CHANGELOG.md

Changelog

0.11.0 - 2024-01-22

BREAKING

We fixed the varity.vcf-to-hgvs implementation. It is confusing to throw the exception in vcf-variant->protein-hgvs when a variant overlaps the exon-intron boundaries, even if coding DNA HGVS is available. So we changed the behavior to return protein HGVS as nil.

Fixed

• Return protein HGVS as nil if a variant overlaps exon-intron boundaries. #89

0.10.1 - 2024-01-15

Fixed

• Add conditional branch of unaffected stop codon to protein-extension. #86

0.10.0 - 2023-12-27

BREAKING

We introduced enhancements to the description of protein changes by varity.vcf-to-hgvs, specifically making deletions more clinically meaningful:

1. exon-intron boundary deletions:

The deletion that overlaps the exon-intron boundary will trigger an Exception because alterations affecting the splice sites are predicted to be splicing abnormalities.

2. stop codon deletions:

In cases where deletions contain a stop codon, varity.vcf-to-hgvs generates the following outputs based on the alteration sequence:

• If the alteration sequence contains a stop codon, varity outputs as deletion-insertion.
• Otherwise, this outputs p.?.

Fixed

• Fix upstream and downstream sequence of sequence-info and delins process. #81
• Fix boundary of exon/intron determining process. #82

0.9.3 - 2023-07-03

Fixed

• Fix 3'-rule errors for certain sequence patterns. #75
• Fix overlapping condition of boundary of exon/intron. #77

0.9.2 - 2023-02-08

Fixed

• Fix the 3’ rule on a trailing sub-sequence. #63
• Fix conditional branch of frameshift caused by insertion. #65
• Fix the position of first amino acid changed by the frame shift. #66
• Fix VCF to protein HGVS conversions of insertions near splice sites. #68

0.9.1 - 2022-10-11

Added

• Feature to filter out refgene index source. #61

Fixed

• Fix frameshift conversion failure. #59

0.9.0 - 2022-07-31

BREAKING

The default value of :prefer-deletion? option is changed to false.

(require '[varity.vcf-to-hgvs :as v2h])

(v2h/vcf-variant->coding-dna-hgvs {:chr "chr7", :pos 140924774, :ref "GGGAGGC", :alt "G"}
                                  "path/to/hg38.fa" "path/to/refGene.txt.gz")
;;=> (#clj-hgvs/hgvs "NM_004333:c.-95GCCTCC[3]")

If you hope the previous behavior, specify :prefer-deletion? true.

(v2h/vcf-variant->coding-dna-hgvs {:chr "chr7", :pos 140924774, :ref "GGGAGGC", :alt "G"}
                                  "path/to/hg38.fa" "path/to/refGene.txt.gz"
                                  {:prefer-deletion? true})
;;=> (#clj-hgvs/hgvs "NM_004333:c.-77_-72delGCCTCC")

Added

• Annotate fusion genes. #52

Changed

• Logging liftover failure caused by different refs. #48
• Change the default :prefer-deletion? to false. #56

Fixed

• Fix the performance of liftover-variants. #47
• Fix alt exon calculation for deletion. #50
• Tweak GENCODE loading performance. #55

0.8.0 - 2021-11-15

Added

• Compatible with GENCODE's GTF and GFF3 format. #42

Changed

• Compat with acession number with version. #43
• Conversions from/to HGVS with GENCODE ID. #45

0.7.1 - 2021-06-22

Fixed

• Fix reference protein seq in fs-ter-substitution. #40

0.7.0 - 2021-01-12

Added

• Add support for vcf lift-over. #35

Changed

• Seek intron, 3'-UTR, and 5'-UTR regions from genomic position. #36
• Update clj-hgvs to 0.4.4.

Fixed

• Error handling in conversion of an invalid coordinate. #37

0.6.2 - 2020-07-06

Changed

• Update dependencies:
  • clj-hgvs 0.4.3
  • cljam 0.8.0
  • commons-compress 1.20
  • tools.logging 1.1.0

Fixed

• Pass nil to cds-end if cds-start equals cds-end in vcf-to-hgvs. #34

0.6.1 - 2020-02-19

Added

• Support repeated sequences caused by deletion on VCF->HGVS. #30
• Support conversion from repeated sequences to VCF deletion. #31
• Add prefer-insertion? option to VCF->HGVS. #32
• Add function for finding alternative HGVS expressions. #33

Fixed

• Fix conversion from reverse-strand repeated sequences to VCF variant. #29

0.6.0 - 2019-12-06

BREAKING

• cdna is renamed to coding-dna to avoid misunderstanding. See #28 for more information.
  • namespace:
    • varity.hgvs-to-vcf.cdna → varity.hgvs-to-vcf.coding-dna
    • varity.vcf-to-hgvs.cdna → varity.vcf-to-hgvs.coding-dna
  • function:
    • e.g. cdna-hgvs->vcf-variants → coding-dna-hgvs->vcf-variants
  • return:
    • {:cdna ...} → {:coding-dna ...}

Changed

• Rename cdna to coding-dna. #28
• Update dependencies:
  • clj-hgvs 0.4.0
  • cljam 0.7.4
  • commons-compress 1.19
  • tools.logging 0.5.0

0.5.1 - 2019-07-12

Added

• Include MNVs in protein HGVS -> VCF conversion results. #26

Changed

• Throw ex-info on hgvs->vcf for a variant containing ambiguous coordinates. #27
• Update dependencies:
  • clj-hgvs 0.3.1
  • cljam 0.7.2
  • proton 0.1.8

Fixed

• Remove incorrect VCF variants from protein HGVS to VCF variants conversion results. #25

0.5.0 - 2019-01-29

BREAKING

clj-hgvs 0.3.0 requires clojure 1.9+ because it uses clojure.spec for HGVS validation. To use varity with clojure 1.8, you must include a dependency on clojure-future-spec.

Changed

• Improve performance of vcf-variant->protein-hgvs. #22
• Update clj-hgvs and proton. #23

Fixed

• Fix pos of hgvs->vcf-variants for genes on reverse strand. #24

0.4.2 - 2018-11-20

Changed

• Use ex-info for varity specific exception. #20

Fixed

• Fix normalization of a variant containing long ref (strand: +). #21

0.4.1 - 2018-11-04

Added

• Add debug printing option. #19

Fixed

• Fix normalization of a variant containing long ref. #17
• Support frame shift with initiation codon change. #18

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.