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

In vivekbhr/icetea: Integrating Cap Enrichment with Transcript Expression Analysis

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)

vivekbhr/icetea documentation built on June 8, 2020, 4:45 a.m.