splitBAM_byIndex {icetea}R Documentation

Split the composite BAM file using internal indexes (MAPCap)

Description

Split the composite BAM file using internal indexes (MAPCap)

Usage

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)


[Package icetea version 1.6.1 Index]