git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/SICtools@115483 bc3139a8-67e5-0310-9ffc-ced21a209358
Xiaobin Xing authored on 31/03/2016 07:38:15
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@@ -8,9 +8,10 @@ test_snpDiff <- function(){
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| 8 | 8 |
refFsa <- system.file(package='SICtools','extdata','example.ref.fasta') |
| 9 | 9 |
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| 10 | 10 |
## check |
| 11 |
- snpTest <- snpDiff(bam1,bam2,refFsa,'chr04',962501,1026983,pValueCutOff=1,baseDistCutOff=0,nCores=2) |
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| 12 |
- checkEquals(nrow(snpTest),16) |
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| 11 |
+ snpTest <- snpDiff(bam1,bam2,refFsa,'chr04',1,1531933,pValueCutOff=1,baseDistCutOff=0,nCores=2) |
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+ checkEquals(nrow(snpTest),17) |
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| 13 | 13 |
checkEquals(subset(snpTest,p.value < 1e-10)$pos,c(962801,1026683)) |
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+ checkEquals(subset(snpTest, A1 == 16)$pos,c(963005,1026599)) |
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| 14 | 15 |
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| 15 | 16 |
## check NULL |
| 16 | 17 |
checkTrue(is.null(snpDiff(bam1,bam2,refFsa,'chr04',962501,1026983,pValueCutOff=0,baseDistCutOff=0,nCores=2))) |