvider dataProvider = new ShardDataProvider( shard, iterator );
|
||||
LocusView view = createView( dataProvider );
|
||||
Shard shard = new LocusShard(GenomeLocParser.createGenomeLoc("chr1", 1, 10));
|
||||
ShardDataProvider dataProvider = new ShardDataProvider(shard, iterator);
|
||||
LocusView view = createView(dataProvider);
|
||||
|
||||
List<SAMRecord> expectedReads = new ArrayList<SAMRecord>();
|
||||
Collections.addAll(expectedReads,read1,read2,read3,read4);
|
||||
testReadsInContext( view, shard.getGenomeLoc(), expectedReads );
|
||||
Collections.addAll(expectedReads, read1, read2, read3, read4);
|
||||
testReadsInContext(view, shard.getGenomeLoc(), expectedReads);
|
||||
}
|
||||
|
||||
@Test
|
||||
public void cascadingReadsAtBoundsTest() {
|
||||
SAMRecord read1 = buildSAMRecord("chr1",1,5);
|
||||
SAMRecord read2 = buildSAMRecord("chr1",2,6);
|
||||
SAMRecord read3 = buildSAMRecord("chr1",3,7);
|
||||
SAMRecord read4 = buildSAMRecord("chr1",4,8);
|
||||
SAMRecord read5 = buildSAMRecord("chr1",5,9);
|
||||
SAMRecord read6 = buildSAMRecord("chr1",6,10);
|
||||
SAMRecordIterator iterator = new SAMRecordIterator(read1,read2,read3,read4,read5,read6);
|
||||
SAMRecord read1 = buildSAMRecord("chr1", 1, 5);
|
||||
SAMRecord read2 = buildSAMRecord("chr1", 2, 6);
|
||||
SAMRecord read3 = buildSAMRecord("chr1", 3, 7);
|
||||
SAMRecord read4 = buildSAMRecord("chr1", 4, 8);
|
||||
SAMRecord read5 = buildSAMRecord("chr1", 5, 9);
|
||||
SAMRecord read6 = buildSAMRecord("chr1", 6, 10);
|
||||
SAMRecordIterator iterator = new SAMRecordIterator(read1, read2, read3, read4, read5, read6);
|
||||
|
||||
Shard shard = new LocusShard(GenomeLocParser.createGenomeLoc("chr1",1,10));
|
||||
ShardDataProvider dataProvider = new ShardDataProvider( shard, iterator );
|
||||
LocusView view = createView( dataProvider );
|
||||
Shard shard = new LocusShard(GenomeLocParser.createGenomeLoc("chr1", 1, 10));
|
||||
ShardDataProvider dataProvider = new ShardDataProvider(shard, iterator);
|
||||
LocusView view = createView(dataProvider);
|
||||
|
||||
List<SAMRecord> expectedReads = new ArrayList<SAMRecord>();
|
||||
Collections.addAll(expectedReads,read1,read2,read3,read4,read5,read6);
|
||||
testReadsInContext( view, shard.getGenomeLoc(), expectedReads );
|
||||
Collections.addAll(expectedReads, read1, read2, read3, read4, read5, read6);
|
||||
testReadsInContext(view, shard.getGenomeLoc(), expectedReads);
|
||||
}
|
||||
|
||||
@Test
|
||||
public void cascadingReadsOverlappingBoundsTest() {
|
||||
SAMRecord read01 = buildSAMRecord("chr1",1,5);
|
||||
SAMRecord read02 = buildSAMRecord("chr1",2,6);
|
||||
SAMRecord read03 = buildSAMRecord("chr1",3,7);
|
||||
SAMRecord read04 = buildSAMRecord("chr1",4,8);
|
||||
SAMRecord read05 = buildSAMRecord("chr1",5,9);
|
||||
SAMRecord read06 = buildSAMRecord("chr1",6,10);
|
||||
SAMRecord read07 = buildSAMRecord("chr1",7,11);
|
||||
SAMRecord read08 = buildSAMRecord("chr1",8,12);
|
||||
