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readme.txt
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readme.txt
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The smallWig tool provides compression/decompression for WIG files.
Copyright by Zhiying Wang, 2015.
Please contact zhiying@uci.edu for any questions and source files.
==============================================
usage
==============================================
To compress a file, please use:
wig2smallwig [InputFile] [OutputFile]
options:
-m [N=0..9, uses 3 + 3*2^N MB memory, decompress should use same N]
context mixing
-r [B, encode block size from 8 to 32]
random access and encode by blocks of size 2^B
-p [total number of processes]
parallel realization, only available if -r is enabled and -m is disabled
To decompress a file, please use:
To use:
smallwig2wig [InputFile] [OutputFile]
options:
-s [ChrmName (e.g. chr1)] [Query Start (integer)] [Query End (integer)]
subsequence query
-p [total number of processes]
parallel realization, only available if -s is disabled and -r is enabled in encoding
==============================================
example
==============================================
1. Compress a file using standard setup:
$ wig2smallwig in.wig out.swig
2. Compress a file allowing random query in the future:
$ wig2smallwig in.wig out.wig -r 9 13
3. Compress a file allowing random query in the future, and use 4 parallel processors:
$ wig2smallwig in.wig out.wig -r 9 13 -p 4
4. Compress a file as much as possible for archive purposes using the maximum amount of memory:
$ wig2smallwig in.wig out.wig -m 9
5. Decompress a whole file:
$ smallwig2wig in.swig out.wig
6. Decompress a file only in chr1, start from location 300, end at location 500:
$ smallwig2wig in.swig out.wig -s chr1 300 500
7. Decompress a file with 4 parallel processors:
$ smallwig2wig in.swig out.wig -p 4