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This class no longer outputs in sequenom format 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1832 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2009-10-14 17:16:36 +00:00
parent 0c95d6906f
commit d89bc2c796
1 changed files with 0 additions and 12 deletions
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12
java/test/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceIntegrationTest.java
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@ -21,22 +21,10 @@ public class FastaAlternateReferenceIntegrationTest extends WalkerTest {
Arrays.asList("3a48986c3832a768b478c3e95f994b0f"));
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("b53b067a3bdada202dba7d3c382ae1d0"));
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);
}
}