Merge pull request #91 from chrovis/chore/prepare-0.11.1-snapshot

Prepare for next development iteration (0.11.1-SNAPSHOT)

CHANGELOG.md

@@ -1,6 +1,13 @@
 # Changelog
 
-## [0.11.0] - date TBD
+## [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
 
@@ -15,7 +22,26 @@
 
 ## [0.10.0] - 2023-12-27
 
- ### Fixed
+### 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](https://github.com/chrovis/varity/pull/81)
 - Fix boundary of exon/intron determining process. [#82](https://github.com/chrovis/varity/pull/82)

README.md

@@ -34,42 +34,6 @@ To use varity with Clojure 1.8, you must include a dependency on
 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`.
 
-## Breaking changes in 0.10.0
-
-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.?`.
-
-## Breaking changes in 0.9.0
-
-The default value of `:prefer-deletion?` option is changed to `false`.
-
-```clojure
-(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`.
-
-```clojure
-(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")
-```
-
 ## Usage
 
 ### Documentation

project.clj

@@ -1,4 +1,4 @@
-(defproject varity "0.11.0"
+(defproject varity "0.11.1-SNAPSHOT"
   :description "Variant translation library for Clojure"
   :url "https://github.com/chrovis/varity"
   :license {:name "Apache License, Version 2.0"