Split the composite BAM file using internal indexes (MAPCap)

Source: R/splitBAM_byIndex.R

Split the composite BAM file using internal indexes (MAPCap)

splitBAM_byIndex(bamFile, index_list, outfile_list, max_mismatch = 0,
  ncores = 1)

Arguments

bamFile	character. Path to a mapped BAM file
index_list	character. A list of indexes for splitting
outfile_list	character. A list of output file names (with order corresponding to that of index_list)
max_mismatch	integer. No. of mismatches allowed in index (maxium 1 recommended)
ncores	integer. Number of cores to use for parallel processing

Value

Filtered files

Examples

bam <- system.file("extdata", "bam/embryo1.bam", package = "icetea")
splitBAM_byIndex(bamFile = bam,
                 index_list = c("CAAGTG", "CAAGTT"),
                 outfile_list = c("test_filt1.bam","test_filt2.bam"),
                 ncores = 1)
#> Creating Filtering Rules
#> Filtering the BAM file
#> Done!