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Right aligning GATKReport numeric columns and updated MD5s in tests. 

PreQC parses file with spaces in sample names by using tabs only.
PostQC allows passing the file names for the evals so that flanks can be evaled.
BaseTest's network temp dir now adds the user name to the path so files aren't created in the root.
HybridSelectionPipeline:
- Updated to latest versions of reference data.
- Refactored Picard parsing code replacing YAML.
This commit is contained in:
Khalid Shakir 2011-12-05 23:04:33 -05:00
parent 1ba03a5e72
commit 677bea0abd
16 changed files with 143 additions and 582 deletions
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44
public/java/src/org/broadinstitute/sting/gatk/report/GATKReportColumn.java
View File

@ -1,6 +1,8 @@
package org.broadinstitute.sting.gatk.report;
import java.util.TreeMap;
import org.apache.commons.lang.math.NumberUtils;
import java.util.*;
/**
* Holds values for a column in a GATK report table
@ -16,12 +18,9 @@ public class GATKReportColumn extends TreeMap<Object, Object> {
*
* @param columnName the name of the column
* @param defaultValue the default value of the column
* @param display if true, the column will be displayed in the final output
* @param display if true, the column will be displayed in the final output
* @param format format string
*/
public GATKReportColumn(String columnName, Object defaultValue, boolean display) {
this(columnName, defaultValue, display, null);
}
public GATKReportColumn(String columnName, Object defaultValue, boolean display, String format) {
this.columnName = columnName;
this.defaultValue = defaultValue;
@ -77,22 +76,47 @@ public class GATKReportColumn extends TreeMap<Object, Object> {
/**
* Get the display width for this column. This allows the entire column to be displayed with the appropriate, fixed width.
* @return the width of this column
* @return the format string for this column
*/
public int getColumnWidth() {
public GATKReportColumnFormat getColumnFormat() {
int maxWidth = columnName.length();
GATKReportColumnFormat.Alignment alignment = GATKReportColumnFormat.Alignment.RIGHT;
for (Object obj : this.values()) {
if (obj != null) {
int width = formatValue(obj).length();
String formatted = formatValue(obj);
int width = formatted.length();
if (width > maxWidth) {
maxWidth = width;
}
if (alignment == GATKReportColumnFormat.Alignment.RIGHT) {
if (!isRightAlign(formatted)) {
alignment = GATKReportColumnFormat.Alignment.LEFT;
}
}
}
}
return maxWidth;
return new GATKReportColumnFormat(maxWidth, alignment);
}
private static final Collection<String> RIGHT_ALIGN_STRINGS = Arrays.asList(
"null",
"NA",
String.valueOf(Double.POSITIVE_INFINITY),
String.valueOf(Double.NEGATIVE_INFINITY),
String.valueOf(Double.NaN));
/**
* Check if the value can be right aligned. Does not trim the values before checking if numeric since it assumes
* the spaces mean that the value is already padded.
* @param value to check
* @return true if the value is a right alignable
*/
protected static boolean isRightAlign(String value) {
return value == null || RIGHT_ALIGN_STRINGS.contains(value) || NumberUtils.isNumber(value);
}
/**

50
public/java/src/org/broadinstitute/sting/pipeline/PipelineSample.java → public/java/src/org/broadinstitute/sting/gatk/report/GATKReportColumnFormat.java
View File

@ -1,5 +1,5 @@
/*
* Copyright (c) 2010, The Broad Institute
* 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
@ -22,41 +22,41 @@
* OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.pipeline;
import java.io.File;
import java.util.Map;
import java.util.TreeMap;
package org.broadinstitute.sting.gatk.report;
/**
* Java bean defining a sample for a pipeline.
* Column width and left/right alignment.
*/
public class PipelineSample {
private String id;
private Map<String, File> bamFiles = new TreeMap<String, File>();
private Map<String, String> tags = new TreeMap<String, String>();
public class GATKReportColumnFormat {
public static enum Alignment { LEFT, RIGHT }
public int width;
public Alignment alignment;
public String getId() {
return id;
public GATKReportColumnFormat(int width, Alignment alignment) {
this.width = width;
this.alignment = alignment;
}
public void setId(String id) {
this.id = id;
public int getWidth() {
return width;
}
public Map<String, File> getBamFiles() {
return bamFiles;
public Alignment getAlignment() {
return alignment;
}
public void setBamFiles(Map<String, File> bamFiles) {
this.bamFiles = bamFiles;
public String getNameFormat() {
return "%-" + width + "s";
}
public Map<String, String> getTags() {
return tags;
}
public void setTags(Map<String, String> tags) {
this.tags = tags;
public String getValueFormat() {
switch (alignment) {
case LEFT:
return "%-" + width + "s";
case RIGHT:
return "%" + width + "s";
default:
throw new UnsupportedOperationException("Unknown alignment: " + alignment);
}
}
}

