export.bedoc: Store GAlignments object as .bedoc

In Roleren/ORFik: Open Reading Frames in Genomics

Store GAlignments object as .bedoc

Description

A fast way to store, load and use bam files. (we now recommend using link{export.ofst} instead!)
.bedoc is .bed ORFik, an optimized bed format for coverage reads with cigar and replicate number.
.bedoc is a text based format with columns (5 maximum):
1. chromosome
2. cigar: (cigar # M's, match/mismatch total)
3. start (left most position)
4. strand (+, -, *)
5. score: duplicates of that read

Usage

export.bedoc(object, out)

Arguments

object	a GAlignments object
out	a character, location on disc (full path)

Details

Positions are 1-based, not 0-based as .bed. Import with import.bedoc

Value

NULL, object saved to disc

Roleren/ORFik documentation built on Nov. 13, 2024, 10 p.m.