contiBAIT (version 1.0.0)

makeChrTable: makeChrTable -- Pulls out chromosome and length data from the header of a bam file

Description

makeChrTable -- Pulls out chromosome and length data from the header of a bam file

Usage

makeChrTable(bamFile, splitFile = NULL, splitBy = NULL, verbose = TRUE)

Arguments

bamFile

string of location of a bam file to extract header data from

splitFile

GRanges object (of type chr, start and end: no strand or meta columns) of locations in which to split the assembly, such as previously determined locations of contig chimerism

splitBy

integer determining the average size contigs should be split by

verbose

if FALSE, no messages appear on terminal

Value

• a GRanges object of class ChrTable, containing information on the organism's chromosomes as extracted from the BAM file header.

Details

makeChrTable creates a table with chromosome name and chromosome length by extracting header data from the supplied bam file.

Examples

#Get an example BAM file and generate a chromosome table featuring fragment names and lengths

example.bam <- list.files(file.path(system.file(package='contiBAIT'), 'extdata'), full.names=TRUE)[1]

chrTable <- makeChrTable(example.bam) 

show(chrTable)

dividedChr <- makeChrTable(example.bam, splitBy=1000000)

show(dividedChr)