name: d4-create - Create a D4 depth Dump
author: Hao Hou <haohou302@gmail.com>
args:
- filter:
short: f
long: filter
value_name: regex
help: A regex that matches the genome name should present in the output file
- ref:
short: r
long: ref
value_name: fai_file_path
help: Reference genome file (Used by CRAM inputs)
- genome:
short: g
long: genome
value_name: genome_file
help: The genome description file (Used by BED inputs)
- threads:
short: t
long: threads
value_name: num_of_threads
help: Specify the number of threads D4 can use for encoding
- dict-range:
short: R
long: dict-range
value_name: dict_spec
help: Dictionary specification, use "a-b" to specify the dictionary is encoding values from A to B(exclusively)
- dict-auto:
short: A
long: dict-auto
help: Automatically determine the dictionary type by random sampling
- dict-file:
short: d
long: dict-file
value_name: dict_spec_file
help: Provide a file that defines the values of the dictionary
- deflate:
short: z
long: deflate
help: Enable the deflate compression
- deflate-level:
long: deflate-level
value_name: level
help: Configure the deflate algorithm, default 5
- sparse:
long: sparse
short: S
help: Sparse mode, this is same as '-zR0-1', which enable secondary table compression and disable primary table
- dump-dict:
long: dump-dict
help: Do not profile the BAM file, only dump the dictionary
- min-mqual:
long: mapping-qual
short: q
value_name: mapping-qual
help: The minimal mapping quality (Only valid with CRAM/BAM inputs)
- bam-flag:
long: bam-flag
short: F
value_name: "bam-flag/+inclusive-mask/[-|~]exclusive-mask"
help: Count the reads with flag (Only valid with BAM/CRAM inputs).
- denominator:
long: denominator
value_name: VALUE
help: Turn on the fix-point mode, this will allow encoding real-number in D4 file
- with-index:
required: false
long: with-index
value_name: INDEX-TYPES
help: Also build the index
- input-file:
required: true
help: Path to the input file
index: 1
- output-file:
required: false
help: Path to the output file
index: 2