Jerry/gzip or standard in as input for matrix #243
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We weren't actually using flate2 anywhere yet, so I have removed the dependency.
Trying to keep the focus on the current version...
Instead of putting this directly in the Python bindings, now this is available in the core library. This way, we can also add a command-line way to do the same thing, for instance.
…hell pipeline approach
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In this PR, we are adding a few features following with #238. We are now supporting to pass in gzip GAF files, and to use CLI command line precessing the files. There are two main changes in this PR.
Integrateingflate 2 decompression into
make_pangenotype_matrixto automatically handle gzip files and plain text files at the same time.Adding a new make_pangenotype_matrix_from_stream that accepts standard input to read pangenotype data from streams.
Currently, the users can pass in gzip files in the python binding, or use CLI command
gzip -dc Chr3.1.gaf.gz | fgfa -I Chr3.gfa matrix --stdinfor matrix constructing. The users can also usefgfa -I Chr3.gfa matrix -f Chr3.1.gaf.gzfor a gzip format orfgfa -I Chr3.gfa matrix -f Chr3.1.gaffor plain text format.