AbamFiles1=c(
"PHR19r-Input.bam")

AbamFiles2=c(
"PHR21r-bcatMono.bam",
"PHR23r-FUBP2.bam",
"PHR20r-bcatPoly.bam",
"PHR22r-TCF4.bam")
AcNAME <- "IgG"

BbamFiles1=c(
"PHR24r-IgG.bam")
BbamFiles2=c(
"PHR21r-bcatMono.bam",
"PHR23r-FUBP2.bam",
"PHR20r-bcatPoly.bam",
"PHR22r-TCF4.bam")
BcNAME <- "IgG"

mrs=function(r,c){
l=strsplit(r,"-")
rn=strsplit(l[[1]][2],"\\.")
l=strsplit(c,"-")
cn=strsplit(l[[1]][2],"\\.")
contrast=paste("RIPSeeker_",rn[[1]][1],"_vs_",cn[[1]][1],"_minus",sep="");
bamFiles=c(r,c)
cNAME <- cn[[1]][1]
outDir <- file.path(getwd(),contrast) 
cat("contrast: ",outDir,"\n")
binSize <- 200     # automatically determine bin size
minBinSize <- 150	 # min bin size in automatic bin size selection
maxBinSize <- 300	 # max bin size in automatic bin size selection
multicore <- TRUE		 # use multicore
biomart <- "ensembl"           # use archive to get ensembl 65
biomaRt_dataset <- "hsapiens_gene_ensembl" # human dataset id name	
goAnno <- "org.Hs.eg.db"                    # GO annotation database
seekOut.CCNT1 <- ripSeek(bamPath = bamFiles, cNAME = cNAME,
                   reverseComplement = TRUE, genomeBuild = "hg19",
		   strandType = "-",  
                   uniqueHit = TRUE, assignMultihits = TRUE, 
                   rerunWithDisambiguatedMultihits = TRUE,
                   binSize=binSize, minBinSize = minBinSize, 
                   maxBinSize = maxBinSize,
                   biomart=biomart, goAnno = goAnno,
                   biomaRt_dataset = biomaRt_dataset,
                   multicore=multicore, outDir=outDir)


contrast=paste("RIPSeeker_",rn[[1]][1],"_vs_",cn[[1]][1],"_plus",sep="");
outDir <- file.path(getwd(),contrast) 
cat("contrast: ",outDir,"\n")
binSize <- 200     # automatically determine bin size
minBinSize <- 150	 # min bin size in automatic bin size selection
maxBinSize <- 300	 # max bin size in automatic bin size selection
multicore <- TRUE		 # use multicore
biomart <- "ensembl"           # use archive to get ensembl 65
biomaRt_dataset <- "hsapiens_gene_ensembl" # human dataset id name	
goAnno <- "org.Hs.eg.db"                    # GO annotation database
seekOut.CCNT1 <- ripSeek(bamPath = bamFiles, cNAME = cNAME,
                   reverseComplement = TRUE, genomeBuild = "hg19",
		   strandType = "+",  
                   uniqueHit = TRUE, assignMultihits = TRUE, 
                   rerunWithDisambiguatedMultihits = TRUE,
                   binSize=binSize, minBinSize = minBinSize, 
                   maxBinSize = maxBinSize,
                   biomart=biomart, goAnno = goAnno,
                   biomaRt_dataset = biomaRt_dataset,
                   multicore=multicore, outDir=outDir)
}

for (i in AbamFiles2){mrs(i,AbamFiles1[1])}