SAMRecord read09 = buildSAMRecord("chr1",9,13);
|
||||
SAMRecord read10 = buildSAMRecord("chr1",10,14);
|
||||
SAMRecord read11 = buildSAMRecord("chr1",11,15);
|
||||
SAMRecord read12 = buildSAMRecord("chr1",12,16);
|
||||
SAMRecordIterator iterator = new SAMRecordIterator(read01,read02,read03,read04,read05,read06,
|
||||
read07,read08,read09,read10,read11,read12);
|
||||
SAMRecord read01 = buildSAMRecord("chr1", 1, 5);
|
||||
SAMRecord read02 = buildSAMRecord("chr1", 2, 6);
|
||||
SAMRecord read03 = buildSAMRecord("chr1", 3, 7);
|
||||
SAMRecord read04 = buildSAMRecord("chr1", 4, 8);
|
||||
SAMRecord read05 = buildSAMRecord("chr1", 5, 9);
|
||||
SAMRecord read06 = buildSAMRecord("chr1", 6, 10);
|
||||
SAMRecord read07 = buildSAMRecord("chr1", 7, 11);
|
||||
SAMRecord read08 = buildSAMRecord("chr1", 8, 12);
|
||||
SAMRecord read09 = buildSAMRecord("chr1", 9, 13);
|
||||
SAMRecord read10 = buildSAMRecord("chr1", 10, 14);
|
||||
SAMRecord read11 = buildSAMRecord("chr1", 11, 15);
|
||||
SAMRecord read12 = buildSAMRecord("chr1", 12, 16);
|
||||
SAMRecordIterator iterator = new SAMRecordIterator(read01, read02, read03, read04, read05, read06,
|
||||
read07, read08, read09, read10, read11, read12);
|
||||
|
||||
Shard shard = new LocusShard(GenomeLocParser.createGenomeLoc("chr1",6,15));
|
||||
ShardDataProvider dataProvider = new ShardDataProvider( shard, iterator );
|
||||
LocusView view = createView( dataProvider );
|
||||
Shard shard = new LocusShard(GenomeLocParser.createGenomeLoc("chr1", 6, 15));
|
||||
ShardDataProvider dataProvider = new ShardDataProvider(shard, iterator);
|
||||
LocusView view = createView(dataProvider);
|
||||
|
||||
List<SAMRecord> expectedReads = new ArrayList<SAMRecord>();
|
||||
Collections.addAll(expectedReads,read01,read02,read03,read04,read05,read06,
|
||||
read07,read08,read09,read10,read11,read12);
|
||||
testReadsInContext( view, shard.getGenomeLoc(), expectedReads );
|
||||
}
|
||||
Collections.addAll(expectedReads, read01, read02, read03, read04, read05, read06,
|
||||
read07, read08, read09, read10, read11, read12);
|
||||
testReadsInContext(view, shard.getGenomeLoc(), expectedReads);
|
||||
}
|
||||
|
||||
/**
|
||||
* Creates a view of the type required for testing.
|
||||
*
|
||||
* @return The correct view to test.
|
||||
*/
|
||||
protected abstract LocusView createView( ShardDataProvider provider );
|
||||
protected abstract LocusView createView(ShardDataProvider provider);
|
||||
|
||||
/**
|
||||
* Test the reads according to an independently derived context.
|
||||
*
|
||||
* @param view
|
||||
* @param bounds
|
||||
* @param reads
|
||||
*/
|
||||
protected abstract void testReadsInContext( LocusView view, GenomeLoc bounds, List<SAMRecord> reads );
|
||||
protected abstract void testReadsInContext(LocusView view, GenomeLoc bounds, List<SAMRecord> reads);
|
||||
|
||||
/**
|
||||
* Fake a reference sequence file. Essentially, seek a header with a bunch of dummy data.
