A command-line utility for converting .hic to .mcool files
Project description
hic2mcool
A command-line utility for converting .hic to .mcool files.
Installation
Install via pip:
pip install hic2mcool
Usage
usage: hic2mcool [-h] --hic_file HIC_FILE --mcool_file MCOOL_FILE [--data_type DATA_TYPE] [--normalization NORMALIZATION] [--temp_dir TEMP_DIR]
Convert .hic to .mcool format using hicstraw and cooler.
optional arguments:
-h, --help show this help message and exit
--hic_file HIC_FILE Input .hic file
--mcool_file MCOOL_FILE
Output .mcool file
--data_type DATA_TYPE
Type of data to extract ("observed", "oe"); default: "observed"
--normalization NORMALIZATION
Normalization method: NONE, VC, VC_SQRT, KR, SCALE, etc; default: "NONE"
--temp_dir TEMP_DIR Specify a temporoary directory location, otherwise system default is used.
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