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Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable

This commit is contained in:
Roger Zurawicki 2011-07-12 16:06:47 -04:00
parent f68064eb95 d21388f0cb
commit d4c6caaed8
17 changed files with 937 additions and 228 deletions
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1
build.xml
View File

@ -981,6 +981,7 @@
<delete dir="out"/>
<delete dir="${build.dir}"/>
<delete dir="${lib.dir}"/>
<delete dir="dump"/>
<delete dir="staging"/>
<delete dir="${dist.dir}"/>
<delete dir="pipelinetests"/>

5
public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/BAMDiffableReader.java
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@ -51,12 +51,11 @@ import java.util.zip.GZIPInputStream;
* Class implementing diffnode reader for VCF
*/
public class BAMDiffableReader implements DiffableReader {
private final static int MAX_RECORDS_TO_READ = 1000;
@Override
public String getName() { return "BAM"; }
@Override
public DiffElement readFromFile(File file) {
public DiffElement readFromFile(File file, int maxElementsToRead) {
final SAMFileReader reader = new SAMFileReader(file, null); // null because we don't want it to look for the index
reader.setValidationStringency(SAMFileReader.ValidationStringency.SILENT);
@ -65,7 +64,7 @@ public class BAMDiffableReader implements DiffableReader {
int count = 0;
while ( iterator.hasNext() ) {
if ( count++ > MAX_RECORDS_TO_READ )
if ( count++ > maxElementsToRead && maxElementsToRead != -1)
break;
final SAMRecord record = iterator.next();

4
public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffElement.java
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@ -115,4 +115,8 @@ public class DiffElement {
else
throw new ReviewedStingException("Illegal request conversion of a DiffValue into a DiffNode: " + this);
}
public int size() {
return 1 + getValue().size();
}
}

149
public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffEngine.java
View File

@ -24,11 +24,9 @@
package org.broadinstitute.sting.gatk.walkers.diffengine;
import com.google.java.contract.Requires;
import org.apache.log4j.Logger;
import org.broadinstitute.sting.gatk.report.GATKReport;
import org.broadinstitute.sting.gatk.report.GATKReportTable;
import org.broadinstitute.sting.gatk.walkers.varianteval.stratifications.VariantStratifier;
import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.classloader.PluginManager;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
@ -60,7 +58,7 @@ public class DiffEngine {
//
// --------------------------------------------------------------------------------
public List<Difference> diff(DiffElement master, DiffElement test) {
public List<SpecificDifference> diff(DiffElement master, DiffElement test) {
DiffValue masterValue = master.getValue();
DiffValue testValue = test.getValue();
@ -70,14 +68,14 @@ public class DiffEngine {
return diff(masterValue, testValue);
} else {
// structural difference in types. one is node, other is leaf
return Arrays.asList(new Difference(master, test));
return Arrays.asList(new SpecificDifference(master, test));
}
}
public List<Difference> diff(DiffNode master, DiffNode test) {
public List<SpecificDifference> diff(DiffNode master, DiffNode test) {
Set<String> allNames = new HashSet<String>(master.getElementNames());
allNames.addAll(test.getElementNames());
List<Difference> diffs = new ArrayList<Difference>();
List<SpecificDifference> diffs = new ArrayList<SpecificDifference>();
for ( String name : allNames ) {
DiffElement masterElt = master.getElement(name);
@ -86,7 +84,7 @@ public class DiffEngine {
throw new ReviewedStingException("BUG: unexceptedly got two null elements for field: " + name);
} else if ( masterElt == null || testElt == null ) { // if either is null, we are missing a value
// todo -- should one of these be a special MISSING item?
diffs.add(new Difference(masterElt, testElt));
diffs.add(new SpecificDifference(masterElt, testElt));
} else {
diffs.addAll(diff(masterElt, testElt));
}
@ -95,11 +93,11 @@ public class DiffEngine {
return diffs;
}
public List<Difference> diff(DiffValue master, DiffValue test) {
public List<SpecificDifference> diff(DiffValue master, DiffValue test) {
if ( master.getValue().equals(test.getValue()) ) {
return Collections.emptyList();
} else {
return Arrays.asList(new Difference(master.getBinding(), test.getBinding()));
return Arrays.asList(new SpecificDifference(master.getBinding(), test.getBinding()));
}
}
@ -147,64 +145,68 @@ public class DiffEngine {
* @param params determines how we display the items
* @param diffs
*/
public void reportSummarizedDifferences(List<Difference> diffs, SummaryReportParams params ) {
public void reportSummarizedDifferences(List<SpecificDifference> diffs, SummaryReportParams params ) {
printSummaryReport(summarizeDifferences(diffs), params );
}
public List<SummarizedDifference> summarizeDifferences(List<Difference> diffs) {
List<String[]> diffPaths = new ArrayList<String[]>(diffs.size());
for ( Difference diff1 : diffs ) {
diffPaths.add(diffNameToPath(diff1.getFullyQualifiedName()));
}
return summarizedDifferencesOfPaths(diffPaths);
public List<Difference> summarizeDifferences(List<SpecificDifference> diffs) {
return summarizedDifferencesOfPaths(diffs);
}
final protected static String[] diffNameToPath(String diffName) {
return diffName.split("\\.");
}
protected List<SummarizedDifference> summarizedDifferencesOfPaths(List<String[]> diffPaths) {
Map<String, SummarizedDifference> summaries = new HashMap<String, SummarizedDifference>();
protected List<Difference> summarizedDifferencesOfPathsFromString(List<String> singletonDiffs) {
List<Difference> diffs = new ArrayList<Difference>();
for ( String diff : singletonDiffs ) {
diffs.add(new Difference(diff));
}
return summarizedDifferencesOfPaths(diffs);
}
protected List<Difference> summarizedDifferencesOfPaths(List<? extends Difference> singletonDiffs) {
Map<String, Difference> summaries = new HashMap<String, Difference>();
// create the initial set of differences
for ( int i = 0; i < diffPaths.size(); i++ ) {
for ( int i = 0; i < singletonDiffs.size(); i++ ) {
for ( int j = 0; j <= i; j++ ) {
String[] diffPath1 = diffPaths.get(i);
String[] diffPath2 = diffPaths.get(j);
if ( diffPath1.length == diffPath2.length ) {
int lcp = longestCommonPostfix(diffPath1, diffPath2);
String path = lcp > 0 ? summarizedPath(diffPath2, lcp) : Utils.join(".", diffPath2);
Difference diffPath1 = singletonDiffs.get(i);
Difference diffPath2 = singletonDiffs.get(j);
if ( diffPath1.length() == diffPath2.length() ) {
int lcp = longestCommonPostfix(diffPath1.getParts(), diffPath2.getParts());
String path = lcp > 0 ? summarizedPath(diffPath2.getParts(), lcp) : diffPath2.getPath();
addSummary(summaries, path, true);
}
}
}
// count differences
for ( String[] diffPath : diffPaths ) {
for ( SummarizedDifference sumDiff : summaries.values() ) {
if ( sumDiff.matches(diffPath) )
for ( Difference diffPath : singletonDiffs ) {
for ( Difference sumDiff : summaries.values() ) {
if ( sumDiff.matches(diffPath.getParts()) )
addSummary(summaries, sumDiff.getPath(), false);
}
}
List<SummarizedDifference> sortedSummaries = new ArrayList<SummarizedDifference>(summaries.values());
List<Difference> sortedSummaries = new ArrayList<Difference>(summaries.values());
Collections.sort(sortedSummaries);
return sortedSummaries;
}
private static void addSummary(Map<String, SummarizedDifference> summaries, String path, boolean onlyCatalog) {
private static void addSummary(Map<String, Difference> summaries, String path, boolean onlyCatalog) {
if ( summaries.containsKey(path) ) {
if ( ! onlyCatalog )
summaries.get(path).incCount();
} else {
SummarizedDifference sumDiff = new SummarizedDifference(path);
Difference sumDiff = new Difference(path);
summaries.put(sumDiff.getPath(), sumDiff);
}
}
protected void printSummaryReport(List<SummarizedDifference> sortedSummaries, SummaryReportParams params ) {
protected void printSummaryReport(List<Difference> sortedSummaries, SummaryReportParams params ) {
GATKReport report = new GATKReport();
final String tableName = "diffences";
report.addTable(tableName, "Summarized differences between the master and test files.\nSee http://www.broadinstitute.org/gsa/wiki/index.php/DiffObjectsWalker_and_SummarizedDifferences for more information");
@ -213,7 +215,7 @@ public class DiffEngine {
table.addColumn("NumberOfOccurrences", 0);
int count = 0, count1 = 0;
for ( SummarizedDifference diff : sortedSummaries ) {
for ( Difference diff : sortedSummaries ) {
if ( diff.getCount() < params.minSumDiffToShow )
// in order, so break as soon as the count is too low
break;
@ -261,76 +263,6 @@ public class DiffEngine {
return Utils.join(".", parts);
}
/**
* TODO -- all of the algorithms above should use SummarizedDifference instead
* TODO -- of some SummarizedDifferences and some low-level String[]
*/
public static class SummarizedDifference implements Comparable<SummarizedDifference> {
final String path; // X.Y.Z
final String[] parts;
int count = 0;
public SummarizedDifference(String path) {
this.path = path;
this.parts = diffNameToPath(path);
}
public void incCount() { count++; }
public int getCount() {
return count;
}
/**
* The fully qualified path object A.B.C etc
* @return
*/
public String getPath() {
return path;
}
/**
* @return the length of the parts of this summary
*/
public int length() {
return this.parts.length;
}
/**
* Returns true if the string parts matches this summary. Matches are
* must be equal() everywhere where this summary isn't *.
* @param otherParts
* @return
*/
public boolean matches(String[] otherParts) {
if ( otherParts.length != length() )
return false;
// TODO optimization: can start at right most non-star element
for ( int i = 0; i < length(); i++ ) {
String part = parts[i];
if ( ! part.equals("*") && ! part.equals(otherParts[i]) )
return false;
}
return true;
}
@Override
public String toString() {
return String.format("%s:%d", getPath(), getCount());
}
@Override
public int compareTo(SummarizedDifference other) {
// sort first highest to lowest count, then by lowest to highest path
int countCmp = Integer.valueOf(count).compareTo(other.count);
return countCmp != 0 ? -1 * countCmp : path.compareTo(other.path);
}
}
// --------------------------------------------------------------------------------
//
// plugin manager
@ -385,12 +317,17 @@ public class DiffEngine {
return findReaderForFile(file) != null;
}
public DiffElement createDiffableFromFile(File file) {
return createDiffableFromFile(file, -1);
}
public DiffElement createDiffableFromFile(File file, int maxElementsToRead) {
DiffableReader reader = findReaderForFile(file);
if ( reader == null )
throw new UserException("Unsupported file type: " + file);
else
return reader.readFromFile(file);
return reader.readFromFile(file, maxElementsToRead);
}
public static boolean simpleDiffFiles(File masterFile, File testFile, DiffEngine.SummaryReportParams params) {
@ -399,7 +336,7 @@ public class DiffEngine {
if ( diffEngine.canRead(masterFile) && diffEngine.canRead(testFile) ) {
DiffElement master = diffEngine.createDiffableFromFile(masterFile);
DiffElement test = diffEngine.createDiffableFromFile(testFile);
List<Difference> diffs = diffEngine.diff(master, test);
List<SpecificDifference> diffs = diffEngine.diff(master, test);
diffEngine.reportSummarizedDifferences(diffs, params);
return true;
} else {