11
public/java/src/org/broadinstitute/sting/gatk/report/GATKReportTable.java
View File

@ -608,12 +608,9 @@ public class GATKReportTable {
*/
public void write(PrintStream out) {
// Get the column widths for everything
HashMap<String, String> columnWidths = new HashMap<String, String>();
HashMap<String, GATKReportColumnFormat> columnFormats = new HashMap<String, GATKReportColumnFormat>();
for (String columnName : columns.keySet()) {
int width = columns.get(columnName).getColumnWidth();
String format = "%-" + String.valueOf(width) + "s";
columnWidths.put(columnName, format);
columnFormats.put(columnName, columns.get(columnName).getColumnFormat());
}
String primaryKeyFormat = "%-" + getPrimaryKeyColumnWidth() + "s";
@ -630,7 +627,7 @@ public class GATKReportTable {
for (String columnName : columns.keySet()) {
if (columns.get(columnName).isDisplayable()) {
if (needsPadding) { out.printf(" "); }
out.printf(columnWidths.get(columnName), columnName);
out.printf(columnFormats.get(columnName).getNameFormat(), columnName);
needsPadding = true;
}
@ -650,7 +647,7 @@ public class GATKReportTable {
if (columns.get(columnName).isDisplayable()) {
if (needsPadding) { out.printf(" "); }
String value = columns.get(columnName).getStringValue(primaryKey);
out.printf(columnWidths.get(columnName), value);
out.printf(columnFormats.get(columnName).getValueFormat(), value);
needsPadding = true;
}

4
public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/GATKReportDiffableReader.java
View File

@ -31,7 +31,6 @@ import org.broadinstitute.sting.gatk.report.GATKReportTable;
import java.io.File;
import java.io.FileReader;
import java.io.IOException;
import java.util.Map;
/**
@ -68,7 +67,8 @@ public class GATKReportDiffableReader implements DiffableReader {
for ( GATKReportColumn column : table.getColumns().values() ) {
DiffNode columnRoot = DiffNode.empty(column.getColumnName(), tableRoot);
columnRoot.add("Width", column.getColumnWidth());
columnRoot.add("Width", column.getColumnFormat().getWidth());
// NOTE: as the values are trimmed during parsing left/right alignment is not currently preserved
columnRoot.add("Displayable", column.isDisplayable());
int n = 1;

62
public/java/src/org/broadinstitute/sting/pipeline/Pipeline.java
View File

@ -1,62 +0,0 @@
/*
* Copyright (c) 2010, The Broad Institute
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
* OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.pipeline;
import java.util.ArrayList;
import java.util.List;
/**
* Java bean for storing a list of samples for a pipeline.
*
* NOTE: This class is used in a very similar way to the classes in
* org.broadinstitute.sting.gatk.datasources.sample.
*
* Both store / load sample information from the file system as YAML.
*
* This package will likely be refactored to share common functionality
* with the other at a future date as requirements coalesce.
*
* - kshakir September 22, 2010
*/
public class Pipeline {
private PipelineProject project = new PipelineProject();
private List<PipelineSample> samples = new ArrayList<PipelineSample>();
public PipelineProject getProject() {
return project;
}
public void setProject(PipelineProject project) {
this.project = project;
}
public List<PipelineSample> getSamples() {
return samples;
}
public void setSamples(List<PipelineSample> samples) {
this.samples = samples;
}
}

115
public/java/src/org/broadinstitute/sting/pipeline/PipelineProject.java
View File

