Changelogs » Hmtnote

Hmtnote

0.7.2

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* Remove pysam from requirements and fix dependencies;
* Change docstrings to Google style;
* Update documentation;
* Update testfiles.

0.7.1

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* Fix issue with echoed string (78);
* Fix issue with CSV format columns (79);
* Update testfiles.

0.7.0

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* Add ``--csv`` command line option to convert output to CSV format;
* Add homoplasmy annotations;
* Update all tests accordingly;
* Update documentation.

0.6.0

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* Use vcfpy2 for VCF files parsing;
* Dump annotation files directly from HmtVar instead of the original API call;
* Add annotation progress bar;
* Check internet connection using httpstat.us;
* Update tests and add more test cases;
* Update documentation with detailed API usage.

0.5.5

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* Fix VCF record parsing issue.

0.5.4

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* Fix installation issue.

0.5.3

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* Update requirements in setup.py.

0.5.2

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* Fix requirements in setup.py file.

0.5.1

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* Fix issue with the new VCFpy implementation where new info where badly reported;
* Update test files restricting the number of entries to 80 for faster testing.

0.5.0

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* Replace VCF parsing using VCFpy instead of cyvcf2;
* Rename ``hmtnote.annotate_vcf()`` to ``hmtnote.annotate()`` for compliance with CLI.

0.4.0

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* Add support for insertion and deletion annotations;
* Add test suite and files for indels.

0.3.1

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* Update installation requirements and documentation.

0.3.0

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* Add options to download the annotation database locally;
* Use local database to annotate variants (instead of calling HmtVar's API);
* Fallback to using local database when no internet connection is available;
* Check if local database actually exists before performing offline annotation;
* Databases are downloaded asynchronously.

0.2.0

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* Add warnings to ``hmtnote`` command to be compliant with future versions;
* Check internet connection before trying to annotate variants.

0.1.5

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* Add HmtVar ID of the variant in basic and full annotation;
* Change ``Disease Score`` annotation to ``DiseaseScore``.

0.1.4

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* Fix issue that prevented importing ``annotate_vcf()`` into Python scripts.

0.1.3

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* Fix issue with ``--predict`` annotation, which didn't retrieve the correct field from HmtVar.

0.1.2

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* Classes and methods are protected where needed;
* Code style is clean.

0.1.1

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* Clean installation requirements for conda;
* Update documentation.

0.1.0

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* First release on PyPI.