makeChrTable: makeChrTable - Pulls out chromosome and length data from the...
In contiBAIT: Improves Early Build Genome Assemblies using Strand-Seq Data

Description Usage Arguments Details Value Examples

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

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

`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

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

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

#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)