17
public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffNode.java
View File

@ -107,11 +107,13 @@ public class DiffNode extends DiffValue {
return getElements(false);
}
/**
* Returns the element bound to name, or null if no such binding exists
* @param name
* @return
*/
public DiffElement getElement(String name) {
for ( DiffElement elt : getElements() )
if ( elt.getName().equals(name) )
return elt;
return null;
return getElementMap().get(name);
}
/**
@ -151,6 +153,13 @@ public class DiffNode extends DiffValue {
add(new DiffElement(name, this.getBinding(), new DiffValue(value)));
}
public int size() {
int count = 0;
for ( DiffElement value : getElements() )
count += value.size();
return count;
}
// ---------------------------------------------------------------------------
//
// toString

24
public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffObjectsWalker.java
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@ -24,7 +24,6 @@
package org.broadinstitute.sting.gatk.walkers.diffengine;
import org.apache.xmlbeans.impl.tool.Diff;
import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.commandline.Output;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
@ -48,11 +47,14 @@ public class DiffObjectsWalker extends RodWalker<Integer, Integer> {
@Output(doc="File to which results should be written",required=true)
protected PrintStream out;
@Argument(fullName="maxRecords", shortName="M", doc="Max. number of records to process", required=false)
int MAX_RECORDS = 0;
@Argument(fullName="maxObjectsToRead", shortName="motr", doc="Max. number of objects to read from the files. -1 [default] means unlimited", required=false)
int MAX_OBJECTS_TO_READ = -1;
@Argument(fullName="maxCount1Records", shortName="M1", doc="Max. number of records occuring exactly once in the file to process", required=false)
int MAX_COUNT1_RECORDS = 0;
@Argument(fullName="maxDiffs", shortName="M", doc="Max. number of diffs to process", required=false)
int MAX_DIFFS = 0;
@Argument(fullName="maxCount1Diffs", shortName="M1", doc="Max. number of diffs occuring exactly once in the file to process", required=false)
int MAX_COUNT1_DIFFS = 0;
@Argument(fullName="minCountForDiff", shortName="MCFD", doc="Min number of observations for a records to display", required=false)
int minCountForDiff = 1;
@ -91,23 +93,25 @@ public class DiffObjectsWalker extends RodWalker<Integer, Integer> {
@Override
public void onTraversalDone(Integer sum) {
out.printf("Reading master file %s%n", masterFile);
DiffElement master = diffEngine.createDiffableFromFile(masterFile);
DiffElement master = diffEngine.createDiffableFromFile(masterFile, MAX_OBJECTS_TO_READ);
out.printf(" Read %d objects%n", master.size());
out.printf("Reading test file %s%n", testFile);
DiffElement test = diffEngine.createDiffableFromFile(testFile);
DiffElement test = diffEngine.createDiffableFromFile(testFile, MAX_OBJECTS_TO_READ);
out.printf(" Read %d objects%n", test.size());
// out.printf("Master diff objects%n");
// out.println(master.toString());
// out.printf("Test diff objects%n");
// out.println(test.toString());
List<Difference> diffs = diffEngine.diff(master, test);
List<SpecificDifference> diffs = diffEngine.diff(master, test);
if ( showItemizedDifferences ) {
out.printf("Itemized results%n");
for ( Difference diff : diffs )
for ( SpecificDifference diff : diffs )
out.printf("DIFF: %s%n", diff.toString());
}
DiffEngine.SummaryReportParams params = new DiffEngine.SummaryReportParams(out, MAX_RECORDS, MAX_COUNT1_RECORDS, minCountForDiff);
DiffEngine.SummaryReportParams params = new DiffEngine.SummaryReportParams(out, MAX_DIFFS, MAX_COUNT1_DIFFS, minCountForDiff);
diffEngine.reportSummarizedDifferences(diffs, params);
}
}

