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RodBinding names are now defaulting to the ArgumentTypeDescriptor fullname 

Nearly all of the tools are passing integrationtests
This commit is contained in:
Mark DePristo 2011-08-03 20:48:11 -04:00
parent d8f1ebf8c6
commit d0279bb28c
5 changed files with 219 additions and 17 deletions
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2
public/java/src/org/broadinstitute/sting/commandline/ArgumentTypeDescriptor.java
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@ -312,7 +312,7 @@ class RodBindingArgumentTypeDescriptor extends ArgumentTypeDescriptor {
ArgumentDefinition defaultDefinition = createDefaultArgumentDefinition(source);
String value = getArgumentValue( defaultDefinition, matches );
try {
String name = source.field.getName();
String name = defaultDefinition.fullName;
String tribbleType;
Tags tags = getArgumentTags(matches);
// must have one or two tag values here

179
public/java/src/org/broadinstitute/sting/gatk/walkers/qc/RodSystemValidationWalker.java 100644
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@ -0,0 +1,179 @@
/*
* 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.qc;
import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.commandline.Output;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
import org.broadinstitute.sting.gatk.refdata.utils.RODRecordList;
import org.broadinstitute.sting.gatk.walkers.Reference;
import org.broadinstitute.sting.gatk.walkers.RodWalker;
import org.broadinstitute.sting.gatk.walkers.Window;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import java.io.*;
import java.math.BigInteger;
import java.security.MessageDigest;
import java.security.NoSuchAlgorithmException;
import java.util.Collection;
import java.util.List;
/**
* a walker for validating (in the style of validating pile-up) the ROD system.
*/
@Reference(window=@Window(start=-40,stop=40))
public class RodSystemValidationWalker extends RodWalker<Integer,Integer> {
// the divider to use in some of the text output
private static final String DIVIDER = ",";
@Output
public PrintStream out;
@Argument(fullName="PerLocusEqual",required=false,doc="Should we check that all records at the same site produce equivilent variant contexts")
public boolean allRecordsVariantContextEquivalent = false;
// used to calculate the MD5 of a file
MessageDigest digest = null;
// we sometimes need to know what rods the engine's seen
List<ReferenceOrderedDataSource> rodList;
/**
* emit the md5 sums for each of the input ROD files (will save up a lot of time if and when the ROD files change
* underneath us).
*/
public void initialize() {
// setup the MD5-er
try {
digest = MessageDigest.getInstance("MD5");
} catch (NoSuchAlgorithmException e) {
throw new ReviewedStingException("Unable to find MD5 checksumer");
}
out.println("Header:");
// enumerate the list of ROD's we've loaded
rodList = this.getToolkit().getRodDataSources();
for (ReferenceOrderedDataSource rod : rodList) {
out.println(rod.getName() + DIVIDER + rod.getType());
out.println(rod.getName() + DIVIDER + rod.getFile());
out.println(rod.getName() + DIVIDER + md5sum(rod.getFile()));
}
out.println("Data:");
}
/**
*
* @param tracker the ref meta data tracker to get RODs
* @param ref reference context
* @param context the reads
* @return an 1 for each site with a rod(s), 0 otherwise
*/
@Override
public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
int ret = 0;
if (tracker != null && tracker.getNTracksWithBoundFeatures() > 0) {
out.print(context.getLocation() + DIVIDER);
for (RODRecordList rod: tracker.getBoundRodTracks())
out.print(rod.getName() + DIVIDER);
out.println(";");
ret++;
}
// if the argument was set, check for equivalence
if (allRecordsVariantContextEquivalent && tracker != null) {
Collection<VariantContext> col = tracker.getValues(VariantContext.class);
VariantContext con = null;
for (VariantContext contextInList : col)
if (con == null) con = contextInList;
else if (!con.equals(col)) out.println("FAIL: context " + col + " doesn't match " + con);
}
return ret;
}
/**
* Provide an initial value for reduce computations.
*
* @return Initial value of reduce.
*/
@Override
public Integer reduceInit() {
return 0;
}
/**
* Reduces a single map with the accumulator provided as the ReduceType.
*
* @param value result of the map.
* @param sum accumulator for the reduce.
* @return accumulator with result of the map taken into account.
*/
@Override
public Integer reduce(Integer value, Integer sum) {
return value + sum;
}
@Override
public void onTraversalDone(Integer result) {
// Double check traversal result to make count is the same.
// TODO: Is this check necessary?
out.println("[REDUCE RESULT] Traversal result is: " + result);
}
// shamelessly absconded and adapted from http://www.javalobby.org/java/forums/t84420.html
private String md5sum(File f) {
InputStream is;
try {
is = new FileInputStream(f);
} catch (FileNotFoundException e) {
return "Not a file";
}
byte[] buffer = new byte[8192];
int read = 0;
try {
while ((read = is.read(buffer)) > 0) {
digest.update(buffer, 0, read);
}
byte[] md5sum = digest.digest();
BigInteger bigInt = new BigInteger(1, md5sum);
return bigInt.toString(16);
}
catch (IOException e) {
throw new RuntimeException("Unable to process file for MD5", e);
}
finally {
try {
is.close();
}
catch (IOException e) {
throw new RuntimeException("Unable to close input stream for MD5 calculation", e);
}
}
}
}