|
||||
*
|
||||
* @return A 'fake' reference sequence file
|
||||
*/
|
||||
private static ReferenceSequenceFile fakeReferenceSequenceFile() {
|
||||
|
|
@ -249,18 +250,27 @@ public abstract class LocusViewTemplate extends BaseTest {
|
|||
SAMSequenceDictionary dictionary = new SAMSequenceDictionary(Collections.singletonList(sequenceRecord));
|
||||
return dictionary;
|
||||
}
|
||||
public ReferenceSequence nextSequence() { throw new UnsupportedOperationException("Fake implementation doesn't support a getter"); }
|
||||
|
||||
public ReferenceSequence nextSequence() {
|
||||
throw new UnsupportedOperationException("Fake implementation doesn't support a getter");
|
||||
}
|
||||
|
||||
public void reset() {
|
||||
return; // TODO MATT FIX ME
|
||||
}
|
||||
};
|
||||
}
|
||||
|
||||
/**
|
||||
* Build a SAM record featuring the absolute minimum required dataset.
|
||||
* @param contig Contig to populate.
|
||||
*
|
||||
* @param contig Contig to populate.
|
||||
* @param alignmentStart start of alignment
|
||||
* @param alignmentEnd end of alignment
|
||||
* @param alignmentEnd end of alignment
|
||||
*
|
||||
* @return New SAM Record
|
||||
*/
|
||||
protected SAMRecord buildSAMRecord( String contig, int alignmentStart, int alignmentEnd ) {
|
||||
protected SAMRecord buildSAMRecord(String contig, int alignmentStart, int alignmentEnd) {
|
||||
SAMFileHeader header = new SAMFileHeader();
|
||||
header.setSequenceDictionary(sequenceSourceFile.getSequenceDictionary());
|
||||
|
||||
|
|
@ -269,18 +279,16 @@ public abstract class LocusViewTemplate extends BaseTest {
|
|||
record.setReferenceIndex(sequenceSourceFile.getSequenceDictionary().getSequenceIndex(contig));
|
||||
record.setAlignmentStart(alignmentStart);
|
||||
Cigar cigar = new Cigar();
|
||||
cigar.add(new CigarElement(alignmentEnd-alignmentStart+1, CigarOperator.M));
|
||||
cigar.add(new CigarElement(alignmentEnd - alignmentStart + 1, CigarOperator.M));
|
||||
record.setCigar(cigar);
|
||||
return record;
|
||||
}
|
||||
|
||||
/**
|
||||
* A simple iterator which iterates over a list of reads.
|
||||
*/
|
||||
/** A simple iterator which iterates over a list of reads. */
|
||||
protected class SAMRecordIterator implements StingSAMIterator {
|
||||
private Iterator<SAMRecord> backingIterator = null;
|
||||
|
||||
public SAMRecordIterator( SAMRecord... reads ) {
|
||||
public SAMRecordIterator(SAMRecord... reads) {
|
||||
List<SAMRecord> backingList = new ArrayList<SAMRecord>();
|
||||
backingList.addAll(Arrays.asList(reads));
|
||||
backingIterator = backingList.iterator();
|
||||
|
|
|
|||
|
|
@ -33,6 +33,12 @@ public class SSGenotypeCallTest extends BaseTest {
|
|||
return null;
|
||||
}
|
||||
|
||||
/** Method for clearing the cache (in case we change the priors) */
|
||||
@Override
|
||||
protected void clearCache() {
|
||||
// do nothing
|
||||
}
|
||||
|
||||
/**
|
||||
* Must be overridden by concrete subclasses
|
||||
*
|
||||
|
|
|
|||
|
|
@ -9,21 +9,21 @@ public class IntervalCleanerIntegrationTest extends WalkerTest {
|
|||
@Test
|
||||
public void testIntervals() {
|
||||
|
||||
String[] md5lod5 = {"bfe1c76bf352b22f79c9b7242197a126", "4aa3637e86822c95af3e2c9b414530c3"};
|
||||
String[] md5lod5 = {"54ba9ef0d90659475f7d694fb97b5f2b", "4aa3637e86822c95af3e2c9b414530c3"};
|
