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Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable

This commit is contained in:
Guillermo del Angel 2011-09-09 18:31:14 -04:00
parent a807205fc3 9e650dfc17
commit e95d484757
8 changed files with 59 additions and 43 deletions
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45
build.xml
View File

@ -821,6 +821,7 @@
<!-- TEST -->
<macrodef name="run-test">
<attribute name="testtype"/>
<attribute name="outputdir"/>
<attribute name="runfailed"/>
<sequential>
@ -828,10 +829,6 @@
<equals arg1="@{runfailed}" arg2="true"/>
</condition>
<condition property="test.output.dir" value="${report}/@{testtype}" else="${report}/failed_rerun">
<not><isset property="run.failed.tests"/></not>
</condition>
<!-- Get the pipeline run type. Default to dry. -->
<condition property="pipeline.run" value="dry" else="${pipeline.run}">
<equals arg1="${pipeline.run}" arg2="$${pipeline.run}" />
@ -841,10 +838,10 @@
<isset property="include.contracts" />
</condition>
<mkdir dir="${test.output.dir}"/>
<mkdir dir="@{outputdir}"/>
<echo message="Sting: Running @{testtype} test cases!"/>
<taskdef resource="testngtasks" classpath="${testng.jar}"/>
<testng outputDir="${test.output.dir}"
<testng outputDir="@{outputdir}"
haltOnFailure="false" failureProperty="test.failure"
verbose="2"
workingDir="${basedir}"
@ -885,23 +882,35 @@
</testng>
<!-- generate a report for Bamboo or Hudson to read in -->
<junitreport todir="${test.output.dir}">
<fileset dir="${test.output.dir}">
<junitreport todir="@{outputdir}">
<fileset dir="@{outputdir}">
<include name="*/*.xml"/>
</fileset>
<report format="noframes" todir="${test.output.dir}"/>
<report format="noframes" todir="@{outputdir}"/>
</junitreport>
<fail message="test failed" if="test.failure" />
</sequential>
</macrodef>
<target name="alltests">
<antcall target="test" inheritAll="false"/>
<antcall target="integrationtest" inheritAll="false"/>
<antcall target="pipelinetest" inheritAll="false"/>
</target>
<target name="alltests.public">
<antcall target="test.public" inheritAll="false"/>
<antcall target="integrationtest.public" inheritAll="false"/>
<antcall target="pipelinetest.public" inheritAll="false"/>
</target>
<!-- Our four different test conditions: Test, IntegrationTest, PerformanceTest, PipelineTest -->
<target name="test" depends="init.buildall,test.compile" description="Run unit tests">
<condition property="ttype" value="*UnitTest" else="${single}">
<not><isset property="single"/></not>
</condition>
<run-test testtype="${ttype}" runfailed="false"/>
<run-test testtype="${ttype}" outputdir="${report}/${ttype}" runfailed="false"/>
</target>
<target name="test.public" depends="init.buildpublic,test"/>
@ -909,7 +918,7 @@
<condition property="itype" value="*IntegrationTest" else="${single}">
<not><isset property="single"/></not>
</condition>
<run-test testtype="${itype}" runfailed="false"/>
<run-test testtype="${itype}" outputdir="${report}/${itype}" runfailed="false"/>
</target>
<target name="integrationtest.public" depends="init.buildpublic,integrationtest"/>
@ -917,7 +926,7 @@
<condition property="ptype" value="*PerformanceTest" else="${single}">
<not><isset property="single"/></not>
</condition>
<run-test testtype="${ptype}" runfailed="false"/>
<run-test testtype="${ptype}" outputdir="${report}/${ptype}" runfailed="false"/>
</target>
<target name="performancetest.public" depends="init.buildpublic,performancetest" />
@ -925,7 +934,7 @@
<condition property="pipetype" value="*PipelineTest" else="${single}">
<not><isset property="single"/></not>
</condition>
<run-test testtype="${pipetype}" runfailed="false"/>
<run-test testtype="${pipetype}" outputdir="${report}/${pipetype}" runfailed="false"/>
</target>
<target name="pipelinetest.public" depends="init.buildpublic,pipelinetest" />
@ -934,24 +943,24 @@
<condition property="pipetype" value="*PipelineTest" else="${single}">
<not><isset property="single"/></not>
</condition>
<run-test testtype="${pipetype}" runfailed="false"/>
<run-test testtype="${pipetype}" outputdir="${report}/${pipetype}" runfailed="false"/>
</target>
<target name="pipelinetestrun.public" depends="init.buildpublic,pipelinetestrun" />
<target name="failed-test" depends="init.buildall,test.compile">
<run-test testtype="${report}/*UnitTest/testng-failed.xml" runfailed="true"/>
<run-test testtype="${report}/*UnitTest/testng-failed.xml" outputdir="${report}/failed_rerun" runfailed="true"/>
</target>
<target name="failed-integration" depends="init.buildall,test.compile">
<run-test testtype="${report}/*IntegrationTest/testng-failed.xml" runfailed="true"/>
<run-test testtype="${report}/*IntegrationTest/testng-failed.xml" outputdir="${report}/failed_rerun" runfailed="true"/>
</target>
<target name="failed-performance" depends="init.buildall,test.compile">
<run-test testtype="${report}/*PerformanceTest/testng-failed.xml" runfailed="true"/>
<run-test testtype="${report}/*PerformanceTest/testng-failed.xml" outputdir="${report}/failed_rerun" runfailed="true"/>
</target>
<target name="failed-pipeline" depends="init.buildall,test.compile">
<run-test testtype="${report}/*PipelineTest/testng-failed.xml" runfailed="true"/>
<run-test testtype="${report}/*PipelineTest/testng-failed.xml" outputdir="${report}/failed_rerun" runfailed="true"/>
</target>
<!-- ******************************************************************************** -->