@ -1,115 +0,0 @@
/*
* Copyright (c) 2010, The Broad Institute
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
* OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.pipeline;
import java.io.File;
import java.util.Map;
import java.util.TreeMap;
/**
* Java bean defining the project for a pipeline.
*/
public class PipelineProject {
private String name;
private File referenceFile;
private File intervalList;
private File genotypeDbsnp;
private File evalDbsnp;
private File refseqTable;
private Map<String, String> tags = new TreeMap<String, String>();
public String getName() {
return name;
}
public void setName(String name) {
this.name = name;
}
public File getIntervalList() {
return intervalList;
}
public void setIntervalList(File intervalList) {
this.intervalList = intervalList;
}
public File getReferenceFile() {
return referenceFile;
}
public void setReferenceFile(File referenceFile) {
this.referenceFile = referenceFile;
}
public File getGenotypeDbsnp() {
return genotypeDbsnp;
}
public void setGenotypeDbsnp(File genotypeDbsnp) {
this.genotypeDbsnp = genotypeDbsnp;
}
public String getGenotypeDbsnpType() {
return getDbsnpType(genotypeDbsnp);
}
public File getEvalDbsnp() {
return evalDbsnp;
}
public void setEvalDbsnp(File evalDbsnp) {
this.evalDbsnp = evalDbsnp;
}
public String getEvalDbsnpType() {
return getDbsnpType(evalDbsnp);
}
public File getRefseqTable() {
return refseqTable;
}
public void setRefseqTable(File refseqTable) {
this.refseqTable = refseqTable;
}
public Map<String, String> getTags() {
return tags;
}
public void setTags(Map<String, String> tags) {
this.tags = tags;
}
private String getDbsnpType(File file) {
if (file == null)
return null;
else if (file.getName().toLowerCase().endsWith(".vcf"))
return "vcf";
else
return "dbsnp";
}
}

23
public/java/src/org/broadinstitute/sting/utils/io/IOUtils.java
View File

@ -362,4 +362,27 @@ public class IOUtils {
org.apache.commons.io.IOUtils.closeQuietly(outputStream);
}
}
/**
* Returns a file throwing a UserException if the file cannot be read.
* @param path File path
* @return LineIterator
*/
public static LineIterator lineIterator(String path) {
return lineIterator(new File(path));
}
/**
* Returns a file throwing a UserException if the file cannot be read.
* @param file File
* @return LineIterator
*/
public static LineIterator lineIterator(File file) {
try {
return FileUtils.lineIterator(file);
} catch (IOException e) {
throw new UserException.CouldNotReadInputFile(file, e);
}
}
}

52
public/java/src/org/broadinstitute/sting/utils/yaml/FieldOrderComparator.java
View File

@ -1,52 +0,0 @@
/*
* Copyright (c) 2010, The Broad Institute
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
* OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.utils.yaml;
import org.yaml.snakeyaml.introspector.Property;
import java.lang.reflect.Field;
import java.util.ArrayList;
import java.util.Comparator;
import java.util.List;
/**
* Orders properties based on the order of the fields in the Java Bean.
*/
class FieldOrderComparator implements Comparator<Property> {
private final List<String> propertyOrder;
public FieldOrderComparator(Class<?> clazz) {
propertyOrder = new ArrayList<String>();
for (Field field : clazz.getDeclaredFields())
propertyOrder.add(field.getName());
}
@Override
public int compare(Property one, Property two) {
Integer index1 = propertyOrder.indexOf(one.getName());
Integer index2 = propertyOrder.indexOf(two.getName());
return index1.compareTo(index2);
}
}

88
public/java/src/org/broadinstitute/sting/utils/yaml/StingYamlRepresenter.java
View File