||||
WalkerTestSpec spec1 = new WalkerTestSpec(
|
||||
"-T IntervalCleaner -LOD 5 -maxConsensuses 100 -greedy 100 -R /broad/1KG/reference/human_b36_both.fasta -I /humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.chrom1.SLX.SRP000032.2009_06.bam -L /humgen/gsa-scr1/GATK_Data/Validation_Data/cleaner.test.intervals --OutputCleaned %s -snps %s",
|
||||
2,
|
||||
Arrays.asList(md5lod5));
|
||||
executeTest("testLod5", spec1);
|
||||
|
||||
String[] md5lod200 = {"4481e4d24d61a3e438323b368ad0eee7", "e39aa718c9810364ebe30964d878d5ff"};
|
||||
String[] md5lod200 = {"55097ed556f41c5d527d7381b8e858dd", "e39aa718c9810364ebe30964d878d5ff"};
|
||||
WalkerTestSpec spec2 = new WalkerTestSpec(
|
||||
"-T IntervalCleaner -LOD 200 -maxConsensuses 100 -greedy 100 -R /broad/1KG/reference/human_b36_both.fasta -I /humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.chrom1.SLX.SRP000032.2009_06.bam -L /humgen/gsa-scr1/GATK_Data/Validation_Data/cleaner.test.intervals --OutputCleaned %s -snps %s",
|
||||
2,
|
||||
Arrays.asList(md5lod200));
|
||||
executeTest("testLod200", spec2);
|
||||
|
||||
String[] md5cleanedOnly = {"c8da42cc2298e05ab4f2bc9e5d7445e1", "4aa3637e86822c95af3e2c9b414530c3"};
|
||||
String[] md5cleanedOnly = {"1f844be094cd30c351586ebf0f8ff38c", "4aa3637e86822c95af3e2c9b414530c3"};
|
||||
WalkerTestSpec spec3 = new WalkerTestSpec(
|
||||
"-T IntervalCleaner -LOD 5 -cleanedOnly -maxConsensuses 100 -greedy 100 -R /broad/1KG/reference/human_b36_both.fasta -I /humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.chrom1.SLX.SRP000032.2009_06.bam -L /humgen/gsa-scr1/GATK_Data/Validation_Data/cleaner.test.intervals --OutputCleaned %s -snps %s",
|
||||
2,
|
||||
|
|
|
|||
|
|
@ -40,7 +40,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
|
|||
@Test
|
||||
public void testTableRecalibrator1() {
|
||||
HashMap<String, String> e = new HashMap<String, String>();
|
||||
e.put( "/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.SLX.SRP000031.2009_06.chr1.10_20mb.bam", "8d2194cf8134800def32d5268033de70" );
|
||||
e.put( "/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.SLX.SRP000031.2009_06.chr1.10_20mb.bam", "3ace4b9b8495429cc32e7008145f4996" );
|
||||
//e.put( "/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12762.SOLID.SRP000031.2009_07.chr1.10_20mb.bam", "" );
|
||||
//e.put( "/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12873.454.SRP000031.2009_06.chr1.10_20mb.bam", "" );
|
||||
|
||||
|
|
|
|||
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|
|
@ -1,3 +1,3 @@
|
|||
<ivy-module version="1.0">
|
||||
<info organisation="edu.mit.broad" module="picard-private" revision="875" status="integration" publication="20090630104500" />
|
||||
<info organisation="edu.mit.broad" module="picard-private" revision="1060" status="integration" publication="20090930104500" />
|
||||
</ivy-module>
|
||||
Binary file not shown.
Binary file not shown.
|
|
@ -1,3 +0,0 @@
|
|||
<ivy-module version="1.0">
|
||||
<info organisation="net.sf" module="picard" revision="1.02.63" status="release" />
|
||||
</ivy-module>
|
||||
Binary file not shown.
|
|
@ -1,3 +0,0 @@
|
|||
<ivy-module version="1.0">
|
||||
<info organisation="net.sf" module="sam" revision="1.01.63" status="release" />
|
||||
</ivy-module>
|
||||
Loading…
Reference in New Issue