13
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
View File

@ -145,10 +145,9 @@ import java.util.*;
* -R ref.fasta \
* -T SelectVariants \
* --variant input.vcf \
* -o output.vcf \
* -SM family.yaml \
* -family NA12891+NA12892=NA12878 \
* -mvq 50
* -mvq 50 \
* -o violations.vcf
*
* Creating a sample of exactly 1000 variants randomly chosen with equal probability from the variant VCF:
* java -Xmx2g -jar GenomeAnalysisTK.jar \
@ -265,17 +264,17 @@ public class SelectVariants extends RodWalker<Integer, Integer> {
private File AF_FILE = new File("");
@Hidden
@Argument(fullName="family_structure_file", shortName="familyFile", doc="USE YAML FILE INSTEAD (-SM) !!! string formatted as dad+mom=child where these parameters determine which sample names are examined", required=false)
@Argument(fullName="family_structure_file", shortName="familyFile", doc="use -family unless you know what you're doing", required=false)
private File FAMILY_STRUCTURE_FILE = null;
/**
* String formatted as dad+mom=child where these parameters determine which sample names are examined.
*/
@Argument(fullName="family_structure", shortName="family", doc="Deprecated; use the -SM argument instead", required=false)
@Argument(fullName="family_structure", shortName="family", doc="string formatted as dad+mom=child where these parameters determine which sample names are examined", required=false)
private String FAMILY_STRUCTURE = "";
/**
* Sample metadata information will be taken from a YAML file (see the -SM argument).
* This activates the mendelian violation module that will select all variants that correspond to a mendelian violation following the rules given by the family structure.
*/
@Argument(fullName="mendelianViolation", shortName="mv", doc="output mendelian violation sites only", required=false)
private Boolean MENDELIAN_VIOLATIONS = false;
@ -306,7 +305,7 @@ public class SelectVariants extends RodWalker<Integer, Integer> {
@Hidden
@Argument(fullName="outMVFile", shortName="outMVFile", doc="USE YAML FILE INSTEAD (-SM) !!! string formatted as dad+mom=child where these parameters determine which sample names are examined", required=false)
@Argument(fullName="outMVFile", shortName="outMVFile", doc="", required=false)
private String outMVFile = null;
/* Private class used to store the intermediate variants in the integer random selection process */

5
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariants.java
View File

@ -56,11 +56,6 @@ import java.util.Set;
* A variant set to filter.
* </p>
*
* <h2>Output</h2>
* <p>
* A filtered VCF.
* </p>
*
* <h2>Examples</h2>
* <pre>
* java -Xmx2g -jar GenomeAnalysisTK.jar \

