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WGLab / LongReadSum

MIT License
12 stars 2 forks source link

BUG: Fix FAST5, sequencing_summary.txt outputs and refactor project structure #16

Closed jonperdomo closed 2 years ago

jonperdomo commented 2 years ago

Enable FAST5 outputs. Also refactor the project structure, which closes #7

jonperdomo commented 2 years ago

FAST5 outputs are now being generated after fixing parse errors. To do this, I first check that the required headers are present. I will now incorporate FAST5 testing into the continuous integration/unit tests workflow

image

jonperdomo commented 2 years ago

I updated the project structure into src/ include/ tests/ and lib/ directories, closing issue #7 . This makes it easier to manage external dependencies needed for the FAST5 implementation.

jonperdomo commented 2 years ago

Created a new module for testing the HDF5 library with the "Create a dataset" example (link)

jonperdomo commented 2 years ago

Completed the unthreaded FAST5 file implementation. Note that the first read does not have a dataset so it's not counted as a read: image

jonperdomo commented 2 years ago

TODO: Fix the base counts. Should be 340189

jonperdomo commented 2 years ago

Oops, used different sample data for the previous output. Here is the actual output: image

jonperdomo commented 2 years ago

Outputs are the same as other tools, see issue #15