perf: optimize STAR memory usage and read orientation defaults

zavolanlab / htsinfer

Infer metadata for your downstream analysis straight from your RNA-seq data

Apache License 2.0

10 stars 22 forks source link

Description

Added --genomeChrBinNbits to get_read_orientation.py to calculate the size of bins for genome storage as min(18,log2[max(GenomeLength/NumberOfReferences,ReadLength)])
Updated the default parameter for --read_orientation_min_mapped_reads to 18
Updated README.md

Fixes #115

Type of change

[X] Bug fix (non-breaking change which fixes an issue)
[X] Documentation update

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 Report

Patch coverage: 100.00% and no project coverage change.

Comparison is base (426177c) 99.78% compared to head (6abd99b) 99.79%.

Additional details and impacted files

```diff @@ Coverage Diff @@ ## dev #125 +/- ## ======================================= Coverage 99.78% 99.79% ======================================= Files 12 12 Lines 948 957 +9 ======================================= + Hits 946 955 +9 Misses 2 2 ``` | [Impacted Files](https://app.codecov.io/gh/zavolanlab/htsinfer/pull/125?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=zavolanlab) | Coverage Δ | | |---|---|---| | [htsinfer/get\_read\_orientation.py](https://app.codecov.io/gh/zavolanlab/htsinfer/pull/125?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=zavolanlab#diff-aHRzaW5mZXIvZ2V0X3JlYWRfb3JpZW50YXRpb24ucHk=) | `99.13% <100.00%> (+0.03%)` | :arrow_up: |

zavolanlab / htsinfer