HISTORY.rst

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.

0.7.2 (2019-08-16)

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