@ -1,88 +0,0 @@
/*
* Copyright (c) 2010, The Broad Institute
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
* OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.utils.yaml;
import org.yaml.snakeyaml.introspector.Property;
import org.yaml.snakeyaml.nodes.*;
import org.yaml.snakeyaml.representer.Represent;
import org.yaml.snakeyaml.representer.Representer;
import java.beans.IntrospectionException;
import java.io.File;
import java.util.Set;
import java.util.TreeSet;
/**
* A representer with Sting prefered settings.
* - Fields are ordered in the order of the class declaration, instead of alphabetically.
* - Empty maps and sequences are not output.
* - Files are converted to their absolute paths.
*/
public class StingYamlRepresenter extends Representer {
public StingYamlRepresenter() {
super();
this.representers.put(File.class, new RepresentFile());
}
@Override
protected Set<Property> getProperties(Class<?> type) throws IntrospectionException {
TreeSet<Property> properties = new TreeSet<Property>(new FieldOrderComparator(type));
properties.addAll(super.getProperties(type));
return properties;
}
@Override
protected NodeTuple representJavaBeanProperty(Object javaBean, Property property,
Object propertyValue, Tag customTag) {
NodeTuple tuple = super.representJavaBeanProperty(javaBean, property, propertyValue, customTag);
Node valueNode = tuple.getValueNode();
if (Tag.NULL.equals(valueNode.getTag())) {
return null;// skip 'null' values
}
if (valueNode instanceof CollectionNode) {
if (Tag.SEQ.equals(valueNode.getTag())) {
SequenceNode seq = (SequenceNode) valueNode;
if (seq.getValue().isEmpty()) {
return null;// skip empty lists
}
}
if (Tag.MAP.equals(valueNode.getTag())) {
MappingNode seq = (MappingNode) valueNode;
if (seq.getValue().isEmpty()) {
return null;// skip empty maps
}
}
}
return tuple;
}
private class RepresentFile implements Represent {
@Override
public Node representData(Object o) {
return StingYamlRepresenter.this.representScalar(Tag.STR, ((File)o).getPath());
}
}
}

107
public/java/src/org/broadinstitute/sting/utils/yaml/YamlUtils.java
View File

@ -1,107 +0,0 @@
/*
* Copyright (c) 2010, The Broad Institute
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
* OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.utils.yaml;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.yaml.snakeyaml.DumperOptions;
import org.yaml.snakeyaml.Yaml;
import org.yaml.snakeyaml.constructor.Constructor;
import org.yaml.snakeyaml.nodes.Tag;
import org.yaml.snakeyaml.representer.Representer;
import java.io.File;
import java.io.FileReader;
import java.io.FileWriter;
import java.io.IOException;
/**
* A collection of utilities for operating on YAML.
* Uses the FLOW style of writing YAML, versus the BLOCK style.
* By default uses a representer that prunes empty lists and maps.
*/
public class YamlUtils {
private static Representer representer = new StingYamlRepresenter();
private static DumperOptions options = new DumperOptions();
static {
options.setCanonical(false);
options.setExplicitRoot(Tag.MAP);
options.setDefaultFlowStyle(DumperOptions.FlowStyle.FLOW);
options.setPrettyFlow(true);
}
/**
* Serialize an object to the file system.
* @param o Object to serialize.
* @param file Path to write the serialized YAML.
*/
public static void dump(Object o, File file) {
dump(o, file, representer);
}
/**
* Serialize an object to the file system.
* @param o Object to serialize.
* @param file Path to write the serialized YAML.
* @param representer Custom representer with rules on how to serialize YAML.
*/
public static void dump(Object o, File file, Representer representer) {
Constructor constructor = new Constructor(o.getClass());
Yaml yaml = new Yaml(constructor, representer, options);
try {
yaml.dump(o, new FileWriter(file));
} catch (IOException ioe) {
throw new UserException.CouldNotCreateOutputFile(file, ioe);
}
}
/**
* Deserialize an object from the file system.
* @param clazz Clazz to deserialize.
* @param file Path to read the deserialized YAML.
* @return Object deserialized from the file system.
*/
public static <T> T load(Class<? extends T> clazz, File file) {
return load(clazz, file, representer);
}
/**
* Deserialize an object from the file system.
* @param clazz Clazz to deserialize.
* @param file Path to read the deserialized YAML.
* @param representer Custom representer with rules on how to deserialize YAML.
* @return Object deserialized from the file system.
*/
@SuppressWarnings("unchecked")
public static <T> T load(Class<? extends T> clazz, File file, Representer representer) {
Constructor constructor = new Constructor(clazz);
Yaml yaml = new Yaml(constructor, representer, options);
try {
return (T) yaml.load(new FileReader(file));
} catch (IOException ioe) {
throw new UserException.CouldNotReadInputFile(file, ioe);
}
}
}

