deleting/archiving as instructed
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3765 348d0f76-0448-11de-a6fe-93d51630548a
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package org.broadinstitute.sting.oneoffprojects.walkers.annotator;
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import org.broad.tribble.vcf.VCFHeaderLineType;
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import org.broad.tribble.vcf.VCFInfoHeaderLine;
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import org.broad.tribble.vcf.VCFRecord;
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import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
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import org.broadinstitute.sting.gatk.contexts.StratifiedAlignmentContext;
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import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContext;
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import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
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import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
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import java.util.HashMap;
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import java.util.Map;
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import java.util.List;
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import java.util.Arrays;
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/**
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* IF THERE IS NO JAVADOC RIGHT HERE, YELL AT chartl
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*
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* @author chartl
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* @date Feb 1, 2010
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*/
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public class ThousandGenomesAnnotator implements InfoFieldAnnotation {
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public List<String> getKeyNames() {
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return Arrays.asList("1KG");
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}
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public List<VCFInfoHeaderLine> getDescriptions() {
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return Arrays.asList(new VCFInfoHeaderLine(getKeyNames().get(0),
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1, VCFHeaderLineType.String,"Is this site seen in Pilot1 or Pilot2 of 1KG?"));
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}
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public Map<String, Object> annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, StratifiedAlignmentContext> context, VariantContext vc) {
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if ( tracker == null )
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return null;
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VCFRecord pilot1 = tracker.lookup("pilot1", VCFRecord.class);
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VCFRecord pilot2 = tracker.lookup("pilot2", VCFRecord.class);
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String result;
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if ( pilot1 == null && pilot2 == null) {
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result = "0";
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} else {
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if ( pilot1 != null && ! pilot1.isFiltered() ) {
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result = "1";
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} else if ( pilot2 != null && !pilot2.isFiltered() ) {
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result = "1";
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} else {
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result = "0";
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}
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}
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Map<String, Object> map = new HashMap<String, Object>();
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map.put(getKeyNames().get(0), result);
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return map;
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}
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}
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package org.broadinstitute.sting.gatk.walkers.annotator;
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import org.broadinstitute.sting.WalkerTest;
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import org.junit.Test;
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import java.util.Arrays;
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/**
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* Created by IntelliJ IDEA.
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* User: chartl
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* Date: Nov 17, 2009
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* Time: 6:58:09 PM
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* To change this template use File | Settings | File Templates.
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*/
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public class SecondBaseSkewIntegrationTest extends WalkerTest {
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// TODO -- reinstitute these integration tests when GELI -> VariantContext is supported
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//@Test
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public void secondBaseSkewTest() {
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for ( int test = 1; test <= 2; test ++ ) {
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String bamFilePath = VariantAnnotatorIntegrationTest.validationDataPath()+VariantAnnotatorIntegrationTest.secondBaseTestFile(test)+".a2b.recal.annotation_subset.bam";
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String callFile = VariantAnnotatorIntegrationTest.validationDataPath()+VariantAnnotatorIntegrationTest.secondBaseTestFile(test)+".a2b.ssg1b.geli.calls";
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String args = VariantAnnotatorIntegrationTest.secondBaseTestString()+" -I "+bamFilePath+" -B variant,Variants,"+callFile+" "+VariantAnnotatorIntegrationTest.secondBaseTestInterval(test)+" -sample variant";
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WalkerTestSpec spec = new WalkerTestSpec(args,1, Arrays.asList(VariantAnnotatorIntegrationTest.secondBaseTestmd5(test)));
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executeTest("Second base skew annotator, test number "+Integer.toString(test), spec);
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}
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}
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//@Test
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public void testOnE2File() {
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String test_args = "-T VariantAnnotator -A SecondBaseSkew "
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+"-R " + seqLocation + "references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta "
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+"-I " + validationDataLocation + "FHSP_pool3_2bannot.bam "
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+"-B variant,Variants," + validationDataLocation + "FHS_pilot_pool3_raw_calls.geli "
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+"-o %s -sample variant -L " + validationDataLocation + "FHS_test_intervals.interval_list";
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String md5_for_this_test = "c1116b3196cc9f553ae2442a4063bc5e";
