$ allcools standardize-allc -h
usage: allcools standardize-allc [-h] --allc_path ALLC_PATH --chrom_size_path
CHROM_SIZE_PATH
[--compress_level COMPRESS_LEVEL]
[--remove_additional_chrom]
optional arguments:
-h, --help show this help message and exit
--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)
--compress_level COMPRESS_LEVEL
Compression level for the output file (default: 5)
--remove_additional_chrom
Whether to remove rows with unknown chromosome instead
of raising KeyError (default: False)
required arguments:
--allc_path ALLC_PATH
Path to 1 ALLC file (default: None)