3
public/java/test/org/broadinstitute/sting/BaseTest.java
View File

@ -78,7 +78,7 @@ public abstract class BaseTest {
public static final String hg19Intervals = intervalsLocation + "whole_exome_agilent_1.1_refseq_plus_3_boosters.Homo_sapiens_assembly19.targets.interval_list";
public static final String hg19Chr20Intervals = intervalsLocation + "whole_exome_agilent_1.1_refseq_plus_3_boosters.Homo_sapiens_assembly19.targets.chr20.interval_list";
public static final String networkTempDir = "/broad/shptmp/";
public static final String networkTempDir = "/broad/shptmp/" + System.getProperty("user.name") + "/";
public static final File networkTempDirFile = new File(networkTempDir);
public static final File testDirFile = new File("public/testdata/");
@ -235,6 +235,7 @@ public abstract class BaseTest {
*/
public static File createNetworkTempFile(String name, String extension) {
try {
FileUtils.forceMkdir(networkTempDirFile);
File file = File.createTempFile(name, extension, networkTempDirFile);
file.deleteOnExit();
return file;

28
public/java/test/org/broadinstitute/sting/gatk/report/GATKReportUnitTest.java
View File

@ -26,6 +26,7 @@ package org.broadinstitute.sting.gatk.report;
import org.broadinstitute.sting.BaseTest;
import org.testng.Assert;
import org.testng.annotations.DataProvider;
import org.testng.annotations.Test;
public class GATKReportUnitTest extends BaseTest {
@ -45,4 +46,31 @@ public class GATKReportUnitTest extends BaseTest {
Object validationReportPK = countVariants.getPrimaryKey("none.eval.none.known");
Assert.assertEquals(validationReport.get(validationReportPK, "sensitivity"), "NaN");
}
@DataProvider(name = "rightAlignValues")
public Object[][] getRightAlignValues() {
return new Object[][] {
new Object[] {null, true},
new Object[] {"null", true},
new Object[] {"NA", true},
new Object[] {"0", true},
new Object[] {"0.0", true},
new Object[] {"-0", true},
new Object[] {"-0.0", true},
new Object[] {String.valueOf(Long.MAX_VALUE), true},
new Object[] {String.valueOf(Long.MIN_VALUE), true},
new Object[] {String.valueOf(Float.MIN_NORMAL), true},
new Object[] {String.valueOf(Double.MAX_VALUE), true},
new Object[] {String.valueOf(Double.MIN_VALUE), true},
new Object[] {String.valueOf(Double.POSITIVE_INFINITY), true},
new Object[] {String.valueOf(Double.NEGATIVE_INFINITY), true},
new Object[] {String.valueOf(Double.NaN), true},
new Object[] {"hello", false}
};
}
@Test(dataProvider = "rightAlignValues")
public void testIsRightAlign(String value, boolean expected) {
Assert.assertEquals(GATKReportColumn.isRightAlign(value), expected, "right align of '" + value + "'");
}
}

4
public/java/test/org/broadinstitute/sting/gatk/walkers/diffengine/DiffObjectsIntegrationTest.java
View File

@ -50,8 +50,8 @@ public class DiffObjectsIntegrationTest extends WalkerTest {
@DataProvider(name = "data")
public Object[][] createData() {
new TestParams(testDir + "diffTestMaster.vcf", testDir + "diffTestTest.vcf", "ed377322c615abc7dceb97025076078d");
new TestParams(testDir + "exampleBAM.bam", testDir + "exampleBAM.simple.bam", "02e46f5d2ebb3d49570850595b3f792e");
new TestParams(testDir + "diffTestMaster.vcf", testDir + "diffTestTest.vcf", "da3dc85a0e35a9aade5520591891b4fa");
new TestParams(testDir + "exampleBAM.bam", testDir + "exampleBAM.simple.bam", "7dc8200730313e6753237a696296fb73");
return TestParams.getTests(TestParams.class);
}

