feat: infer lib type if mate info not in seq IDs

[BorisYourich]

Description

I have added a GetOrientation class instance in the GetLibType class so that when the sequence identifiers do not match, the files will be mapped separately. Then the alignments for each file are compared and if at least a cutoff fraction of the reads can be considered concordant, the results.relationship is changed to "split_mates".

Note that this implementation is completely written in Python and will easily become the bottleneck of the program as the logic by which the mappings are compared is all-vs-all for the two mates, so if a high fraction of reads are multi-mapping, the execution will get significantly slower

Fixes #85

Type of change

Please delete options that are not relevant.

• [x] New feature (non-breaking change which adds functionality)

Checklist

Please carefully read these items and tick them off if the statements are true or do not apply.

• [x] I have performed a self-review of my own code
• [x] My code follows the existing coding style, lints and generates no new warnings
• [x] I have added type annotations to all function/method signatures, and I have added type annotations for any local variables that are non-trivial, potentially ambiguous or might otherwise benefit from explicit typing.
• [x] I have commented my code in hard-to-understand areas
• [x] I have added ["Google-style docstrings"] to all new modules, classes, methods/functions or updated previously existing ones
• [x] I have added tests that prove my fix is effective or that my feature works
• [x] New and existing unit tests pass locally with my changes and I have not reduced the code coverage relative to the previous state
• [x] I have updated any sections of the app's documentation that are affected by the proposed changes

If for some reason you are unable to tick off all boxes, please leave a comment explaining the issue you are facing so that we can work on it together.

[codecov[bot]]

Codecov Report

Patch coverage: 100.00% and project coverage change: +0.01 :tada:

Comparison is base (bf11484) 99.79% compared to head (2a4b122) 99.80%.

Additional details and impacted files

```diff @@ Coverage Diff @@ ## dev #129 +/- ## ========================================== + Coverage 99.79% 99.80% +0.01% ========================================== Files 12 12 Lines 957 1024 +67 ========================================== + Hits 955 1022 +67 Misses 2 2 ``` | [Impacted Files](https://app.codecov.io/gh/zavolanlab/htsinfer/pull/129?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=zavolanlab) | Coverage Δ | | |---|---|---| | [htsinfer/cli.py](https://app.codecov.io/gh/zavolanlab/htsinfer/pull/129?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=zavolanlab#diff-aHRzaW5mZXIvY2xpLnB5) | `100.00% <100.00%> (ø)` | | | [htsinfer/get\_library\_type.py](https://app.codecov.io/gh/zavolanlab/htsinfer/pull/129?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=zavolanlab#diff-aHRzaW5mZXIvZ2V0X2xpYnJhcnlfdHlwZS5weQ==) | `100.00% <100.00%> (ø)` | | | [htsinfer/htsinfer.py](https://app.codecov.io/gh/zavolanlab/htsinfer/pull/129?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=zavolanlab#diff-aHRzaW5mZXIvaHRzaW5mZXIucHk=) | `100.00% <100.00%> (ø)` | | | [htsinfer/models.py](https://app.codecov.io/gh/zavolanlab/htsinfer/pull/129?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=zavolanlab#diff-aHRzaW5mZXIvbW9kZWxzLnB5) | `100.00% <100.00%> (ø)` | |

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[balajtimate]

Sure, I'll run some tests and get back to it soon

[BorisYourich]

Sure, thanks for taking the time, I will fix that soon as possible.

[BorisYourich]

The issue was that I didn't consider reads that do not map at all, there is no need to include such alignments, therefore I added a check.

[BorisYourich]

Okay, I just pushed the changes that Alex recommended, I think you can merge this.