d4_create: Create d4 file(s) from inputs
In snystrom/rd4tools: An Interface to d4tools

Description Usage Arguments Details Value additional arguments Examples

View source: R/create.R

This function will create a new d4 file for each file passed to input. Additional command arguments can be passed to ... to configure

1	d4_create(input, output = NULL, ..., d4tools = NULL)

`input`	path to BigWig, BAM, or CRAM files to convert to d4.
`output`	path to save d4 output. If unset, the file is named identically and in the same path as the input file, but with the .d4 extension.
`...`	see additional arguments table below for valid arguments
`d4tools`	path to d4tools (or use options("d4tools" = "path/to/d4tools"))

Note there is no type checking on inputs, so using inputs with heterogeneous file types may produce unintended consequences when using file-type specific arguments in ....

path to new d4 object

name	data type	description
deflate	`logical(1)`	Enable deflate compression
dict_auto	`logical(1)`	Automatically determine dictionary type by random sampling
dump_dict	`logical(1)`	do not profile BAM file, only dump dictionary
sparse	`logical(1)`	Sparse mode, same as `deflate = TRUE, dict_range = "0-1"`. Enables secondary table compression and disable primary table
deflate_level	`integer(1)`	Configure the deflate algorithm, default 5
dict_file	`character(1)`	Path to a file defining the values of the dictionary
dict_range	`character(1)`	Dictionary specification as a range: "a-b" encoding values from A to B (exclusive)
filter	`character(1)`	A regex matching the genome name should present in the output file (note: use a shell regex, not R-style regexes)
genome	`character(1)`	genome description file (Used by BED inputs)
mapping_qual	`integer(1)`	minimal mapping quality (only valid with CRAM/BAM inputs)
ref	`character(1)`	path to reference genome file (only used with CRAM inputs)
threads	`integer(1)`	number of threads to use for encoding

## Not run: 
# Will create "example.d4"
d4_create("example.fq")

# Explicit naming is done by passing a name to "output"
d4_create("example.fq", "my_new_file.d4")

## End(Not run)