1
public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffValue.java
View File

@ -87,4 +87,5 @@ public class DiffValue {
public boolean isAtomic() { return true; }
public boolean isCompound() { return ! isAtomic(); }
public int size() { return 1; }
}

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

@ -43,7 +43,7 @@ public interface DiffableReader {
@Ensures("result != null")
@Requires("file != null")
public DiffElement readFromFile(File file);
public DiffElement readFromFile(File file, int maxElementsToRead);
@Requires("file != null")
public boolean canRead(File file);

83
public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/Difference.java
View File

@ -24,35 +24,72 @@
package org.broadinstitute.sting.gatk.walkers.diffengine;
/**
* Created by IntelliJ IDEA.
* User: depristo
* Date: 7/4/11
* Time: 12:53 PM
*
* Represents a specific difference between two specific DiffElements
*/
public class Difference {
DiffElement master, test;
public class Difference implements Comparable<Difference> {
final String path; // X.Y.Z
final String[] parts;
int count = 0;
public Difference(DiffElement master, DiffElement test) {
if ( master == null && test == null ) throw new IllegalArgumentException("Master and test both cannot be null");
this.master = master;
this.test = test;
public Difference(String path) {
this.path = path;
this.parts = DiffEngine.diffNameToPath(path);
}
public String[] getParts() {
return parts;
}
public void incCount() { count++; }
public int getCount() {
return count;
}
/**
* The fully qualified path object A.B.C etc
* @return
*/
public String getPath() {
return path;
}
/**
* @return the length of the parts of this summary
*/
public int length() {
return this.parts.length;
}
/**
* Returns true if the string parts matches this summary. Matches are
* must be equal() everywhere where this summary isn't *.
* @param otherParts
* @return
*/
public boolean matches(String[] otherParts) {
if ( otherParts.length != length() )
return false;
// TODO optimization: can start at right most non-star element
for ( int i = 0; i < length(); i++ ) {
String part = parts[i];
if ( ! part.equals("*") && ! part.equals(otherParts[i]) )
return false;
}
return true;
}
@Override
public String toString() {
return String.format("%s:%s!=%s",
getFullyQualifiedName(),
getOneLineString(master),
getOneLineString(test));
return String.format("%s:%d", getPath(), getCount());
}
public String getFullyQualifiedName() {
return (master == null ? test : master).fullyQualifiedName();
@Override
public int compareTo(Difference other) {
// sort first highest to lowest count, then by lowest to highest path
int countCmp = Integer.valueOf(count).compareTo(other.count);
return countCmp != 0 ? -1 * countCmp : path.compareTo(other.path);
}
private static String getOneLineString(DiffElement elt) {
return elt == null ? "MISSING" : elt.getValue().toOneLineString();
}
}

59
public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/SpecificDifference.java 100644
View File

@ -0,0 +1,59 @@
/*
* Copyright (c) 2011, The Broad Institute
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
* OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.gatk.walkers.diffengine;
/**
* Created by IntelliJ IDEA.
* User: depristo
* Date: 7/4/11
* Time: 12:53 PM
*
* Represents a specific difference between two specific DiffElements
*/
public class SpecificDifference extends Difference {
DiffElement master, test;
public SpecificDifference(DiffElement master, DiffElement test) {
super(createName(master, test));
if ( master == null && test == null ) throw new IllegalArgumentException("Master and test both cannot be null");
this.master = master;
this.test = test;
}
public String toString() {
return String.format("%s:%s!=%s",
getPath(),
getOneLineString(master),
getOneLineString(test));
}
private static String createName(DiffElement master, DiffElement test) {
return (master == null ? test : master).fullyQualifiedName();
}
private static String getOneLineString(DiffElement elt) {
return elt == null ? "MISSING" : elt.getValue().toOneLineString();
}
}

10
public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/VCFDiffableReader.java
View File

@ -51,15 +51,21 @@ public class VCFDiffableReader implements DiffableReader {
public String getName() { return "VCF"; }
@Override
public DiffElement readFromFile(File file) {
public DiffElement readFromFile(File file, int maxElementsToRead) {
DiffNode root = DiffNode.rooted(file.getName());
try {
LineReader lineReader = new AsciiLineReader(new FileInputStream(file));
VCFCodec vcfCodec = new VCFCodec();
VCFHeader header = (VCFHeader)vcfCodec.readHeader(lineReader);
// must be read as state is stored in reader itself
vcfCodec.readHeader(lineReader);
String line = lineReader.readLine();
int count = 0;
while ( line != null ) {
if ( count++ > maxElementsToRead && maxElementsToRead != -1)
break;
VariantContext vc = (VariantContext)vcfCodec.decode(line);
String name = vc.getChr() + ":" + vc.getStart();
DiffNode vcRoot = DiffNode.empty(name, root);

3
public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CountCovariatesWalker.java
View File

@ -27,6 +27,7 @@ package org.broadinstitute.sting.gatk.walkers.recalibration;
import org.broad.tribble.bed.BEDCodec;
import org.broad.tribble.dbsnp.DbSNPCodec;
import org.broadinstitute.sting.gatk.filters.MappingQualityUnavailableReadFilter;
import org.broadinstitute.sting.utils.codecs.vcf.VCF3Codec;
import org.broadinstitute.sting.utils.codecs.vcf.VCFCodec;
import org.broadinstitute.sting.commandline.Gather;
@ -75,7 +76,7 @@ import java.util.Map;
@BAQMode(ApplicationTime = BAQ.ApplicationTime.FORBIDDEN)
@By( DataSource.READS ) // Only look at covered loci, not every loci of the reference file
@ReadFilters( {MappingQualityZeroReadFilter.class} ) // Filter out all reads with zero mapping quality
@ReadFilters( {MappingQualityZeroReadFilter.class, MappingQualityUnavailableReadFilter.class} ) // Filter out all reads with zero or unavailable mapping quality
@Requires( {DataSource.READS, DataSource.REFERENCE, DataSource.REFERENCE_BASES} ) // This walker requires both -I input.bam and -R reference.fasta
@PartitionBy(PartitionType.LOCUS)
public class CountCovariatesWalker extends LocusWalker<CountCovariatesWalker.CountedData, CountCovariatesWalker.CountedData> implements TreeReducible<CountCovariatesWalker.CountedData> {

