Commit 6e163f45 authored by Sander van der Zeeuw's avatar Sander van der Zeeuw
Browse files

added bcftools singlesample to the test

parent f17e2175
......@@ -44,12 +44,13 @@ class ShivaVariantcallingTest extends TestNGSuite with Matchers {
bams <- 0 to 2;
raw <- bool;
bcftools <- bool;
bcftools_singlesample <- bool;
haplotypeCallerGvcf <- bool;
haplotypeCallerAllele <- bool;
unifiedGenotyperAllele <- bool;
unifiedGenotyper <- bool;
haplotypeCaller <- bool
) yield Array[Any](bams, raw, bcftools, unifiedGenotyper, haplotypeCaller, haplotypeCallerGvcf, haplotypeCallerAllele, unifiedGenotyperAllele)
) yield Array[Any](bams, raw, bcftools, bcftools_singlesample, unifiedGenotyper, haplotypeCaller, haplotypeCallerGvcf, haplotypeCallerAllele, unifiedGenotyperAllele)
).toArray
}
......@@ -57,6 +58,7 @@ class ShivaVariantcallingTest extends TestNGSuite with Matchers {
def testShivaVariantcalling(bams: Int,
raw: Boolean,
bcftools: Boolean,
bcftools_singlesample: Boolean,
unifiedGenotyper: Boolean,
haplotypeCaller: Boolean,
haplotypeCallerGvcf: Boolean,
......@@ -65,6 +67,7 @@ class ShivaVariantcallingTest extends TestNGSuite with Matchers {
val callers: ListBuffer[String] = ListBuffer()
if (raw) callers.append("raw")
if (bcftools) callers.append("bcftools")
if (bcftools_singlesample) callers.append("bcftools_singlesample")
if (unifiedGenotyper) callers.append("unifiedgenotyper")
if (haplotypeCallerGvcf) callers.append("haplotypecaller_gvcf")
if (haplotypeCallerAllele) callers.append("haplotypecaller_allele")
......@@ -78,7 +81,8 @@ class ShivaVariantcallingTest extends TestNGSuite with Matchers {
val illegalArgumentException = pipeline.inputBams.isEmpty ||
(!raw && !bcftools &&
!haplotypeCaller && !unifiedGenotyper &&
!haplotypeCallerGvcf && !haplotypeCallerAllele && !unifiedGenotyperAllele)
!haplotypeCallerGvcf && !haplotypeCallerAllele && !unifiedGenotyperAllele &&
!bcftools_singlesample)
if (illegalArgumentException) intercept[IllegalArgumentException] {
pipeline.script()
......
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