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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
This commit is contained in:
ebanks 2009-09-10 03:13:11 +00:00
parent 8ca89279aa
commit 1362a56227
4 changed files with 68 additions and 2 deletions
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2
java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceWalker.java
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@ -66,7 +66,7 @@ public class FastaAlternateReferenceWalker extends FastaReferenceWalker {
return new Pair<GenomeLoc, String>(context.getLocation(), (SEQUENOM ? refBase.concat("[-/"+variant.getAltBasesFWD()+"]") : refBase.concat(variant.getAltBasesFWD())));
} else if ( variant.isSNP() ) {
basesSeen++;
return new Pair<GenomeLoc, String>(context.getLocation(), (rod.getName().startsWith("snpmask") ? "N" : ("[" + refBase + "/" + variant.getAltBasesFWD() + "]")));
return new Pair<GenomeLoc, String>(context.getLocation(), (rod.getName().startsWith("snpmask") ? "N" : (SEQUENOM ? "[" + refBase + "/" + variant.getAltBasesFWD() + "]" : variant.getAltBasesFWD())));
}
}

24
java/test/org/broadinstitute/sting/gatk/walkers/fasta/BamToFastqIntegrationTest.java 100755
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@ -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);
}
}

42
java/test/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceIntegrationTest.java 100755
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@ -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);
}
}

2
java/test/org/broadinstitute/sting/gatk/walkers/indels/IntervalCleanerIntegrationTest.java
View File

@ -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);