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WalkerTestSpec spec = new WalkerTestSpec(test_args,1, Arrays.asList(md5_for_this_test));
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executeTest("Testing on E2 annotated but not Q2 annotated file ",spec);
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}
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//@Test
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public void testOnUnannotatedFile() {
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String test_args = "-T VariantAnnotator -A SecondBaseSkew "
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+"-R " + seqLocation + "references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta "
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+"-I " + validationDataLocation + "FHSP_pool3_test.bam "
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+"-B variant,Variants," + validationDataLocation + "FHS_pilot_pool3_raw_calls.geli "
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+"-o %s -sample variant -L " + validationDataLocation + "FHS_test_intervals.interval_list";
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String md5_for_this_test = "a297259694ac88f769a45bce96a08e51";
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WalkerTestSpec spec = new WalkerTestSpec(test_args,1, Arrays.asList(md5_for_this_test));
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executeTest("Testing on bam file without 2bb annotations ",spec);
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}
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@Test
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public void testOnIndels() {
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String test_args = "-T VariantAnnotator -I " + validationDataLocation + "FHS_Pileup_Test.bam"
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+ " -R " + seqLocation + "references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta -A SecondBaseSkew"
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+ " -sample variant -B variant,VCF," + validationDataLocation + "FHS_pileup_test_chr15.vcf"
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+ " -o %s -L chr15:46347148";
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String expected_md5 = "f4aff94a713fcf4dc5750d6a6a884ad3";
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WalkerTestSpec spec = new WalkerTestSpec(test_args,1,Arrays.asList(expected_md5));
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executeTest("Testing on locus with many indels", spec);
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}
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// todo -- chris needs to fix this
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// @Test
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// public void testPrimaryBaseSecondaryBaseOnIndels() {
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// String test_args = "-T VariantAnnotator -I /humgen/gsa-scr1/GATK_Data/Validation_Data/FHS_Pileup_Test.bam"
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// + " -R /seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta -A PrimaryBaseSecondaryBaseSymmetry"
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// + " -sample variant -B variant,VCF,/humgen/gsa-scr1/GATK_Data/Validation_Data/FHS_pileup_test_chr15.vcf"
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// + " -vcf %s -L chr15:46347148";
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// String expected_md5 = "9b587be7a270c6df7e0affcfc61a861a";
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// WalkerTestSpec spec = new WalkerTestSpec(test_args,1,Arrays.asList(expected_md5));
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// executeTest("Testing PrimaryBaseSeHcondaryBaseSymmetry on locus with many indels", spec);
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// }
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}
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@ -1,51 +1,16 @@
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package org.broadinstitute.sting.gatk.walkers.annotator;
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import org.broadinstitute.sting.WalkerTest;
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import org.broadinstitute.sting.utils.StingException;
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import org.junit.Test;
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import java.util.Arrays;
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public class VariantAnnotatorIntegrationTest extends WalkerTest {
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public static String secondBaseTestString() {
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return "-T VariantAnnotator -R " + seqLocation + "references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta -vcf %s -A SecondBaseSkew";
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}
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public static String validationDataPath() {
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return validationDataLocation + "";
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}
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public static String secondBaseTestFile( int testNo ) {
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switch ( testNo ) {
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case 1: return "NA12891";
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case 2: return "NA20762";
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default: throw new StingException("Impossible test has been run: secondbasetest number "+ testNo);
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}
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}
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public static String secondBaseTestInterval ( int testNo ) {
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switch ( testNo ) {
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case 1: return "-L chr1:14,000,000-18,000,000";
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case 2: return "-L chr22:20660081-20660083 -L chr22:29198100-29198104 -L chr22:29821330-29821334";
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default: throw new StingException("Impossible test has been run: secondbasetest number "+testNo);
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}
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}
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public static String secondBaseTestmd5( int testNo ) {
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switch ( testNo ) {
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case 1: return "bf64bac186fd682018dd7f0419d90190";
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case 2: return "67f40627b12be31efe02c9d853fbcf37";
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default: throw new StingException("Impossible test has been run: secondbasetest number "+testNo);
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}
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}
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public static String baseTestString() {
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return "-T VariantAnnotator -R " + oneKGLocation + "reference/human_b36_both.fasta -o %s";
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}
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@Test
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public void testHasAnnotsNotAsking1() {
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WalkerTestSpec spec = new WalkerTestSpec(
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