11
public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java
View File

@ -1085,14 +1085,15 @@ public class VariantContext implements Feature { // to enable tribble intergrati
}
public void validateReferenceBases(Allele reference, Byte paddedRefBase) {
// don't validate if we're an insertion or complex event
if ( !reference.isNull() && getReference().length() == 1 && !reference.basesMatch(getReference()) ) {
throw new TribbleException.InternalCodecException(String.format("the REF allele is incorrect for the record at position %s:%d, %s vs. %s", getChr(), getStart(), reference.getBaseString(), getReference().getBaseString()));
// don't validate if we're a complex event
if ( !isComplexIndel() && !reference.isNull() && !reference.basesMatch(getReference()) ) {
throw new TribbleException.InternalCodecException(String.format("the REF allele is incorrect for the record at position %s:%d, fasta says %s vs. VCF says %s", getChr(), getStart(), reference.getBaseString(), getReference().getBaseString()));
}
// we also need to validate the padding base for simple indels
if ( hasReferenceBaseForIndel() && !getReferenceBaseForIndel().equals(paddedRefBase) )
throw new TribbleException.InternalCodecException(String.format("the padded REF base is incorrect for the record at position %s:%d, %s vs. %s", getChr(), getStart(), (char)getReferenceBaseForIndel().byteValue(), (char)paddedRefBase.byteValue()));
if ( hasReferenceBaseForIndel() && !getReferenceBaseForIndel().equals(paddedRefBase) ) {
throw new TribbleException.InternalCodecException(String.format("the padded REF base is incorrect for the record at position %s:%d, fasta says %s vs. VCF says %s", getChr(), getStart(), (char)paddedRefBase.byteValue(), (char)getReferenceBaseForIndel().byteValue()));
}
}
public void validateRSIDs(Set<String> rsIDs) {

8
public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java
View File

@ -256,7 +256,7 @@ 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("2df4f8911ffc3c8d042298723ed465f8"));
1, Arrays.asList("f70997b6a3e7fdc89d11e1d61a2463d4"));
executeTestParallel("testSelect1", spec);
}
@ -273,7 +273,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
@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("ed54aa127b173d8ad8b6482f2a929a42"));
WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("407682de41dcf139ea635e9cda21b912"));
executeTestParallel("testCompVsEvalAC",spec);
}
@ -303,7 +303,7 @@ 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("18c44636e36d6657110bf984f8eac181"));
WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("424c9d438b1faa59b2c29413ba32f37b"));
executeTestParallel("testEvalTrackWithoutGenotypes",spec);
}
@ -315,7 +315,7 @@ 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("1b8ae4fd10de0888bd843f833859d990"));
WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("18fa0b89ebfff51141975d7e4ce7a159"));
executeTestParallel("testMultipleEvalTracksWithoutGenotypes",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("ea09bf764adba9765b99921c5ba2c709")
Arrays.asList("d46a735ffa898f4aa6b3758c5b03f06d")
);
executeTest("testVCFStreamingChain", selectTestSpec);

12
public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariantsIntegrationTest.java
View File

@ -113,4 +113,16 @@ public class ValidateVariantsIntegrationTest extends WalkerTest {
executeTest("test bad alt allele", spec);
}
@Test
public void testBadAllele2() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString("validationExampleBad3.vcf", "REF"),
0,
UserException.MalformedFile.class
);
executeTest("test bad ref allele in deletion", spec);
}
}

6
public/scala/qscript/org/broadinstitute/sting/queue/qscripts/MethodsDevelopmentCallingPipeline.scala
View File

@ -22,8 +22,8 @@ class MethodsDevelopmentCallingPipeline extends QScript {
@Argument(shortName="noBAQ", doc="turns off BAQ calculation", required=false)
var noBAQ: Boolean = false
@Argument(shortName="indels", doc="calls indels with the Unified Genotyper", required=false)
var callIndels: Boolean = false
@Argument(shortName="noIndels", doc="do not call indels with the Unified Genotyper", required=false)
var noIndels: Boolean = false
@Argument(shortName="LOCAL_ET", doc="Doesn't use the AWS S3 storage for ET option", required=false)
var LOCAL_ET: Boolean = false
@ -165,7 +165,7 @@ class MethodsDevelopmentCallingPipeline extends QScript {
val goldStandard = true
for (target <- targets) {
if( !skipCalling ) {
if (callIndels) add(new indelCall(target), new indelFilter(target), new indelEvaluation(target))
if (!noIndels) add(new indelCall(target), new indelFilter(target), new indelEvaluation(target))
add(new snpCall(target))
add(new VQSR(target, !goldStandard))
add(new applyVQSR(target, !goldStandard))