229
public/java/test/org/broadinstitute/sting/gatk/walkers/diffengine/DiffEngineUnitTest.java 100644
View File

@ -0,0 +1,229 @@
/*
* Copyright (c) 2011, The Broad Institute
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
* OTHER DEALINGS IN THE SOFTWARE.
*/
// our package
package org.broadinstitute.sting.gatk.walkers.diffengine;
// the imports for unit testing.
import org.broadinstitute.sting.BaseTest;
import org.testng.Assert;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.DataProvider;
import org.testng.annotations.Test;
import java.util.*;
/**
* Basic unit test for DifferableReaders in reduced reads
*/
public class DiffEngineUnitTest extends BaseTest {
DiffEngine engine;
@BeforeClass(enabled = true)
public void createDiffEngine() {
engine = new DiffEngine();
}
// --------------------------------------------------------------------------------
//
// Difference testing routines
//
// --------------------------------------------------------------------------------
private class DifferenceTest extends TestDataProvider {
public DiffElement tree1, tree2;
public List<String> differences;
private DifferenceTest(String tree1, String tree2) {
this(tree1, tree2, Collections.<String>emptyList());
}
private DifferenceTest(String tree1, String tree2, String difference) {
this(tree1, tree2, Arrays.asList(difference));
}
private DifferenceTest(String tree1, String tree2, List<String> differences) {
super(DifferenceTest.class);
this.tree1 = DiffNode.fromString(tree1);
this.tree2 = DiffNode.fromString(tree2);
this.differences = differences;
}
public String toString() {
return String.format("tree1=%s tree2=%s diff=%s",
tree1.toOneLineString(), tree2.toOneLineString(), differences);
}
}
@DataProvider(name = "trees")
public Object[][] createTrees() {
new DifferenceTest("A=X", "A=X");
new DifferenceTest("A=X", "A=Y", "A:X!=Y");
new DifferenceTest("A=X", "B=X", Arrays.asList("A:X!=MISSING", "B:MISSING!=X"));
new DifferenceTest("A=(X=1)", "B=(X=1)", Arrays.asList("A:(X=1)!=MISSING", "B:MISSING!=(X=1)"));
new DifferenceTest("A=(X=1)", "A=(X=1)");
new DifferenceTest("A=(X=1 Y=2)", "A=(X=1 Y=2)");
new DifferenceTest("A=(X=1 Y=2 B=(Z=3))", "A=(X=1 Y=2 B=(Z=3))");
new DifferenceTest("A=(X=1)", "A=(X=2)", "A.X:1!=2");
new DifferenceTest("A=(X=1 Y=2 B=(Z=3))", "A=(X=1 Y=2 B=(Z=4))", "A.B.Z:3!=4");
new DifferenceTest("A=(X=1)", "A=(X=1 Y=2)", "A.Y:MISSING!=2");
new DifferenceTest("A=(X=1 Y=2 B=(Z=3))", "A=(X=1 Y=2)", "A.B:(Z=3)!=MISSING");
return DifferenceTest.getTests(DifferenceTest.class);
}
@Test(enabled = true, dataProvider = "trees")
public void testDiffs(DifferenceTest test) {
logger.warn("Test tree1: " + test.tree1.toOneLineString());
logger.warn("Test tree2: " + test.tree2.toOneLineString());
List<SpecificDifference> diffs = engine.diff(test.tree1, test.tree2);
logger.warn("Test expected diff : " + test.differences);
logger.warn("Observed diffs : " + diffs);
}
// --------------------------------------------------------------------------------
//
// Low-level routines for summarizing differences
//
// --------------------------------------------------------------------------------
@Test(enabled = true)
public void testLongestCommonPostfix() {
testLongestCommonPostfixHelper("A", "A", 1);
testLongestCommonPostfixHelper("A", "B", 0);
testLongestCommonPostfixHelper("A.B", "A.B", 2);
testLongestCommonPostfixHelper("A.B.C", "A.B.C", 3);
testLongestCommonPostfixHelper("A.B.C", "X.B.C", 2);
testLongestCommonPostfixHelper("A.B.C", "X.Y.C", 1);
testLongestCommonPostfixHelper("A.B.C", "X.Y.Z", 0);
testLongestCommonPostfixHelper("A.B.C", "A.X.C", 1);
testLongestCommonPostfixHelper("A.B.C", "A.X.Z", 0);
testLongestCommonPostfixHelper("A.B.C", "A.B.Z", 0);
}
public void testLongestCommonPostfixHelper(String p1, String p2, int expected) {
String[] parts1 = p1.split("\\.");
String[] parts2 = p2.split("\\.");
int obs = DiffEngine.longestCommonPostfix(parts1, parts2);
Assert.assertEquals(obs, expected, "p1=" + p1 + " p2=" + p2 + " failed");
}
@Test(enabled = true, dependsOnMethods = "testLongestCommonPostfix")
public void testSummarizePath() {
testSummarizePathHelper("A", "A", "A");
testSummarizePathHelper("A", "B", "*");
testSummarizePathHelper("A.B", "A.B", "A.B");
testSummarizePathHelper("A.B", "X.B", "*.B");
testSummarizePathHelper("A.B", "X.Y", "*.*");
testSummarizePathHelper("A.B.C", "A.B.C", "A.B.C");
testSummarizePathHelper("A.B.C", "X.B.C", "*.B.C");
testSummarizePathHelper("A.B.C", "X.Y.C", "*.*.C");
testSummarizePathHelper("A.B.C", "X.Y.Z", "*.*.*");
testSummarizePathHelper("A.B.C", "A.X.C", "*.*.C");
testSummarizePathHelper("A.B.C", "A.X.Z", "*.*.*");
testSummarizePathHelper("A.B.C", "A.B.Z", "*.*.*");
}
public void testSummarizePathHelper(String p1, String p2, String expected) {
String[] parts1 = DiffEngine.diffNameToPath(p1);
String[] parts2 = DiffEngine.diffNameToPath(p2);
int obs = DiffEngine.longestCommonPostfix(parts1, parts2);
String path = DiffEngine.summarizedPath(parts2, obs);
Assert.assertEquals(path, expected, "p1=" + p1 + " p2=" + p2 + " failed");
}
// --------------------------------------------------------------------------------
//
// High-level difference summary
//
// --------------------------------------------------------------------------------
private class SummarizeDifferenceTest extends TestDataProvider {
List<String> diffs = new ArrayList<String>();
List<String> expecteds = new ArrayList<String>();
public SummarizeDifferenceTest() { super(SummarizeDifferenceTest.class); }
public SummarizeDifferenceTest addDiff(String... diffsToAdd) {
diffs.addAll(Arrays.asList(diffsToAdd));
return this;
}
public SummarizeDifferenceTest addSummary(String... expectedSummary) {
expecteds.addAll(Arrays.asList(expectedSummary));
return this;
}
public String toString() {
return String.format("diffs=%s => expected=%s", diffs, expecteds);
}
public void test() {
List<String[]> diffPaths = new ArrayList<String[]>(diffs.size());
for ( String diff : diffs ) { diffPaths.add(DiffEngine.diffNameToPath(diff)); }
List<Difference> sumDiffs = engine.summarizedDifferencesOfPathsFromString(diffs);
Assert.assertEquals(sumDiffs.size(), expecteds.size(), "Unexpected number of summarized differences: " + sumDiffs);
for ( int i = 0; i < sumDiffs.size(); i++ ) {
Difference sumDiff = sumDiffs.get(i);
String expected = expecteds.get(i);
String[] pathCount = expected.split(":");
String path = pathCount[0];
int count = Integer.valueOf(pathCount[1]);
Assert.assertEquals(sumDiff.getPath(), path, "Unexpected path at: " + expected + " obs=" + sumDiff + " all=" + sumDiffs);
Assert.assertEquals(sumDiff.getCount(), count, "Unexpected counts at: " + expected + " obs=" + sumDiff + " all=" + sumDiffs);
}
}
}
@DataProvider(name = "summaries")
public Object[][] createSummaries() {
new SummarizeDifferenceTest().addDiff("A", "A").addSummary("A:2");
new SummarizeDifferenceTest().addDiff("A", "B").addSummary("A:1", "B:1");
new SummarizeDifferenceTest().addDiff("A", "A", "A").addSummary("A:3");
new SummarizeDifferenceTest().addDiff("A", "A", "A", "B").addSummary("A:3", "B:1");
new SummarizeDifferenceTest().addDiff("A", "A", "A", "B", "B").addSummary("A:3", "B:2");
new SummarizeDifferenceTest().addDiff("A", "A", "A", "B", "B", "C").addSummary("A:3", "B:2", "C:1");
new SummarizeDifferenceTest().addDiff("A.X", "A.X").addSummary("A.X:2");
new SummarizeDifferenceTest().addDiff("A.X", "A.X", "B.X").addSummary("*.X:3", "A.X:2", "B.X:1");
new SummarizeDifferenceTest().addDiff("A.X", "A.X", "B.X", "B.X").addSummary("*.X:4", "A.X:2", "B.X:2");
new SummarizeDifferenceTest().addDiff("A.B.C", "X.B.C").addSummary("*.B.C:2", "A.B.C:1", "X.B.C:1");
new SummarizeDifferenceTest().addDiff("A.B.C", "X.Y.C", "X.Y.C").addSummary("*.*.C:3", "X.Y.C:2", "A.B.C:1");
new SummarizeDifferenceTest().addDiff("A.B.C", "A.X.C", "X.Y.C").addSummary("*.*.C:3", "A.B.C:1", "A.X.C:1", "X.Y.C:1");
new SummarizeDifferenceTest().addDiff("A.B.C", "A.X.C", "B.X.C").addSummary("*.*.C:3", "*.X.C:2", "A.B.C:1", "A.X.C:1", "B.X.C:1");
new SummarizeDifferenceTest().addDiff("A.B.C", "A.X.C", "B.X.C", "B.X.C").addSummary("*.*.C:4", "*.X.C:3", "B.X.C:2", "A.B.C:1", "A.X.C:1");
return SummarizeDifferenceTest.getTests(SummarizeDifferenceTest.class);
}
@Test(enabled = true, dependsOnMethods = "testSummarizePath", dataProvider = "summaries")
public void testSummarizeDifferences(SummarizeDifferenceTest test) {
test.test();
}
}

