From 221e01fb27d2f4a3d2da6413e8cb44b2f6a407ac Mon Sep 17 00:00:00 2001 From: ebanks Date: Mon, 12 Jul 2010 16:59:45 +0000 Subject: [PATCH] deleting/archiving as instructed git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3765 348d0f76-0448-11de-a6fe-93d51630548a --- .../sting/annotations}/SecondBaseSkew.java | 0 .../annotator/ThousandGenomesAnnotator.java | 59 ------------- .../SecondBaseSkewIntegrationTest.java | 83 ------------------- .../VariantAnnotatorIntegrationTest.java | 35 -------- 4 files changed, 177 deletions(-) rename {java/src/org/broadinstitute/sting/gatk/walkers/annotator => archive/java/src/org/broadinstitute/sting/annotations}/SecondBaseSkew.java (100%) delete mode 100644 java/src/org/broadinstitute/sting/oneoffprojects/walkers/annotator/ThousandGenomesAnnotator.java delete mode 100755 java/test/org/broadinstitute/sting/gatk/walkers/annotator/SecondBaseSkewIntegrationTest.java diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SecondBaseSkew.java b/archive/java/src/org/broadinstitute/sting/annotations/SecondBaseSkew.java similarity index 100% rename from java/src/org/broadinstitute/sting/gatk/walkers/annotator/SecondBaseSkew.java rename to archive/java/src/org/broadinstitute/sting/annotations/SecondBaseSkew.java diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/annotator/ThousandGenomesAnnotator.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/annotator/ThousandGenomesAnnotator.java deleted file mode 100644 index de1c6c1c5..000000000 --- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/annotator/ThousandGenomesAnnotator.java +++ /dev/null @@ -1,59 +0,0 @@ -package org.broadinstitute.sting.oneoffprojects.walkers.annotator; - -import org.broad.tribble.vcf.VCFHeaderLineType; -import org.broad.tribble.vcf.VCFInfoHeaderLine; -import org.broad.tribble.vcf.VCFRecord; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.contexts.StratifiedAlignmentContext; -import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContext; -import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; - -import java.util.HashMap; -import java.util.Map; -import java.util.List; -import java.util.Arrays; - -/** - * IF THERE IS NO JAVADOC RIGHT HERE, YELL AT chartl - * - * @author chartl - * @date Feb 1, 2010 - */ -public class ThousandGenomesAnnotator implements InfoFieldAnnotation { - - public List getKeyNames() { - return Arrays.asList("1KG"); - } - - public List getDescriptions() { - return Arrays.asList(new VCFInfoHeaderLine(getKeyNames().get(0), - 1, VCFHeaderLineType.String,"Is this site seen in Pilot1 or Pilot2 of 1KG?")); - } - - public Map annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map context, VariantContext vc) { - if ( tracker == null ) - return null; - - VCFRecord pilot1 = tracker.lookup("pilot1", VCFRecord.class); - VCFRecord pilot2 = tracker.lookup("pilot2", VCFRecord.class); - - String result; - - if ( pilot1 == null && pilot2 == null) { - result = "0"; - } else { - if ( pilot1 != null && ! pilot1.isFiltered() ) { - result = "1"; - } else if ( pilot2 != null && !pilot2.isFiltered() ) { - result = "1"; - } else { - result = "0"; - } - } - Map map = new HashMap(); - map.put(getKeyNames().get(0), result); - return map; - } -} - diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/annotator/SecondBaseSkewIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/annotator/SecondBaseSkewIntegrationTest.java deleted file mode 100755 index bc4a098ed..000000000 --- a/java/test/org/broadinstitute/sting/gatk/walkers/annotator/SecondBaseSkewIntegrationTest.java +++ /dev/null @@ -1,83 +0,0 @@ -package org.broadinstitute.sting.gatk.walkers.annotator; - -import org.broadinstitute.sting.WalkerTest; -import org.junit.Test; - -import java.util.Arrays; - -/** - * Created by IntelliJ IDEA. - * User: chartl - * Date: Nov 17, 2009 - * Time: 6:58:09 PM - * To change this template use File | Settings | File Templates. - */ -public class SecondBaseSkewIntegrationTest extends WalkerTest { - - // TODO -- reinstitute these integration tests when GELI -> VariantContext is supported - - //@Test - public void secondBaseSkewTest() { - for ( int test = 1; test <= 2; test ++ ) { - String bamFilePath = VariantAnnotatorIntegrationTest.validationDataPath()+VariantAnnotatorIntegrationTest.secondBaseTestFile(test)+".a2b.recal.annotation_subset.bam"; - String callFile = VariantAnnotatorIntegrationTest.validationDataPath()+VariantAnnotatorIntegrationTest.secondBaseTestFile(test)+".a2b.ssg1b.geli.calls"; - String args = VariantAnnotatorIntegrationTest.secondBaseTestString()+" -I "+bamFilePath+" -B variant,Variants,"+callFile+" "+VariantAnnotatorIntegrationTest.secondBaseTestInterval(test)+" -sample variant"; - WalkerTestSpec spec = new