History

0.1.0 (2019-03-03)

  • First release on PyPI.

0.1.1 (2019-03-04)

  • Clean installation requirements for conda;

  • Update documentation.

0.1.2 (2019-03-15)

  • Classes and methods are protected where needed;

  • Code style is clean.

0.1.3 (2019-03-17)

  • Fix issue with --predict annotation, which didn’t retrieve the correct field from HmtVar.

0.1.4 (2019-03-19)

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

0.1.5 (2019-03-20)

  • Add HmtVar ID of the variant in basic and full annotation;

  • Change Disease Score annotation to DiseaseScore.

0.2.0 (2019-03-25)

  • Add warnings to hmtnote command to be compliant with future versions;

  • Check internet connection before trying to annotate variants.

0.3.0 (2019-03-27)

  • 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.

0.3.1 (2019-03-29)

  • Update installation requirements and documentation.

0.4.0 (2019-04-03)

  • Add support for insertion and deletion annotations;

  • Add test suite and files for indels.

0.5.0 (2019-04-28)

  • Replace VCF parsing using VCFpy instead of cyvcf2;

  • Rename hmtnote.annotate_vcf() to hmtnote.annotate() for compliance with CLI.

0.5.1 (2019-04-29)

  • 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.

0.5.2 (2019-04-30)

  • Fix requirements in setup.py file.

0.5.3 (2019-05-06)

  • Update requirements in setup.py.

0.5.4 (2019-05-06)

  • Fix installation issue.

0.5.5 (2019-05-06)

  • Fix VCF record parsing issue.

0.6.0 (2019-06-25)

  • 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.

0.7.0 (2019-07-26)

  • Add --csv command line option to convert output to CSV format;

  • Add homoplasmy annotations;

  • Update all tests accordingly;

  • Update documentation.

0.7.1 (2019-07-30)

  • Fix issue with echoed string (#78);

  • Fix issue with CSV format columns (#79);

  • Update testfiles.