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/*
* Copyright (c) 2011, The Broad Institute
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
* OTHER DEALINGS IN THE SOFTWARE.
*/
// our package
package org.broadinstitute.sting.gatk.walkers.diffengine;
// the imports for unit testing.
import org.broadinstitute.sting.BaseTest;
import org.testng.Assert;
import org.testng.annotations.DataProvider;
import org.testng.annotations.Test;
import java.util.*;
/**
* Basic unit test for DifferableReaders in reduced reads
*/
public class DiffNodeUnitTest extends BaseTest {
// Data is:
// MY_ROOT
// fields: A=A, B=B
// nodes: C, D
// C: fields: E=E, nodes: none
// D: fields: F=F, G=G, nodes: none
static DiffNode MY_ROOT = DiffNode.rooted("MY_ROOT");
static DiffValue Value_A = new DiffValue("A", MY_ROOT, "A");
static DiffValue Value_B = new DiffValue("B", MY_ROOT, "B");
static DiffNode NODE_C = DiffNode.empty("C", MY_ROOT);
static DiffNode NODE_D = DiffNode.empty("D", MY_ROOT);
static DiffValue Value_E = new DiffValue("E", NODE_C, "E");
static DiffValue Value_F = new DiffValue("F", NODE_D, "F");
static DiffValue Value_G = new DiffValue("G", NODE_D, "G");
static {
MY_ROOT.add(Value_A);
MY_ROOT.add(Value_B);
MY_ROOT.add(NODE_C);
MY_ROOT.add(NODE_D);
NODE_C.add(Value_E);
NODE_D.add(Value_F);
NODE_D.add(Value_G);
}
// --------------------------------------------------------------------------------
//
// Element testing routines
//
// --------------------------------------------------------------------------------
private class ElementTest extends TestDataProvider {
public DiffElement elt;
public String name;
public String fullName;
public DiffElement parent;
private ElementTest(DiffValue elt, DiffValue parent, String name, String fullName) {
this(elt.getBinding(), parent.getBinding(), name, fullName);
}
private ElementTest(DiffElement elt, DiffElement parent, String name, String fullName) {
super(ElementTest.class);
this.elt = elt;
this.name = name;
this.fullName = fullName;
this.parent = parent;
}
public String toString() {
return String.format("ElementTest elt=%s name=%s fullName=%s parent=%s",
elt.toOneLineString(), name, fullName, parent.getName());
}
}
@DataProvider(name = "elementdata")
public Object[][] createElementData() {
new ElementTest(MY_ROOT.getBinding(), DiffElement.ROOT, "MY_ROOT", "MY_ROOT");
new ElementTest(NODE_C, MY_ROOT, "C", "MY_ROOT.C");
new ElementTest(NODE_D, MY_ROOT, "D", "MY_ROOT.D");
new ElementTest(Value_A, MY_ROOT, "A", "MY_ROOT.A");
new ElementTest(Value_B, MY_ROOT, "B", "MY_ROOT.B");
new ElementTest(Value_E, NODE_C, "E", "MY_ROOT.C.E");
new ElementTest(Value_F, NODE_D, "F", "MY_ROOT.D.F");
new ElementTest(Value_G, NODE_D, "G", "MY_ROOT.D.G");
return TestDataProvider.getTests(ElementTest.class);
}
@Test(enabled = true, dataProvider = "elementdata")
public void testElementMethods(ElementTest test) {
Assert.assertNotNull(test.elt.getName());
Assert.assertNotNull(test.elt.getParent());
Assert.assertEquals(test.elt.getName(), test.name);
Assert.assertEquals(test.elt.getParent(), test.parent);
Assert.assertEquals(test.elt.fullyQualifiedName(), test.fullName);
}
// --------------------------------------------------------------------------------
//
// DiffValue testing routines
//
// --------------------------------------------------------------------------------
private class LeafTest extends TestDataProvider {
public DiffValue diffvalue;
public Object value;
private LeafTest(DiffValue diffvalue, Object value) {
super(LeafTest.class);
this.diffvalue = diffvalue;
this.value = value;
}
public String toString() {
return String.format("LeafTest diffvalue=%s value=%s", diffvalue.toOneLineString(), value);
}
}
@DataProvider(name = "leafdata")
public Object[][] createLeafData() {
new LeafTest(Value_A, "A");
new LeafTest(Value_B, "B");
new LeafTest(Value_E, "E");
new LeafTest(Value_F, "F");
new LeafTest(Value_G, "G");
return TestDataProvider.getTests(LeafTest.class);
}
@Test(enabled = true, dataProvider = "leafdata")
public void testLeafMethods(LeafTest test) {
Assert.assertNotNull(test.diffvalue.getValue());
Assert.assertEquals(test.diffvalue.getValue(), test.value);
}
// --------------------------------------------------------------------------------
//
// Node testing routines
//
// --------------------------------------------------------------------------------
private class NodeTest extends TestDataProvider {
public DiffNode node;
public Set<String> fields;
public Set<String> subnodes;
public Set<String> allNames;
private NodeTest(DiffNode node, List<String> fields, List<String> subnodes) {
super(NodeTest.class);
this.node = node;
this.fields = new HashSet<String>(fields);
this.subnodes = new HashSet<String>(subnodes);
this.allNames = new HashSet<String>(fields);
allNames.addAll(subnodes);
}
public String toString() {
return String.format("NodeTest node=%s fields=%s subnodes=%s",
node.toOneLineString(), fields, subnodes);
}
}
@DataProvider(name = "nodedata")
public Object[][] createData1() {
new NodeTest(MY_ROOT, Arrays.asList("A", "B"), Arrays.asList("C", "D"));
new NodeTest(NODE_C, Arrays.asList("E"), Collections.<String>emptyList());
new NodeTest(NODE_D, Arrays.asList("F", "G"), Collections.<String>emptyList());
return TestDataProvider.getTests(NodeTest.class);
}
@Test(enabled = true, dataProvider = "nodedata")
public void testNodeAccessors(NodeTest test) {
Assert.assertNotNull(test.node.getElements());
for ( String name : test.allNames ) {
DiffElement elt = test.node.getElement(name);
Assert.assertNotNull(elt, "Failed to find field " + elt + " in " + test.node);
Assert.assertEquals(elt.getName(), name);
Assert.assertEquals(elt.getValue().isAtomic(), test.fields.contains(name), "Failed atomic/compound expectation: " + test.node);
}
}
// NOTE: add routines are being implicitly tested by the creation of the data structures
@Test(enabled = true, dataProvider = "nodedata")
public void testCounts(NodeTest test) {
Assert.assertEquals(test.node.getElements().size(), test.allNames.size());
Assert.assertEquals(test.node.getElementNames(), test.allNames);
}
// --------------------------------------------------------------------------------
//
// fromString testing routines
//
// --------------------------------------------------------------------------------
private class FromStringTest extends TestDataProvider {
public String string;
public DiffElement expected;
private FromStringTest(String string, DiffElement expected) {
super(FromStringTest.class);
this.string = string;
this.expected = expected;
}
public String toString() {
return String.format("FromStringTest string=%s expected=%s", string, expected.toOneLineString());
}
}
@DataProvider(name = "fromstringdata")
public Object[][] createFromData() {
new FromStringTest("A=A", Value_A.getBinding());
new FromStringTest("B=B", Value_B.getBinding());
new FromStringTest("C=(E=E)", NODE_C.getBinding());
new FromStringTest("D=(F=F G=G)", NODE_D.getBinding());
return TestDataProvider.getTests(FromStringTest.class);
}
@Test(enabled = true, dataProvider = "fromstringdata")
public void parseFromString(FromStringTest test) {
logger.warn("Testing from string: " + test.string);
DiffElement elt = DiffNode.fromString(test.string);
Assert.assertEquals(elt.toOneLineString(), test.expected.toOneLineString());
}
}

