output gzipped data

[tao-bioinfo]

If the input is gzipped data, the output should be automatically gzipped. Otherwise users would encounter large files

[sfchen]

Actually I implemented this feature but finally discarded it since the python gzip lib is too slow for direct gz output.

Currently I suggest to add a gzip after AfterQC is done. I am considering to reimplement AfterQC with C++ for some performance and threading issue.

[antonkulaga]

Some tools have --gzip parameter to allow users decide whether to gzip output or not

[sfchen]

gzip output has been enabled on master branch.

For gzipped input, then the output will be also gzipped. If the input is not gzipped, you can enable --gzip or -z option to force gzip compression.

gzip input --> gzip output
ungzip input --> ungzip output
ungzip input + --gzip (-z) option --> gzip output

Use --compression to change the compression level (0~9), default is 2. The better the compression, the lower the speed.