From 1362a5622707209caa56043d0bb990cf58799b06 Mon Sep 17 00:00:00 2001 From: ebanks Date: Thu, 10 Sep 2009 03:13:11 +0000 Subject: [PATCH] Added fasta tests and small fix to cleaner test git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1575 348d0f76-0448-11de-a6fe-93d51630548a --- .../fasta/FastaAlternateReferenceWalker.java | 2 +- .../fasta/BamToFastqIntegrationTest.java | 24 +++++++++++ ...astaAlternateReferenceIntegrationTest.java | 42 +++++++++++++++++++ .../IntervalCleanerIntegrationTest.java | 2 +- 4 files changed, 68 insertions(+), 2 deletions(-) create mode 100755 java/test/org/broadinstitute/sting/gatk/walkers/fasta/BamToFastqIntegrationTest.java create mode 100755 java/test/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceIntegrationTest.java diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceWalker.java index 078b16a5a..6337c460f 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceWalker.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceWalker.java @@ -66,7 +66,7 @@ public class FastaAlternateReferenceWalker extends FastaReferenceWalker { return new Pair(context.getLocation(), (SEQUENOM ? refBase.concat("[-/"+variant.getAltBasesFWD()+"]") : refBase.concat(variant.getAltBasesFWD()))); } else if ( variant.isSNP() ) { basesSeen++; - return new Pair(context.getLocation(), (rod.getName().startsWith("snpmask") ? "N" : ("[" + refBase + "/" + variant.getAltBasesFWD() + "]"))); + return new Pair(context.getLocation(), (rod.getName().startsWith("snpmask") ? "N" : (SEQUENOM ? "[" + refBase + "/" + variant.getAltBasesFWD() + "]" : variant.getAltBasesFWD()))); } } diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/fasta/BamToFastqIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/fasta/BamToFastqIntegrationTest.java new file mode 100755 index 000000000..c46e76951 --- /dev/null +++ b/java/test/org/broadinstitute/sting/gatk/walkers/fasta/BamToFastqIntegrationTest.java @@ -0,0 +1,24 @@ +package org.broadinstitute.sting.gatk.walkers.fasta; + +import org.broadinstitute.sting.WalkerTest; +import org.junit.Test; + +import java.util.Arrays; + +public class BamToFastqIntegrationTest extends WalkerTest { + @Test + public void testIntervals() { + + WalkerTestSpec spec1 = new WalkerTestSpec( + "-T BamToFastq -R /broad/1KG/reference/human_b36_both.fasta -I /humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,100-10,000,500;1:10,100,000-10,101,000;1:10,900,000-10,900,001 -o %s", + 1, + Arrays.asList("f742731e17fba105c7daae0e4f80ca1d")); + executeTest("testBamToFasta", spec1); + + WalkerTestSpec spec2 = new WalkerTestSpec( + "-T BamToFastq -reverse -R /broad/1KG/reference/human_b36_both.fasta -I /humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,100-10,000,500;1:10,100,000-10,101,000;1:10,900,000-10,900,001 -o %s", + 1, + Arrays.asList("19a5418fdf7b53dac8badb67bb1e1b88")); + executeTest("testBamToFastaReverse", spec2); + } +} diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceIntegrationTest.java new file mode 100755 index 000000000..0ae8b80a3 --- /dev/null +++ b/java/test/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceIntegrationTest.java @@ -0,0 +1,42 @@ +package org.broadinstitute.sting.gatk.walkers.fasta; + +import org.broadinstitute.sting.WalkerTest; +import org.junit.Test; + +import java.util.Arrays; + +public class FastaAlternateReferenceIntegrationTest extends WalkerTest { + @Test + public void testIntervals() { + + WalkerTestSpec spec1 = new WalkerTestSpec( + "-T FastaAlternateReferenceMaker -R /broad/1KG/reference/human_b36_both.fasta -L 1:10,000,100-10,000,500;1:10,100,000-10,101,000;1:10,900,000-10,900,001 -o %s", + 1, + Arrays.asList("328d2d52cedfdc52da7d1abff487633d")); + executeTest("testFastaReference", spec1); + + WalkerTestSpec spec2 = new WalkerTestSpec( + "-T FastaAlternateReferenceMaker -R /broad/1KG/reference/human_b36_both.fasta -B indels,PointIndel,/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.chr1_10mb_11mb.slx.indels -B snpmask,dbsnp,/humgen/gsa-scr1/GATK_Data/dbsnp_129_b36.rod -L 1:10,075,000-10,075,380;1:10,093,447-10,093,847;1:10,271,252-10,271,452 -o %s", + 1, + Arrays.asList("b7c0d95c1bf1ea69f5a7a58dd4d57685")); + executeTest("testFastaAlternateReferenceIndels", spec2); + + WalkerTestSpec spec3 = new WalkerTestSpec( + "-T FastaAlternateReferenceMaker -sequenom -R /broad/1KG/reference/human_b36_both.fasta -B indels,PointIndel,/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.chr1_10mb_11mb.slx.indels -B snpmask,dbsnp,/humgen/gsa-scr1/GATK_Data/dbsnp_129_b36.rod -L 1:10,075,000-10,075,380;1:10,093,447-10,093,847;1:10,271,252-10,271,452 -o %s", + 1, + Arrays.asList("3137b0c90ba13fb648be51c14fdb296f")); + executeTest("testFastaAlternateReferenceIndelSequenom", spec3); + + WalkerTestSpec spec4 = new WalkerTestSpec( + "-T FastaAlternateReferenceMaker -R /broad/1KG/reference/human_b36_both.fasta -B snps,Variants,/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.chr1_10mb_11mb.slx.geli.calls -B snpmask,dbsnp,/humgen/gsa-scr1/GATK_Data/dbsnp_129_b36.rod -L 1:10,023,400-10,023,500;1:10,029,200-10,029,500 -o %s", + 1, + Arrays.asList("82705a88f6fc25880dd2331183531d9a")); + executeTest("testFastaAlternateReferenceSnps", spec4); + + WalkerTestSpec spec5 = new WalkerTestSpec( + "-T FastaAlternateReferenceMaker -sequenom -R /broad/1KG/reference/human_b36_both.fasta -B snps,Variants,/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.chr1_10mb_11mb.slx.geli.calls -B snpmask,dbsnp,/humgen/gsa-scr1/GATK_Data/dbsnp_129_b36.rod -L 1:10,023,400-10,023,500;1:10,029,200-10,029,500 -o %s", + 1, + Arrays.asList("c6744c61009a7c15899ce4ef1faa0000")); + executeTest("testFastaAlternateReferenceSnpsSequenom", spec5); + } +} diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/indels/IntervalCleanerIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/indels/IntervalCleanerIntegrationTest.java index e24c26144..900831595 100755 --- a/java/test/org/broadinstitute/sting/gatk/walkers/indels/IntervalCleanerIntegrationTest.java +++ b/java/test/org/broadinstitute/sting/gatk/walkers/indels/IntervalCleanerIntegrationTest.java @@ -11,7 +11,7 @@ public class IntervalCleanerIntegrationTest extends WalkerTest { String[] md5lod5 = {"bfe1c76bf352b22f79c9b7242197a126", "4aa3637e86822c95af3e2c9b414530c3"}; WalkerTestSpec spec1 = new WalkerTestSpec( - "-T IntervalCleaner -stats blah1.stats -LOD 5 -maxConsensuses 100 -greedy 100 -R /broad/1KG/reference/human_b36_both.fasta -I /humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.chrom1.SLX.SRP000032.2009_06.bam -L /humgen/gsa-scr1/GATK_Data/Validation_Data/cleaner.test.intervals --OutputCleaned %s -snps %s", + "-T IntervalCleaner -LOD 5 -maxConsensuses 100 -greedy 100 -R /broad/1KG/reference/human_b36_both.fasta -I /humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.chrom1.SLX.SRP000032.2009_06.bam -L /humgen/gsa-scr1/GATK_Data/Validation_Data/cleaner.test.intervals --OutputCleaned %s -snps %s", 2, Arrays.asList(md5lod5)); executeTest("testLod5", spec1);