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[WIP] Hdf5 io #4

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[WIP] Hdf5 io #4

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Commits on Jul 30, 2021

  1. hdf5 io funcs

    @alexey0308
    alexey0308 committed Jul 30, 2021
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  2. add h5py to prepare

    @alexey0308
    alexey0308 committed Jul 30, 2021
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  3. move cycle within with open()

    @alexey0308
    alexey0308 committed Jul 30, 2021
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Commits on Aug 2, 2021

  1. correct level

    @alexey0308
    alexey0308 committed Aug 2, 2021
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  2. add iteration over chr and test

    @alexey0308
    alexey0308 committed Aug 2, 2021
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  3. use w to substitute hdf5 file if exists

    @alexey0308
    alexey0308 committed Aug 2, 2021
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  4. upd version in test to silence it

    @alexey0308
    alexey0308 committed Aug 2, 2021
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  5. add read_chromosome and use it to load chr matrix

    @alexey0308
    alexey0308 committed Aug 2, 2021
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  6. add reading from hdf5 in smooth

    @alexey0308
    alexey0308 committed Aug 2, 2021
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  7. rename to scan

    @alexey0308
    alexey0308 committed Aug 2, 2021
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Commits on Aug 5, 2021

  1. fix imports

    @alexey0308
    alexey0308 committed Aug 5, 2021
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Commits on Aug 16, 2021

  1. hdf5 io funcs

    @alexey0308
    alexey0308 committed Aug 16, 2021
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  2. add h5py to prepare

    @alexey0308
    alexey0308 committed Aug 16, 2021
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  3. move cycle within with open()

    @alexey0308
    alexey0308 committed Aug 16, 2021
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  4. correct level

    @alexey0308
    alexey0308 committed Aug 16, 2021
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  5. add iteration over chr and test

    @alexey0308
    alexey0308 committed Aug 16, 2021
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  6. use w to substitute hdf5 file if exists

    @alexey0308
    alexey0308 committed Aug 16, 2021
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  7. upd version in test to silence it

    @alexey0308
    alexey0308 committed Aug 16, 2021
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  8. add read_chromosome and use it to load chr matrix

    @alexey0308
    alexey0308 committed Aug 16, 2021
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  9. add reading from hdf5 in smooth

    @alexey0308
    alexey0308 committed Aug 16, 2021
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  10. rename to scan

    @alexey0308
    alexey0308 committed Aug 16, 2021
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Commits on Aug 18, 2021

  1. rm class annotation

    @alexey0308
    alexey0308 committed Aug 18, 2021
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  2. corrected import of packages

    @LeonieKuechenhoff
    LeonieKuechenhoff committed Aug 18, 2021
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  3. Merge branch 'hdf5' of https://github.com/LKremer/scbs into hdf5

    @LeonieKuechenhoff
    LeonieKuechenhoff committed Aug 18, 2021
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  4. ADD streamed writing of hd5f from coo matrix

    @alexey0308
    alexey0308 committed Aug 18, 2021
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Commits on Aug 19, 2021

  1. upd doc

    @alexey0308
    alexey0308 committed Aug 19, 2021
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  2. ADD calculate number of entries in the chromosome file

    @alexey0308
    alexey0308 committed Aug 19, 2021
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  3. ADD ExitStack to avoid not closed files in exceptions

    @alexey0308
    alexey0308 committed Aug 19, 2021
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  4. Merge branch 'hdf5' into hdf5-streaming

    @alexey0308
    alexey0308 committed Aug 19, 2021
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  5. ADD calculate number of entries in the chromosome file

    @alexey0308
    alexey0308 committed Aug 19, 2021
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  6. ADD ExitStack to avoid not closed files in exceptions

    @alexey0308
    alexey0308 committed Aug 19, 2021
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  7. ADD test write from stream -> read hdf5

    @alexey0308
    alexey0308 committed Aug 19, 2021
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  8. UPD version

    @alexey0308
    alexey0308 committed Aug 19, 2021
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Commits on Aug 20, 2021

  1. extract transformation of coo to csr

    @alexey0308
    alexey0308 committed Aug 20, 2021
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  2. extract format class to file

    @alexey0308
    alexey0308 committed Aug 20, 2021
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  3. return file names, but not closed descriptors

    @alexey0308
    alexey0308 committed Aug 20, 2021
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  4. move return level

    @alexey0308
    alexey0308 committed Aug 20, 2021
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  5. fix level

    @alexey0308
    alexey0308 committed Aug 20, 2021
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  6. add description of chromosome class

    @alexey0308
    alexey0308 committed Aug 20, 2021
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  7. use to strategies to save 

    streamed and all-at-once chromosome file saving
    @alexey0308
    alexey0308 committed Aug 20, 2021
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Commits on Aug 23, 2021

  1. use compression and types

    @alexey0308
    alexey0308 committed Aug 23, 2021
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  2. add test with zeros in the end

    @alexey0308
    alexey0308 committed Aug 23, 2021
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  3. add streamed write to the prepare main func

    @alexey0308
    alexey0308 committed Aug 23, 2021
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Commits on Aug 25, 2021

  1. ADD sparse facade object

    @alexey0308
    alexey0308 committed Aug 25, 2021
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  2. ADD doc

    @alexey0308
    alexey0308 committed Aug 25, 2021
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  3. Merge branch 'hdf5-streaming' into hdf5

    @alexey0308
    alexey0308 committed Aug 25, 2021
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  4. fix imports

    @alexey0308
    alexey0308 committed Aug 25, 2021
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  5. import only if use

    @alexey0308
    alexey0308 committed Aug 25, 2021
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Commits on Aug 26, 2021

  1. add missing import

    @alexey0308
    alexey0308 committed Aug 26, 2021
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  2. sort imports

    @alexey0308
    alexey0308 committed Aug 26, 2021
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Commits on Sep 27, 2021

  1. add streaming flag

    @alexey0308
    alexey0308 committed Sep 27, 2021
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