Changelog

0.4.0 - 2018-10-03

BREAKING

Strand representation is changed from string (+, -) to keyword (:forward, :reverse).

Added

• Support promoter on variant conversion. #10
• Profile for Clojure 1.10. #11
• Add several functions to work with refGene exon sequences. #13

Changed

• Return p.? w/ warning when CDS is indivisible by 3. #12
• Use :forward/:reverse as values for the key ':strand'. #14
• Update dependencies:
  • clj-hgvs 0.2.4
  • cljam 0.6.0
  • commons-compress 1.18

Fixed

• Fix nonsense substitution in del case. #9
• Fix the translation condition of termination substitution with frameshift. #15
• Fix conversion of no change substitution. #16

0.3.7 - 2018-04-27

Added

• Add benchmark code for liftover. #8

Changed

• Improve the performance of liftover. #7
• Update dependencies:
  • cavia 0.5.0
  • commons-compress 1.16.1
  • proton 0.1.6

0.3.6 - 2018-02-06

Added

• Add function to retrieve exon regions. #4

Changed

• Update dependencies:
  • commons-compress 1.16
  • proton 0.1.4

Fixed

• Fix mistranslation from HGVS to vcf variant. #5

0.3.5 - 2017-12-26

Changed

• Parse scores and exon-frames in refGene.txt. #3
• Update dependencies:
  • cavia 0.4.3
  • clj-hgvs 0.2.3
  • cljam 0.5.1
  • proton 0.1.3

Fixed

• Fix incorrect conversion of nonsense substitution.

0.3.4 - 2017-08-21

Changed

• Update cljam (0.4.1) and proton (0.1.2) version.

Fixed

• Fix errors for some uncommon variants. #2

0.3.3 - 2017-06-30

Added

• Add tests.
• Support TwoBit format as reference sequence file.

Fixed

• Fix the process of calculating alt protein sequence.

0.3.2 - 2017-06-15

Changed

• Bump clj-hgvs version up to 0.2.0.

0.3.1 - 2017-05-15

Changed

• Improve cDNA HGVS -> VCF variant support.
• ref-seq info can be used for HGVS -> VCF.
• Bump dependencies version up.

Fixed

• Fix missed arguments.
• Fix arguments of lift in README.md. #1
• Fix reflection/boxing warnings.

0.3.0 - 2017-05-08

Added

• Normalize chromosome of VCF->HGVS inputs.

Changed

• Use :chr instead of :chrom as chromosome of ref-gene.
• Use record as ref-gene index instead of map.
• Modify arguments of VCF<->HGVS.
• Modify arguments of lift.
• Bump clj-hgvs version up to 0.1.2.

0.2.0 - 2017-04-20

First release.