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