35
public/java/test/org/broadinstitute/sting/commandline/ParsingEngineUnitTest.java
View File

@ -631,7 +631,7 @@ public class ParsingEngineUnitTest extends BaseTest {
// --------------------------------------------------------------------------------
private class SingleRodBindingArgProvider {
@Input(shortName="V", required=false)
@Input(fullName="binding", shortName="V", required=false)
public RodBinding<Feature> binding = RodBinding.makeUnbound(Feature.class);
}
@ -653,6 +653,29 @@ public class ParsingEngineUnitTest extends BaseTest {
Assert.assertEquals(argProvider.binding.getTags().getPositionalTags().size(), 1, "Tags aren't correctly set");
}
private class ShortNameOnlyRodBindingArgProvider {
@Input(shortName="short", required=false)
public RodBinding<Feature> binding = RodBinding.makeUnbound(Feature.class);
}
@Test
public void shortNameOnlyRodBindingArgumentTest() {
final String[] commandLine = new String[] {"-short:vcf","foo.vcf"};
parsingEngine.addArgumentSource( ShortNameOnlyRodBindingArgProvider.class );
parsingEngine.parse( commandLine );
parsingEngine.validate();
ShortNameOnlyRodBindingArgProvider argProvider = new ShortNameOnlyRodBindingArgProvider();
parsingEngine.loadArgumentsIntoObject( argProvider );
Assert.assertEquals(argProvider.binding.getName(), "binding", "Name isn't set properly");
Assert.assertEquals(argProvider.binding.getSource(), "foo.vcf", "Source isn't set to its expected value");
Assert.assertEquals(argProvider.binding.getType(), Feature.class, "Type isn't set to its expected value");
Assert.assertEquals(argProvider.binding.isBound(), true, "Bound() isn't returning its expected value");
Assert.assertEquals(argProvider.binding.getTags().getPositionalTags().size(), 1, "Tags aren't correctly set");
}
@Test
public void unbasicRodBindingArgumentTest() {
final String[] commandLine = new String[] {};
@ -696,7 +719,7 @@ public class ParsingEngineUnitTest extends BaseTest {
}
private class VariantContextRodBindingArgProvider {
@Input(shortName="V")
@Input(fullName = "binding", shortName="V")
public RodBinding<VariantContext> binding;
}
@ -735,7 +758,7 @@ public class ParsingEngineUnitTest extends BaseTest {
}
private class ListRodBindingArgProvider {
@Input(shortName="V", required=false)
@Input(fullName = "binding", shortName="V", required=false)
public List<RodBinding<Feature>> bindings;
}
@ -752,7 +775,7 @@ public class ParsingEngineUnitTest extends BaseTest {
Assert.assertEquals(argProvider.bindings.size(), 1, "Unexpected number of bindings");
RodBinding<Feature> binding = argProvider.bindings.get(0);
Assert.assertEquals(binding.getName(), "bindings", "Name isn't set properly");
Assert.assertEquals(binding.getName(), "binding", "Name isn't set properly");
Assert.assertEquals(binding.getSource(), "foo.vcf", "Source isn't set to its expected value");
Assert.assertEquals(binding.getType(), Feature.class, "Type isn't set to its expected value");
Assert.assertEquals(binding.getTags().getPositionalTags().size(), 1, "Tags aren't correctly set");
@ -772,13 +795,13 @@ public class ParsingEngineUnitTest extends BaseTest {
Assert.assertEquals(argProvider.bindings.size(), 2, "Unexpected number of bindings");
RodBinding<Feature> binding = argProvider.bindings.get(0);
Assert.assertEquals(binding.getName(), "bindings", "Name isn't set properly");
Assert.assertEquals(binding.getName(), "binding", "Name isn't set properly");
Assert.assertEquals(binding.getSource(), "foo.vcf", "Source isn't set to its expected value");
Assert.assertEquals(binding.getType(), Feature.class, "Type isn't set to its expected value");
Assert.assertEquals(binding.getTags().getPositionalTags().size(), 1, "Tags aren't correctly set");
RodBinding<Feature> binding2 = argProvider.bindings.get(1);
Assert.assertEquals(binding2.getName(), "bindings2", "Name isn't set properly");
Assert.assertEquals(binding2.getName(), "binding2", "Name isn't set properly");
Assert.assertEquals(binding2.getSource(), "bar.vcf", "Source isn't set to its expected value");
Assert.assertEquals(binding2.getType(), Feature.class, "Type isn't set to its expected value");
Assert.assertEquals(binding2.getTags().getPositionalTags().size(), 1, "Tags aren't correctly set");

