git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/SICtools@115484 bc3139a8-67e5-0310-9ffc-ced21a209358
Xiaobin Xing authored on 31/03/2016 08:14:30
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@@ -2,26 +2,7 @@ indelDiff <- |
| 2 | 2 |
function(bam1,bam2,refFsa,regChr,regStart,regEnd,minBaseQuality = 13, |
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minMapQuality = 0,nCores = 1,pValueCutOff = 0.05,gtDistCutOff = 0.1,verbose=TRUE){
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- ## for test |
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-# library(doParallel) |
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-# library(Rsamtools) |
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-# library(matrixStats) |
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-# library(plyr) |
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-# |
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-# bam1 <- '/g/steinmetz/xing/SICtoolsDebug/20160319/debug/ER.sorted.bam' |
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-# bam2 <- '/g/steinmetz/xing/SICtoolsDebug/20160319/debug/d1c.0.01.bam' |
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-# refFsa <- '/g/steinmetz/xing/SICtoolsDebug/20160319/debug/S288c.fa' |
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-# regChr <- 'chr2' |
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-# regStart <- 1 |
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-# regEnd <- 230218 |
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-# minBaseQuality <- 13 |
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-# minMapQuality <- 0 |
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-# nCores <- 10 |
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-# pValueCutOff <- 0.05 |
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-# gtDistCutOff <- 0.1 |
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-# verbose <- TRUE |
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-# |
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- |
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+ |
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## disable dimention dropping for matrix |
| 26 | 7 |
`[` <- function(...) base::`[`(...,drop=FALSE) |
| 27 | 8 |
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| ... | ... |
@@ -2,26 +2,6 @@ snpDiff <- |
| 2 | 2 |
function(bam1,bam2,refFsa,regChr,regStart,regEnd,minBaseQuality = 13, |
| 3 | 3 |
minMapQuality = 0,nCores = 1,pValueCutOff= 0.05,baseDistCutOff = 0.1,verbose=TRUE){
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| 4 | 4 |
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- |
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- ## for test |
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-# library(doParallel) |
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-# library(Rsamtools) |
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-# library(matrixStats) |
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-# library(plyr) |
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-# |
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-# bam1 <- '/g/steinmetz/xing/SICtoolsDebug/20160319/debug/ER.sorted.bam' |
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-# bam2 <- '/g/steinmetz/xing/SICtoolsDebug/20160319/debug/d1c.0.01.bam' |
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-# refFsa <- '/g/steinmetz/xing/SICtoolsDebug/20160319/debug/S288c.fa' |
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-# regChr <- 'chr1' |
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-# regStart <- 1 |
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-# regEnd <- 230218 |
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-# minBaseQuality <- 13 |
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-# minMapQuality <- 0 |
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-# nCores <- 10 |
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-# pValueCutOff <- 0.05 |
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-# baseDistCutOff <- 0.1 |
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-# verbose <- TRUE |
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- |
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| 25 | 5 |
## disable dimention dropping for matrix |
| 26 | 6 |
`[` <- function(...) base::`[`(...,drop=FALSE) |
| 27 | 7 |
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