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output gzipped data #26

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billzt opened this issue Oct 7, 2017 · 3 comments
Open

output gzipped data #26

billzt opened this issue Oct 7, 2017 · 3 comments

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@billzt
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billzt commented Oct 7, 2017

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

@sfchen
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sfchen commented Oct 7, 2017

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

sfchen added a commit that referenced this issue Oct 28, 2017
gzip input --> gzip output
ungzip input --> ungzip output
ungzip input + --gzip (-z) option --> gzip output

issues:
#26
#14
@sfchen
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sfchen commented Oct 28, 2017

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.

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