- For compiling: C++ 11
- At least 2GB of RAM and 50GB of storage
- [optional] multi-core CPU for parallel decoding.
The bedMethyl files are "revised" bed files. A typical bedMethyl file has 9 + 2 columns, with the first 9 columns matching those of the bed file and 2 additional columns containing coverage and percentage information
| column 1 | column 2 | column 3 | column 4 | column 5 | column 6 | column 7 | column 8 | column 9 | column 10 | column 11 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| definition | chrom | chromStart | chromEnd | name | score | strand | thickStart | thickEnd | itemRGB | coverage | percentage |
| datatype | string | int32_t | int32_t | string | int32_t | string | int32_t | int32_t | string | int32_t | uint8_t |
Sample files can be download from the ENCODE database, for example the WGBS experiment of forebrain embryo. Here, we provide a small test file in the folder data
# download METHCOMP
git clone https://github.com/jianhao2016/METHCOMP
# compile
make
To run METHCOMP on the test file, use the following command:
./output full ../data/test .
This command will compress the test file into "compressed_test-0" and then decompress it to "reconstructed_test-0". The compressed files and decompressed files are stored in the folder DerivedData/
To run the compression/decompression algorithm on an arbitrary methylation data file, use the following command:
./output <mode> <path to file> <output folder path> [optional <number of line per block> <line to be decoded>]
Or use the scripts for block-mode compression:
source auto_compress.sh <path to file> <output path> [optional <lines in each block>]
And block-mode decompression:
source auto_decompress.sh <file name> <file directory> <output path> [optional <lines in each block>]
mode can be chosen from the following menu: full (joint compression and decompression), compress and decompress. When <output folder path> is omitted, the default output folder is DerivedData/.
Two optional arguments, <number of line per block> and <line to be decoded>, are used for random access. To
compress the original file in blocks, enter the number of lines in each block you would like to. To decoded a specific
line, enter the line number to decode the block it belongs to.
The auto_script is for parallel decoding.
The compressed files and decompressed files are named "compressed_<file name>" and "reconstructed_<file name>"