Magnipore

Added

- [read5](https://github.com/JannesSP/read5) to internaly handle the input formats:
- fast5,
- [slow5, blow5](https://github.com/hasindu2008/slow5tools) and
- potentially [pod5](https://github.com/nanoporetech/pod5-file-format) in the future
- [magnipore now via pip available](https://pypi.org/project/magnipore/)
- more tests
- testing file formats fast5, slow5 & blow5
- testing event aggregation

Changed

1. replaced [nanopolish](https://github.com/jts/nanopolish) eventalign with [f5c](https://github.com/hasindu2008/f5c) eventalign
2. pod5 is now available via [conda](https://anaconda.org/JannesSP/pod5), no need for `pip install pod5` anymore

Parameters

Changed
a lot of parameter names were shortened and short parameter names were added
- --path_to_fast5_first_sample -> --raw_data_first_sample
- --path_to_reference_first_sample -> --reference_first_sample
- --first_sample_label -> --label_first_sample
- --path_to_fast5_sec_sample -> --raw_data_sec_sample
- --path_to_reference_sec_sample -> --reference_sec_sample
- --sec_sample_label -> --label_sec_sample
- --path_to_first_basecalls -> -b1, --basecalls_first_sample
- --path_to_sec_basecalls -> -b2, --basecalls_sec_sample
- --path_to_first_sequencing_summary -> -s1, --sequencing_summary_first_sample
- --path_to_sec_sequencing_summary -> -s2, --sequencing_summary_sec_sample

Removed
- -f5, --fast5_out

Added
- -rna
- -r10
- -km, --kmer_model

Changed OMV size back to 30

changed OMV size to 10 by mistake - lead to much longer runtime!

- Change default minimap2 string from 'splice' to 'map-ont'
- Add sequencing summary parameter, if sequencing summary is not in the same dir as basecalls
- Fixed Typos in README

Reference Difference File (.refdiff) handles complete IUPAC code now

- introducing possible substitutions for set-characters like Y, R, S, W, M, K and N
- similar to Ns in the reference, we cannot make a clear statement

Ref1: ACTTG
Ref2: ACTTG
-> match

Ref1: ACCTG
Ref2: ACTTG
-> substitution

Ref1: ACYTG
Ref2: ACTTG
-> possible substitution

Ref1: ACYTG
Ref2: ACATG
-> substitution

Removed

1. removed parameters:
- strict
- r2

2. removed coverage plots from nanosherlock

3. Reduce stored data in RED file
- removed base & motif columns

Added

1. Pytests
- added first tests, more to be written
- added tests to meta.yml, will be executed when using building conda package

2. Updated Help Message in README.md

Changed

1. Use IUPAC code for refdiff substitutions
- Example: Y:C or Y:T is no subsitution mutation anymore, as Y = {C, T}

2. Reduced storage of plotting data in magnipore.py

Remove Filter For 0 Coverage Positions

Before:

- positions with 0 coverage (in at least 1 of both samples) did not show up in the .magnipore output files, only in the .red files

Now:

- they show up containing 0s for mean and stdev and nans for tdscore and kl divergence