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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
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smallWig: Tool for Parallel RNAseq Compression
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