143
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/*
* Copyright (c) 2011, The Broad Institute
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
* OTHER DEALINGS IN THE SOFTWARE.
*/
// our package
package org.broadinstitute.sting.gatk.walkers.diffengine;
// the imports for unit testing.
import net.sf.samtools.SAMRecord;
import org.broadinstitute.sting.BaseTest;
import org.broadinstitute.sting.utils.variantcontext.Allele;
import org.testng.Assert;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
import java.io.File;
import java.util.*;
/**
* Basic unit test for DifferableReaders in reduced reads
*/
public class DiffableReaderUnitTest extends BaseTest {
DiffEngine engine;
File vcfFile = new File(testDir + "diffTestMaster.vcf");
File bamFile = new File(testDir + "exampleBAM.bam");
@BeforeClass(enabled = true)
public void createDiffEngine() {
engine = new DiffEngine();
}
@Test(enabled = true)
public void testPluggableDiffableReaders() {
logger.warn("testPluggableDiffableReaders");
Map<String, DiffableReader> readers = engine.getReaders();
Assert.assertNotNull(readers);
Assert.assertTrue(readers.size() > 0);
Assert.assertNotNull(readers.get("VCF"));
for ( Map.Entry<String, DiffableReader> e : engine.getReaders().entrySet() ) {
logger.warn("Found diffable reader: " + e.getKey());
Assert.assertEquals(e.getValue().getName(), e.getKey());
Assert.assertEquals(e.getValue(), engine.getReader(e.getKey()));
}
}
private static void testLeaf(DiffNode rec, String field, Object expected) {
DiffElement value = rec.getElement(field);
Assert.assertNotNull(value, "Expected to see leaf named " + field + " in rec " + rec);
Assert.assertEquals(value.getValue().getValue(), expected, "Expected to leaf named " + field + " to have value " + expected + " in rec " + rec);
}
@Test(enabled = true, dependsOnMethods = "testPluggableDiffableReaders")
public void testVCF1() {
logger.warn("testVCF1");
DiffableReader vcfReader = engine.getReader("VCF");
Assert.assertTrue(vcfReader.canRead(vcfFile));
Assert.assertFalse(vcfReader.canRead(bamFile));
DiffElement diff = vcfReader.readFromFile(vcfFile, -1);
Assert.assertNotNull(diff);
Assert.assertEquals(diff.getName(), vcfFile.getName());
Assert.assertSame(diff.getParent(), DiffElement.ROOT);
DiffNode node = diff.getValueAsNode();
Assert.assertEquals(node.getElements().size(), 9);
// chr1 2646 rs62635284 G A 0.15 PASS AC=2;AF=1.00;AN=2 GT:AD:DP:GL:GQ 1/1:53,75:3:-12.40,-0.90,-0.00:9.03
DiffNode rec1 = node.getElement("chr1:2646").getValueAsNode();
testLeaf(rec1, "CHROM", "chr1");
testLeaf(rec1, "POS", 2646);
testLeaf(rec1, "ID", "rs62635284");
testLeaf(rec1, "REF", Allele.create("G", true));
testLeaf(rec1, "ALT", new HashSet<Allele>(Arrays.asList(Allele.create("A"))));
testLeaf(rec1, "QUAL", 0.15);
testLeaf(rec1, "FILTER", Collections.<Object>emptySet());
testLeaf(rec1, "AC", "2");
testLeaf(rec1, "AF", "1.00");
testLeaf(rec1, "AN", "2");
}
@Test(enabled = true, dependsOnMethods = "testPluggableDiffableReaders")
public void testBAM() {
logger.warn("testBAM");
DiffableReader bamReader = engine.getReader("BAM");
Assert.assertTrue(bamReader.canRead(bamFile));
Assert.assertFalse(bamReader.canRead(vcfFile));
DiffElement diff = bamReader.readFromFile(bamFile, -1);
Assert.assertNotNull(diff);
Assert.assertEquals(diff.getName(), bamFile.getName());
Assert.assertSame(diff.getParent(), DiffElement.ROOT);
DiffNode node = diff.getValueAsNode();
Assert.assertEquals(node.getElements().size(), 33);
// 30PPJAAXX090125:1:42:512:1817#0 99 chr1 200 0 76M =
// 255 -130 ACCCTAACCCTAACCCTAACCCTAACCATAACCCTAAGACTAACCCTAAACCTAACCCTCATAATCGAAATACAAC
// BBBBC@C?AABCBB<63>=B@>+B9-9+)2B8,+@327B5A>90((>-+''3?(/'''A)(''19('7.,**%)3:
// PG:Z:0 RG:Z:exampleBAM.bam SM:Z:exampleBAM.bam
DiffNode rec1 = node.getElement("30PPJAAXX090125:1:42:512:1817#0_1").getValueAsNode();
testLeaf(rec1, "NAME", "30PPJAAXX090125:1:42:512:1817#0");
testLeaf(rec1, "FLAGS", 99);
testLeaf(rec1, "RNAME", "chr1");
testLeaf(rec1, "POS", 200);
testLeaf(rec1, "MAPQ", 0);
testLeaf(rec1, "CIGAR", "76M");
testLeaf(rec1, "RNEXT", "chr1");
testLeaf(rec1, "PNEXT", 255);
testLeaf(rec1, "TLEN", -130);
testLeaf(rec1, "SEQ", "ACCCTAACCCTAACCCTAACCCTAACCATAACCCTAAGACTAACCCTAAACCTAACCCTCATAATCGAAATACAAC");
testLeaf(rec1, "QUAL", "BBBBC@C?AABCBB<63>=B@>+B9-9+)2B8,+@327B5A>90((>-+''3?(/'''A)(''19('7.,**%)3:");
testLeaf(rec1, "PG", "0");
testLeaf(rec1, "RG", "exampleBAM.bam");
testLeaf(rec1, "SM", "exampleBAM.bam");
}
}