44
public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java
View File

@ -30,7 +30,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
"-o %s"
),
1,
Arrays.asList("abe943d1aac120d7e75b9b9e5dac2399")
Arrays.asList("f909fd8374f663e983b9b3fda4cf5cf1")
);
executeTest("testFunctionClassWithSnpeff", spec);
}
@ -50,7 +50,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
"-o %s"
),
1,
Arrays.asList("5fd9624c7a35ffb79d0feb1e233fc757")
Arrays.asList("081fcaa532c7ba8f23da739389e6f7c3")
);
executeTest("testStratifySamplesAndExcludeMonomorphicSites", spec);
}
@ -70,7 +70,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
"-o %s"
),
1,
Arrays.asList("4a8765cd02d36e63f6d0f0c10a6c674b")
Arrays.asList("b3852f84d07c270b8a12874083c3e31b")
);
executeTest("testFundamentalsCountVariantsSNPsandIndels", spec);
}
@ -91,7 +91,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
"-o %s"
),
1,
Arrays.asList("4106ab8f742ad1c3138c29220151503c")
Arrays.asList("cf70468b5ebaec408419da69b0a7fcb9")
);
executeTest("testFundamentalsCountVariantsSNPsandIndelsWithNovelty", spec);
}
@ -113,7 +113,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
"-o %s"
),
1,
Arrays.asList("6cee3a8d68307a118944f2df5401ac89")
Arrays.asList("5e3b8b85acfc41365c8208c23abf746b")
);
executeTest("testFundamentalsCountVariantsSNPsandIndelsWithNoveltyAndFilter", spec);
}
@ -134,7 +134,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
"-o %s"
),
1,
Arrays.asList("af5dd27354d5dfd0d2fe03149af09b55")
Arrays.asList("ccdbc50d30ece6d0d3b199c397f03ed3")
);
executeTest("testFundamentalsCountVariantsSNPsandIndelsWithCpG", spec);
}
@ -155,7 +155,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
"-o %s"
),
1,
Arrays.asList("062a231e203671e19aa9c6507710d762")
Arrays.asList("95c690d5af8ed51573eb2f0503dcd9c2")
);
executeTest("testFundamentalsCountVariantsSNPsandIndelsWithFunctionalClass", spec);
}
@ -176,7 +176,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
"-o %s"
),
1,
Arrays.asList("75abdd2b17c0a5e04814b6969a3d4d7e")
Arrays.asList("8e8547eb38b34bec0095b0500fd9641d")
);
executeTest("testFundamentalsCountVariantsSNPsandIndelsWithDegeneracy", spec);
}
@ -197,7 +197,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
"-o %s"
),
1,
Arrays.asList("bdbb5f8230a4a193058750c5e506c733")
Arrays.asList("158a4651a656aea7f84c79548f6fe519")
);
executeTest("testFundamentalsCountVariantsSNPsandIndelsWithSample", spec);
}
@ -220,7 +220,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
"-o %s"
),
1,
Arrays.asList("f076120da22930294840fcc396f5f141")
Arrays.asList("76c8a0b28d2993644120f7afa5833ab2")
);
executeTest("testFundamentalsCountVariantsSNPsandIndelsWithJexlExpression", spec);
}
@ -245,7 +245,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
"-o %s"
),
1,
Arrays.asList("69201f4a2a7a44b38805a4aeeb8830b6")
Arrays.asList("34682193f458b93b39efac00b4fc6723")
);
executeTest("testFundamentalsCountVariantsSNPsandIndelsWithMultipleJexlExpressions", spec);
}
@ -264,7 +264,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
"-o %s"
),
1,
Arrays.asList("c3bd3cb6cfb21a8c2b4d5f69104bf6c2")
Arrays.asList("52f6655f1532bcea24b402010d93ce73")
);
executeTest("testFundamentalsCountVariantsNoCompRod", spec);
}
@ -277,7 +277,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
" --eval " + validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf" +
" --comp:comp_genotypes,VCF3 " + validationDataLocation + "yri.trio.gatk.ug.head.vcf";
WalkerTestSpec spec = new WalkerTestSpec(withSelect(tests, "DP < 50", "DP50") + " " + extraArgs + " -ST CpG -o %s",
1, Arrays.asList("861f94e3237d62bd5bc00757319241f7"));
1, Arrays.asList("6fa6e77f149de3d13c31d410a98043a0"));
executeTestParallel("testSelect1", spec);
}