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

@ -38,7 +38,7 @@ public class LeftAlignVariantsIntegrationTest extends WalkerTest {
@Test
public void testLeftAlignment() {
WalkerTestSpec spec = new WalkerTestSpec(
"-T LeftAlignVariants -o %s -R " + b37KGReference + " --variant:vcf " + validationDataLocation + "forLeftAlignVariantsTest.vcf -NO_HEADER",
"-T LeftAlignVariants -o %s -R " + b37KGReference + " --variants:vcf " + validationDataLocation + "forLeftAlignVariantsTest.vcf -NO_HEADER",
1,
Arrays.asList("158b1d71b28c52e2789f164500b53732"));
executeTest("test left alignment", spec);

18
public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextIntegrationTest.java
View File

@ -30,15 +30,15 @@ public class VariantContextIntegrationTest extends WalkerTest {
@DataProvider(name = "VCITTestData")
public Object[][] createVCITTestData() {
new VCITTest("--printPerLocus", "f36b81b8bcd210c0e3a1058d791b78ec");
new VCITTest("--printPerLocus --onlyContextsOfType SNP", "a77492ba003a1fca8d8e0227fa642f34");
new VCITTest("--printPerLocus --onlyContextsOfType INDEL", "9e0375a1b680d7df0971dbf256944d7a");
new VCITTest("--printPerLocus --onlyContextsOfType MIXED", "93628cbba30033398e7e680b92cb3680");
new VCITTest("--printPerLocus --onlyContextsOfType NO_VARIATION", "39335acdb34c8a2af433dc50d619bcbc");
new VCITTest("--printPerLocus --takeFirstOnly", "c4a3d7545d26880635e0e5e4e69952e2");
new VCITTest("--printPerLocus --onlyContextsOfType INDEL --onlyContextsStartinAtCurrentPosition", "22a7bb9e63d5f2950322c26397670e5c");
new VCITTest("--printPerLocus --onlyContextsStartinAtCurrentPosition", "6387c1a400d1872ae4394d01e533c296");
new VCITTest("--printPerLocus --takeFirstOnly --onlyContextsStartinAtCurrentPosition", "dde3a3db4d9c57f5042e0dfe03380987");
new VCITTest("--printPerLocus", "");
new VCITTest("--printPerLocus --onlyContextsOfType SNP", "");
new VCITTest("--printPerLocus --onlyContextsOfType INDEL", "");
new VCITTest("--printPerLocus --onlyContextsOfType MIXED", "");
new VCITTest("--printPerLocus --onlyContextsOfType NO_VARIATION", "");
new VCITTest("--printPerLocus --takeFirstOnly", "");
new VCITTest("--printPerLocus --onlyContextsOfType INDEL --onlyContextsStartinAtCurrentPosition", "");
new VCITTest("--printPerLocus --onlyContextsStartinAtCurrentPosition", "");
new VCITTest("--printPerLocus --takeFirstOnly --onlyContextsStartinAtCurrentPosition", "");
return VCITTest.getTests(VCITTest.class);
}