comp.index.files: Compress and index BED-like files

In jmonlong/PopSV: Population-based detection of structural variants from Read-Depth signal

Description

Compress and index BED-like files. The first three columns must define chromosome location, start and end position.

Usage

comp.index.files(files, outprefix = files, rm.input = TRUE,
  overwrite.out = TRUE, reorder = FALSE)

Arguments

files	the names of the files to compress and index.
outprefix	the prefix to use when naming the output files. By default, the original file names.
rm.input	should the original input file be removed after compression/indexing ? Default is TRUE.
overwrite.out	should a compressed file be overwritten if it already exists ? Default is TRUE.
reorder	should the files be read and reordered before compression/indexation. Default is FALSE.

Details

The files should be ordered by genomic position. If not 'reorder=TRUE' will force the files to be imported in R, reordered and written back.

Value

a character vector confirming the creation of the new files.

Author(s)

Jean Monlong

jmonlong/PopSV documentation built on Sept. 15, 2019, 9:29 p.m.