WalkerTestSpec(args,1, Arrays.asList(VariantAnnotatorIntegrationTest.secondBaseTestmd5(test))); - executeTest("Second base skew annotator, test number "+Integer.toString(test), spec); - } - } - - //@Test - public void testOnE2File() { - String test_args = "-T VariantAnnotator -A SecondBaseSkew " - +"-R " + seqLocation + "references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta " - +"-I " + validationDataLocation + "FHSP_pool3_2bannot.bam " - +"-B variant,Variants," + validationDataLocation + "FHS_pilot_pool3_raw_calls.geli " - +"-o %s -sample variant -L " + validationDataLocation + "FHS_test_intervals.interval_list"; - - String md5_for_this_test = "c1116b3196cc9f553ae2442a4063bc5e"; - - WalkerTestSpec spec = new WalkerTestSpec(test_args,1, Arrays.asList(md5_for_this_test)); - executeTest("Testing on E2 annotated but not Q2 annotated file ",spec); - - - } - - //@Test - public void testOnUnannotatedFile() { - String test_args = "-T VariantAnnotator -A SecondBaseSkew " - +"-R " + seqLocation + "references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta " - +"-I " + validationDataLocation + "FHSP_pool3_test.bam " - +"-B variant,Variants," + validationDataLocation + "FHS_pilot_pool3_raw_calls.geli " - +"-o %s -sample variant -L " + validationDataLocation + "FHS_test_intervals.interval_list"; - - String md5_for_this_test = "a297259694ac88f769a45bce96a08e51"; - - WalkerTestSpec spec = new WalkerTestSpec(test_args,1, Arrays.asList(md5_for_this_test)); - executeTest("Testing on bam file without 2bb annotations ",spec); - } - - @Test - public void testOnIndels() { - String test_args = "-T VariantAnnotator -I " + validationDataLocation + "FHS_Pileup_Test.bam" - + " -R " + seqLocation + "references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta -A SecondBaseSkew" - + " -sample variant -B variant,VCF," + validationDataLocation + "FHS_pileup_test_chr15.vcf" - + " -o %s -L chr15:46347148"; - String expected_md5 = "f4aff94a713fcf4dc5750d6a6a884ad3"; - WalkerTestSpec spec = new WalkerTestSpec(test_args,1,Arrays.asList(expected_md5)); - executeTest("Testing on locus with many indels", spec); - } - - // todo -- chris needs to fix this -// @Test -// public void testPrimaryBaseSecondaryBaseOnIndels() { -// String test_args = "-T VariantAnnotator -I /humgen/gsa-scr1/GATK_Data/Validation_Data/FHS_Pileup_Test.bam" -// + " -R /seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta -A PrimaryBaseSecondaryBaseSymmetry" -// + " -sample variant -B variant,VCF,/humgen/gsa-scr1/GATK_Data/Validation_Data/FHS_pileup_test_chr15.vcf" -// + " -vcf %s -L chr15:46347148"; -// String expected_md5 = "9b587be7a270c6df7e0affcfc61a861a"; -// WalkerTestSpec spec = new WalkerTestSpec(test_args,1,Arrays.asList(expected_md5)); -// executeTest("Testing PrimaryBaseSeHcondaryBaseSymmetry on locus with many indels", spec); -// } - -} diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java index 37b4b12b7..64565b658 100755 --- a/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java +++ b/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java @@ -1,51 +1,16 @@ package org.broadinstitute.sting.gatk.walkers.annotator; import org.broadinstitute.sting.WalkerTest; -import org.broadinstitute.sting.utils.StingException; import org.junit.Test; import java.util.Arrays; public class VariantAnnotatorIntegrationTest extends WalkerTest { - public static String secondBaseTestString() { - return "-T VariantAnnotator -R " + seqLocation + "references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta -vcf %s -A SecondBaseSkew"; - } - - public static String validationDataPath() { - return validationDataLocation + ""; - } - - public static String secondBaseTestFile( int testNo ) { - switch ( testNo ) { - case 1: return "NA12891"; - case 2: return "NA20762"; - default: throw new StingException("Impossible test has been run: secondbasetest number "+ testNo); - } - } - - public static String secondBaseTestInterval ( int testNo ) { - switch ( testNo ) { - case 1: return "-L chr1:14,000,000-18,000,000"; - case 2: return "-L chr22:20660081-20660083 -L chr22:29198100-29198104 -L chr22:29821330-29821334"; - default: throw new StingException("Impossible test has been run: secondbasetest number "+testNo); - } - } - - public static String secondBaseTestmd5( int testNo ) { - switch ( testNo ) { - case 1: return "bf64bac186fd682018dd7f0419d90190"; - case 2: return "67f40627b12be31efe02c9d853fbcf37"; - default: throw new StingException("Impossible test has been run: secondbasetest number "+testNo); - } - } - public static String baseTestString() { return "-T VariantAnnotator -R " + oneKGLocation + "reference/human_b36_both.fasta -o %s"; } - - @Test public void testHasAnnotsNotAsking1() { WalkerTestSpec spec = new WalkerTestSpec(