95
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/*
* Copyright (c) 2011, The Broad Institute
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
* OTHER DEALINGS IN THE SOFTWARE.
*/
// our package
package org.broadinstitute.sting.gatk.walkers.diffengine;
// the imports for unit testing.
import org.broadinstitute.sting.BaseTest;
import org.testng.Assert;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.DataProvider;
import org.testng.annotations.Test;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collections;
import java.util.List;
/**
* Basic unit test for DifferableReaders in reduced reads
*/
public class DifferenceUnitTest extends BaseTest {
// --------------------------------------------------------------------------------
//
// testing routines
//
// --------------------------------------------------------------------------------
private class DifferenceTest extends TestDataProvider {
public DiffElement tree1, tree2;
public String difference;
private DifferenceTest(String tree1, String tree2, String difference) {
this(DiffNode.fromString(tree1), DiffNode.fromString(tree2), difference);
}
private DifferenceTest(DiffElement tree1, DiffElement tree2, String difference) {
super(DifferenceTest.class);
this.tree1 = tree1;
this.tree2 = tree2;
this.difference = difference;
}
public String toString() {
return String.format("tree1=%s tree2=%s diff=%s",
tree1 == null ? "null" : tree1.toOneLineString(),
tree2 == null ? "null" : tree2.toOneLineString(),
difference);
}
}
@DataProvider(name = "data")
public Object[][] createTrees() {
new DifferenceTest("A=X", "A=Y", "A:X!=Y");
new DifferenceTest("A=Y", "A=X", "A:Y!=X");
new DifferenceTest(DiffNode.fromString("A=X"), null, "A:X!=MISSING");
new DifferenceTest(null, DiffNode.fromString("A=X"), "A:MISSING!=X");
return DifferenceTest.getTests(DifferenceTest.class);
}
@Test(enabled = true, dataProvider = "data")
public void testDiffToString(DifferenceTest test) {
logger.warn("Test tree1: " + (test.tree1 == null ? "null" : test.tree1.toOneLineString()));
logger.warn("Test tree2: " + (test.tree2 == null ? "null" : test.tree2.toOneLineString()));
logger.warn("Test expected diff : " + test.difference);
SpecificDifference diff = new SpecificDifference(test.tree1, test.tree2);
logger.warn("Observed diffs : " + diff);
Assert.assertEquals(diff.toString(), test.difference, "Observed diff string " + diff + " not equal to expected difference string " + test.difference );
}
}