@ -287,14 +287,14 @@ public class VariantEvalIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec(cmdRoot + " -ST CpG --eval:VCF3 " + validationDataLocation + vcfFile + " --comp:VCF3 " + validationDataLocation + "GenotypeConcordanceComp.vcf -noEV -EV GenotypeConcordance -o %s",
1,
Arrays.asList("96f27163f16bb945f19c6623cd6db34e"));
Arrays.asList("9a56c20a7b9a554a7b530f2cb1dd776d"));
executeTestParallel("testVEGenotypeConcordance" + vcfFile, spec);
}
@Test
public void testCompVsEvalAC() {
String extraArgs = "-T VariantEval -R "+b36KGReference+" -o %s -ST CpG -EV GenotypeConcordance --eval:evalYRI,VCF3 " + validationDataLocation + "yri.trio.gatk.ug.very.few.lines.vcf --comp:compYRI,VCF3 " + validationDataLocation + "yri.trio.gatk.fake.genotypes.ac.test.vcf";
WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("955c33365e017679047fabec0f14d5e0"));
WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("aeff16bb43be03a2a7e5b9d0108b4999"));
executeTestParallel("testCompVsEvalAC",spec);
}
@ -312,7 +312,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
@Test
public void testCompOverlap() {
String extraArgs = "-T VariantEval -R " + b37KGReference + " -L " + validationDataLocation + "VariantEval/pacbio.hg19.intervals --comp:comphapmap " + comparisonDataLocation + "Validated/HapMap/3.3/genotypes_r27_nr.b37_fwd.vcf --eval " + validationDataLocation + "VariantEval/pacbio.ts.recalibrated.vcf -noEV -EV CompOverlap -sn NA12878 -noST -ST Novelty -o %s";
WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("fb7d989e44bd74c5376cb5732f9f3f64"));
WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("9002023b8aa8fc2c9aac58b8a79bca1e"));
executeTestParallel("testCompOverlap",spec);
}
@ -324,7 +324,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
" --dbsnp " + b37dbSNP132 +
" --eval:evalBI " + validationDataLocation + "VariantEval/ALL.20100201.chr20.bi.sites.vcf" +
" -noST -ST Novelty -o %s";
WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("da5bcb305c5ef207ce175821efdbdefd"));
WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("38ed9d216bd43f1cceceea24146fae38"));
executeTestParallel("testEvalTrackWithoutGenotypes",spec);
}
@ -336,7 +336,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
" --eval:evalBI " + validationDataLocation + "VariantEval/ALL.20100201.chr20.bi.sites.vcf" +
" --eval:evalBC " + validationDataLocation + "VariantEval/ALL.20100201.chr20.bc.sites.vcf" +
" -noST -ST Novelty -o %s";
WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("fde839ece1442388f21a2f0b936756a8"));
WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("453c6b1f7165913e8b1787e22bac1281"));
executeTestParallel("testMultipleEvalTracksWithoutGenotypes",spec);
}
@ -353,13 +353,13 @@ public class VariantEvalIntegrationTest extends WalkerTest {
" -noST -noEV -ST Novelty -EV CompOverlap" +
" -o %s";
WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("1efae6b3b88c752b771e0c8fae24464e"));
WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("61052c19211e7eb61fbbb62db5e40b56"));
executeTestParallel("testMultipleCompTracks",spec);
}
@Test
public void testPerSampleAndSubsettedSampleHaveSameResults1() {
String md5 = "bc9bcabc3105e2515d9a2d41506d2de1";
String md5 = "0edded1cd578db62fa296c99c34a909d";
WalkerTestSpec spec = new WalkerTestSpec(
buildCommandLine(
@ -414,7 +414,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
"-o %s"
),
1,
Arrays.asList("e53546243250634fc03e83b4e61ec55f")
Arrays.asList("ee22604616b3e9fc48a6dcbbf73a056d")
);
executeTest("testAlleleCountStrat", spec);
}
@ -435,7 +435,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
"-o %s"
),
1,
Arrays.asList("c8086f0525bc13e666afeb670c2e13ae")
Arrays.asList("240369cd651c77e05e8a6659f4a6237e")
);
executeTest("testIntervalStrat", spec);
}

