$ allcools merge-allc -h
usage: allcools merge-allc [-h] --allc_paths ALLC_PATHS [ALLC_PATHS ...]
--output_path OUTPUT_PATH --chrom_size_path
CHROM_SIZE_PATH [--cpu CPU]
[--bin_length BIN_LENGTH] [--snp]
optional arguments:
-h, --help show this help message and exit
--cpu CPU Number of processes to use in parallel. The real CPU
usage is ~1.5 times than this number, due to the sub
processes of handling ALLC files using tabix/bgzip.
Monitor the CPU and Memory usage when running this
function. (default: 10)
--bin_length BIN_LENGTH
Length of the genome bin in each parallel job, large
number means more memory usage. (default: 10000000)
--snp If true, means the input allc contain snp information,
and the allc processing will take care that. (default:
False)
required arguments:
--allc_paths ALLC_PATHS [ALLC_PATHS ...]
Single ALLC path contain wildcard OR multiple space
separated ALLC paths OR a file contains 1 ALLC path in
each row. (default: None)
--output_path OUTPUT_PATH
Path to the output merged ALLC file. (default: None)
--chrom_size_path CHROM_SIZE_PATH
Path to UCSC chrom size file. This can be generated
from the genome fasta or downloaded via UCSC
fetchChromSizes tools. All ALLCools functions will
refer to this file whenever possible to check for
chromosome names and lengths, so it is crucial to use
a chrom size file consistent to the reference fasta
file ever since mapping. ALLCools functions will not
change or infer chromosome names. (default: None)