91
public/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java
View File

@ -19,9 +19,9 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
public void testCountCovariates1() {
HashMap<String, String> e = new HashMap<String, String>();
e.put( validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.bam", "7b5832d4b2a23b8ef2bb639eb59bfa88" );
e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SOLID.bam", "f4f8a49bb5764d2a8f61e055f64dcce4");
e.put( validationDataLocation + "NA19240.chr1.BFAST.SOLID.bam", "9c006f8e9fb5752b1c139f5a8cc7ea88");
e.put( validationDataLocation + "NA12873.454.SRP000031.2009_06.chr1.10_20mb.bam", "e6f7b4ab9aa291022e0ba8b7dbe4c77e" );
e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.bam", "570506533f079d738d70934dfe1c02cd" );
e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.bam", "e6b98af01c5a08e4954b79ec42db6fc3" );
for ( String parallelism : Arrays.asList("", " -nt 4")) {
for ( Map.Entry<String, String> entry : e.entrySet() ) {
@ -53,9 +53,9 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
public void testTableRecalibrator1() {
HashMap<String, String> e = new HashMap<String, String>();
e.put( validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.bam", "0278cce4cfdab869dc0c11d6852a984b" );
e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SOLID.bam", "344d4252143df8c2cce6b568747553a5");
e.put( validationDataLocation + "NA19240.chr1.BFAST.SOLID.bam", "6797d7ffa4ef6c48413719ba32696ccf");
e.put( validationDataLocation + "NA12873.454.SRP000031.2009_06.chr1.10_20mb.bam", "2bb3374dde131791d7638031ae3b3e10" );
e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.bam", "064c4a7bdd23974c3a9c5f924540df76" );
e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.bam", "1f9d8944b73169b367cb83b0d22e5432" );
for ( Map.Entry<String, String> entry : e.entrySet() ) {
String bam = entry.getKey();
@ -107,7 +107,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
@Test
public void testTableRecalibratorMaxQ70() {
HashMap<String, String> e = new HashMap<String, String>();
e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SOLID.bam", "344d4252143df8c2cce6b568747553a5" );
e.put( validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.bam", "0278cce4cfdab869dc0c11d6852a984b" );
for ( Map.Entry<String, String> entry : e.entrySet() ) {
String bam = entry.getKey();
@ -133,12 +133,10 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
}
}
@Test
public void testCountCovariatesSolidIndelsRemoveRefBias() {
HashMap<String, String> e = new HashMap<String, String>();
e.put( validationDataLocation + "NA19240.chr1.BFAST.SOLID.bam", "0a6cdb9611e5880ea6611205080aa267" );
e.put( validationDataLocation + "NA19240.chr1.BFAST.SOLID.bam", "c9ea5f995e1e2b7a5688533e678dcedc" );
for ( Map.Entry<String, String> entry : e.entrySet() ) {
String bam = entry.getKey();
@ -164,7 +162,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
@Test
public void testTableRecalibratorSolidIndelsRemoveRefBias() {
HashMap<String, String> e = new HashMap<String, String>();
e.put( validationDataLocation + "NA19240.chr1.BFAST.SOLID.bam", "9bc7e1ad223ba759fe5e8ddb4c07369c" );
e.put( validationDataLocation + "NA19240.chr1.BFAST.SOLID.bam", "993fae4270e7e1e15986f270acf247af" );
for ( Map.Entry<String, String> entry : e.entrySet() ) {
String bam = entry.getKey();
@ -189,13 +187,10 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
}
}
@Test
public void testCountCovariatesVCF() {
HashMap<String, String> e = new HashMap<String, String>();
e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SOLID.bam", "3700eaf567e4937f442fc777a226d6ad");
e.put( validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.bam", "170f0c3cc4b8d72c539136effeec9a16");
for ( Map.Entry<String, String> entry : e.entrySet() ) {
String bam = entry.getKey();
@ -219,7 +214,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
@Test
public void testCountCovariatesBED() {
HashMap<String, String> e = new HashMap<String, String>();
e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SOLID.bam", "6803891a3398821fc8a37e19ea8e5a00");
e.put( validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.bam", "b460478d9683e827784e42bc352db8bb");
for ( Map.Entry<String, String> entry : e.entrySet() ) {
String bam = entry.getKey();
@ -243,7 +238,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
@Test
public void testCountCovariatesVCFPlusDBsnp() {
HashMap<String, String> e = new HashMap<String, String>();
e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SOLID.bam", "f224c42fbc4026db973ccc91265ab5c7");
e.put( validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.bam", "a3d892bd60d8f679affda3c1e3af96c1");
for ( Map.Entry<String, String> entry : e.entrySet() ) {
String bam = entry.getKey();
@ -268,69 +263,10 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
}
}
@Test
public void testCountCovariatesNoReadGroups() {
HashMap<String, String> e = new HashMap<String, String>();
e.put( validationDataLocation + "NA12762.SOLID.SRP000031.2009_07.chr1.10_20mb.bam", "c024e03f019aeceaf364fa58c8295ad8" );
for ( Map.Entry<String, String> entry : e.entrySet() ) {
String bam = entry.getKey();
String md5 = entry.getValue();
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-R " + b36KGReference +
" --DBSNP " + GATKDataLocation + "dbsnp_129_b36.rod" +
" -T CountCovariates" +
" -I " + bam +
" -L 1:10,000,000-10,200,000" +
" -cov ReadGroupCovariate" +
" -cov QualityScoreCovariate" +
" -cov CycleCovariate" +
" -cov DinucCovariate" +
" --default_read_group DefaultReadGroup" +
" --default_platform illumina" +
" --solid_recal_mode SET_Q_ZERO" +
" -recalFile %s",
1, // just one output file
Arrays.asList(md5));
List<File> result = executeTest("testCountCovariatesNoReadGroups", spec).getFirst();
paramsFilesNoReadGroupTest.put(bam, result.get(0).getAbsolutePath());
}
}
@Test
public void testTableRecalibratorNoReadGroups() {
HashMap<String, String> e = new HashMap<String, String>();
e.put( validationDataLocation + "NA12762.SOLID.SRP000031.2009_07.chr1.10_20mb.bam", "1eefbe7ac0376fc1ed1392d85242171e" );
for ( Map.Entry<String, String> entry : e.entrySet() ) {
String bam = entry.getKey();
String md5 = entry.getValue();
String paramsFile = paramsFilesNoReadGroupTest.get(bam);
System.out.printf("PARAMS FOR %s is %s%n", bam, paramsFile);
if ( paramsFile != null ) {
WalkerTestSpec spec = new WalkerTestSpec(
"-R " + b36KGReference +
" -T TableRecalibration" +
" -I " + bam +
" -L 1:10,100,000-10,300,000" +
" -o %s" +
" --no_pg_tag" +
" --solid_recal_mode SET_Q_ZERO" +
" --default_read_group DefaultReadGroup" +
" --default_platform illumina" +
" -recalFile " + paramsFile,
1, // just one output file
Arrays.asList(md5));
executeTest("testTableRecalibratorNoReadGroups", spec);
}
}
}
@Test
public void testCountCovariatesNoIndex() {
HashMap<String, String> e = new HashMap<String, String>();
e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.noindex.bam", "cfc31bb6f51436d1c3b34f62bb801dc8" );
e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.noindex.bam", "284ccac1f8fe485e52c86333cac7c2d4" );
for ( Map.Entry<String, String> entry : e.entrySet() ) {
String bam = entry.getKey();
@ -356,7 +292,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
@Test
public void testTableRecalibratorNoIndex() {
HashMap<String, String> e = new HashMap<String, String>();
e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.noindex.bam", "83b848a16034c2fb423d1bb0f5be7784" );
e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.noindex.bam", "c167799c2d9cab815d7c9b23337f162e" );
for ( Map.Entry<String, String> entry : e.entrySet() ) {
String bam = entry.getKey();
@ -380,11 +316,10 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
}
}
@Test
public void testCountCovariatesFailWithoutDBSNP() {
HashMap<String, String> e = new HashMap<String, String>();
e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SOLID.bam", "");
e.put( validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.bam", "");
for ( Map.Entry<String, String> entry : e.entrySet() ) {
String bam = entry.getKey();