@@ -7,19 +7,19 @@ test_indelDiff <- function(){

 	refFsa <- system.file(package='SICtools','extdata','example.ref.fasta')

 	## test deletion

-	deletionTest <- indelDiff(bam1,bam2,refFsa,'chr04',962501,1026983,pValueCutOff=1,gtDistCutOff=0,verbose=FALSE)

+	deletionTest <- indelDiff(bam1,bam2,refFsa,'chr04',962501,1026983,pValueCutOff=1,gtDistCutOff=0,verbose=FALSE,nCores=2)

 	checkEquals(deletionTest$pos, 1026860)

 	checkEquals(deletionTest$ref, 'TCG')

 	checkEquals(deletionTest$altGt1, 'T')

 	## test insertion

-	insertionTest <- indelDiff(bam1,bam2,refFsa,'chr07',828514,828914,pValueCutOff=1,gtDistCutOff=0) 

-	checkEquals(insertionTest$pos, 828714)

-	checkEquals(insertionTest$ref, 'CAAAAAAA')

-	checkEquals(insertionTest$altGt1, 'CAAAAAAAA')

+	insertionTest <- indelDiff(bam1,bam2,refFsa,'chr07',828514,828914,pValueCutOff=1,gtDistCutOff=0,nCores=2) 

+	checkEquals(insertionTest$pos, c(828636,828714))

+	checkEquals(insertionTest$ref, c('GCCA','CAAAAAAA'))

+	checkEquals(insertionTest$altGt1, c('GCCACCA','CAAAAAAAA'))

 	## test NULL

-	checkTrue(is.null(indelDiff(bam1,bam2,refFsa,'chr04',962501,1026983,pValueCutOff=1,gtDistCutOff=2,verbose=FALSE)))

+	checkTrue(is.null(indelDiff(bam1,bam2,refFsa,'chr04',962501,1026983,pValueCutOff=1,gtDistCutOff=2,verbose=FALSE,nCores=2)))

 }

@@ -8,12 +8,12 @@ test_snpDiff <- function(){

 	refFsa <- system.file(package='SICtools','extdata','example.ref.fasta')

 	## check

-	snpTest <- snpDiff(bam1,bam2,refFsa,'chr04',962501,1026983,pValueCutOff=1,baseDistCutOff=0)

+	snpTest <- snpDiff(bam1,bam2,refFsa,'chr04',962501,1026983,pValueCutOff=1,baseDistCutOff=0,nCores=2)

 	checkEquals(nrow(snpTest),16)

 	checkEquals(subset(snpTest,p.value < 1e-10)$pos,c(962801,1026683))

 	## check NULL

-	checkTrue(is.null(snpDiff(bam1,bam2,refFsa,'chr04',962501,1026983,pValueCutOff=0,baseDistCutOff=0)))

+	checkTrue(is.null(snpDiff(bam1,bam2,refFsa,'chr04',962501,1026983,pValueCutOff=0,baseDistCutOff=0,nCores=2)))

 }