Methlab

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- Fixed ``install_requires``.
- SAM files now return the SAM flag.

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- Class to manipulate aligned SAM files from Bismark.
- Included docs on how to use.

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* Documentaion for align_fastq_with_plate_positions and CytosineCoverageFile.

Renamed to methlab to conform to Python standards

20th July 2023

Corrected how versioning is done - this ought to be done in __init__.py and be imported to setup.py
I'm not really sure what setup.cfg is doing.

Initial commit

Changes to be committed:
new file: AUTHORS.rst
new file: CONTRIBUTING.rst
new file: HISTORY.rst
new file: LICENSE
new file: MANIFEST.in
new file: README.rst
new file: methlab/align_fastq_with_plate_positions.py
new file: methlab/data/nordborg_nextera_index_sets.csv
new file: methlab/data/plate_2022-007.csv
new file: methlab/data/unique_nextera_dual_xt.csv
new file: setup.cfg
new file: setup.py
new file: tests/test_align_fastq_with_plate_positions.py
new file: tests/test_methlab.py

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- Initial commit
- Function `align_fastq_with_plate_positions.py`` looks up adaptor index positions from bam file names


methlab

A class for disecting allc files

25th July 2023

Created a class to import and take apart cytosine coverage files from Bismark.

* `count_reads` counts up methylated and unmethylated reads, plus total number
of cytosines in each sequence context.
* `methylation_over_features` takes series of genome coordinates (from an
annotation file, for example), pulls out each part of the coverage file and
calls `count_reads` on each.
* `conversion_rate` calculates mean methylation on each chromosome
* `methylation_in_windows` partitions the genome in to windows of fixed size and
calls `count_reads` on each.

Added test data and a test file.