export.bedoc: Store GAlignments object as .bedoc

In ORFik: Open Reading Frames in Genomics

Description

A much faster way to store, load and use bam files.
.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

ORFik documentation built on March 27, 2021, 6 p.m.