splitBAM_byIndex: Split the composite BAM file using internal indexes (MAPCap)

Description Usage Arguments Value Examples

View source: R/splitBAM_byIndex.R

Description

Split the composite BAM file using internal indexes (MAPCap)

Usage

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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

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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)

icetea documentation built on Nov. 8, 2020, 6:57 p.m.