2
public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VCFStreamingIntegrationTest.java
View File

@ -98,7 +98,7 @@ public class VCFStreamingIntegrationTest extends WalkerTest {
" -EV CompOverlap -noEV -noST" +
" -o %s",
1,
Arrays.asList("1f7ed8c0f671dd227ab764624ef0d64c")
Arrays.asList("addf5f4596ddacef40808f6d3d281111")
);
executeTest("testVCFStreamingChain", selectTestSpec);

88
public/java/test/org/broadinstitute/sting/pipeline/PipelineUnitTest.java
View File

@ -1,88 +0,0 @@
/*
* Copyright (c) 2010, The Broad Institute
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
* OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.pipeline;
import org.broadinstitute.sting.pipeline.Pipeline;
import org.broadinstitute.sting.pipeline.PipelineSample;
import org.testng.Assert;
import org.broadinstitute.sting.utils.yaml.YamlUtils;
import org.testng.annotations.Test;
import java.io.File;
import java.util.Map;
public class PipelineUnitTest {
@Test
public void testDumpAndLoad() throws Exception {
Pipeline pipeline = new Pipeline();
pipeline.getProject().setName("PRJ_NAME");
pipeline.getProject().setReferenceFile(new File("my.fasta"));
pipeline.getProject().setGenotypeDbsnp(new File("my.vcf"));
pipeline.getProject().setEvalDbsnp(new File("my.dbsnp"));
pipeline.getProject().getTags().put("testProjectTag", "project value here");
PipelineSample sample = new PipelineSample();
sample.setId("SMP_ID");
sample.getBamFiles().put("recalibrated", new File("recalibrated.bam"));
sample.getBamFiles().put("cleaned", new File("/absolute/path/to/cleaned.bam"));
sample.getTags().put("testSampleTag", "sample value here");
pipeline.getSamples().add(sample);
File file = File.createTempFile("testDumpAndLoad", ".yaml");
YamlUtils.dump(pipeline, file);
Pipeline pipelineLoad = YamlUtils.load(Pipeline.class, file);
Assert.assertEquals(pipelineLoad.getProject().getName(), pipeline.getProject().getName());
Assert.assertEquals(pipeline.getProject().getReferenceFile(), pipelineLoad.getProject().getReferenceFile());
Assert.assertEquals(pipeline.getProject().getIntervalList(), pipelineLoad.getProject().getIntervalList());
Assert.assertEquals(pipeline.getProject().getGenotypeDbsnp(), pipelineLoad.getProject().getGenotypeDbsnp());
Assert.assertEquals(pipeline.getProject().getGenotypeDbsnpType(), pipelineLoad.getProject().getGenotypeDbsnpType());
Assert.assertEquals(pipeline.getProject().getEvalDbsnp(), pipelineLoad.getProject().getEvalDbsnp());
Assert.assertEquals(pipeline.getProject().getEvalDbsnpType(), pipelineLoad.getProject().getEvalDbsnpType());
Assert.assertEquals(pipelineLoad.getProject().getTags().size(), pipeline.getProject().getTags().size());
for (Map.Entry<String, String> entry : pipeline.getProject().getTags().entrySet())
Assert.assertEquals(pipeline.getProject().getTags().get(entry.getKey()), entry.getValue());
Assert.assertEquals(pipelineLoad.getSamples().size(), pipeline.getSamples().size());
for (int i = 0; i < pipeline.getSamples().size(); i++) {
PipelineSample pipelineSample = pipeline.getSamples().get(i);
PipelineSample pipelineLoadSample = pipelineLoad.getSamples().get(i);
Assert.assertEquals(pipelineLoadSample.getId(), pipelineSample.getId());
Assert.assertEquals(pipelineLoadSample.getBamFiles().size(), pipelineSample.getBamFiles().size());
for (Map.Entry<String, File> entry : pipelineSample.getBamFiles().entrySet())
Assert.assertEquals(entry.getValue(), pipelineSample.getBamFiles().get(entry.getKey()));
Assert.assertEquals(pipelineLoadSample.getTags().size(), pipelineSample.getTags().size());
for (Map.Entry<String, String> entry : pipelineSample.getTags().entrySet())
Assert.assertEquals(pipelineSample.getTags().get(entry.getKey()), entry.getValue());
}
}
}