13. Version History

13.1. v0.4.x release series

0.4.8 (2020.09.30) :

  • check redundancy of VEP fields in full-annotation

0.4.7 (2020.09.24) :

  • add preprocessing functions

0.4.7 (2020.09.23) :

  • debug VEP annotation missing error of some multiallele variants in preproc module

0.4.6 (2020.09.18) :

  • add multiple data source files.

0.4.5 (2020.08.28) :

  • bug fix in download module. add -silence option

0.4.4 (2020.08.25) :

  • bug fix missing genotype for multiallelic variant when -split_multi_allelic_variant option is applied. (issue #5)

0.4.3 (2020.08.09) :

  • add -fixpl option when converting multi-allelic variant to biallelic variants.

  • change for full-annotation data source v0.4.8

  • update value mapping order in external function.

  • add configration jsonfile (./data/conf.json)

  • add download sub-command

  • add tqdm library for downloading progress bar

0.4.2 (2020.06.25) :

  • add parameter set in data structure json file.

0.4.1 (2020.06.08) :

  • turn to be ‘single_source_mode = True’ when data structure file has only single source file.

  • allocate all sample names when users use -genoinfo without indicating sample names.

0.4.0 (2020.06.05) :

  • add variant type

  • support multiple datasources for vcf annotation

  • remove block-size option

  • make MUTANNO source name for ‘samplevariantkey’, ‘hgvsg’, and ‘variant_class’

  • add ‘-variant_class’ option

  • refactoring

  • add multi-source mode

  • refactoring makedata mode

13.2. v0.3.x release series

0.3.19 (2020.05.25) :

  • split pred and score in pathogenicity score from VEP (SIFT and Polyphen)

  • add ‘region_vcf’ option in ‘makedata’

0.3.18 (2020.05.13) :

  • add chain file option for pyliftover

0.3.17 (2020.05.06) :

  • add is_most_severe_transcript in external function.py

  • add keep_equal_str filter in data structure file

  • update -geno_info option to get sample ID list (ex. -geno_info HG002 HG003 HG004 )

  • update hgvs chromosome.

0.3.16 (2020.04.27) :

  • add GENE_MAIN_CHROM, CODING_GENE_MAIN_CHROM in -vartype option

0.3.15 (2020.03.26) :

  • add ‘web’ option

0.3.14 (2020.03.21) :

  • implement pypi installation

  • apply pytest

0.3.13 (2020.03.10) :

  • add ‘add_genoinfo’ option

  • add ‘split_multi_allelic_variant’ option

  • add ‘clean_tag’ option

0.3.12 (2020.03.05) :

  • add ‘default’ value

0.3.11 (2020.02.28) :

  • add SAMPLEGENO tag

  • minor fix in header

0.3.10 (2020.02.26) :

  • minor update in version tag

0.3.9 (2020.02.26) :

  • remove unannotated variant (-remove_unannotated_variant)

  • update the format of multiallele tag

0.3.8 (2020.02.25)

  • debugged first variant missing in annot module

0.3.7

  • update annot module

0.3.6

  • add makedata

0.3.5

  • merge some dbNSFP fields into transcript table (dbNSFPTranscript)

0.3.4

  • change type of dbNSFP SiPhy_29way_pi to list

0.3.3

  • encode ‘space’ to ‘%20’ (remove blank space)