bambi: bambi

In mskilab/bambi: R to query barcode indices on bam files

Description

motivation explanation queries WGS and SS 10x BAMs

Arguments

p

A process object.

command

Character scalar, the command to run. It will be escaped via shQuote.

args

Character vector, arguments to the command. The will be escaped via shQuote.

commandline

A character scalar, a full command line. No escaping will be performed on it.

stdout

What to do with the standard output. Possible values: FALSE: discard it; a string, redirect it to this file, TRUE: redirect it to a temporary file.

stdout

What to do with the standard error. Possible values: FALSE: discard it; a string, redirect it to this file, TRUE: redirect it to a temporary file.

grace

Grace pediod between the TERM and KILL signals, in seconds.

...

Extra arguments are passed to the readLines function.

Details

$grab_bx() grab BX tags (if exist)

grab_bx = function(query, data.table = FALSE, verbose = FALSE, mc.cores = 1)

$grab_cb() grab CB tags (if exist)

grab_cb = function(query, data.table = FALSE, verbose = FALSE, mc.cores = 1)

$grab_ub() grab CB tags (if exist)

grab_ub = function(query, data.table = FALSE, verbose = FALSE, mc.cores = 1)

$fetch_by_tag() grab CB tags (if exist)

fetch_by_tag = function(tag, query, data.table = FALSE, verbose = FALSE, mc.cores = 1)

mskilab/bambi documentation built on May 14, 2019, 4:04 a.m.