diff --git a/CHANGELOG.md b/CHANGELOG.md index 57839ed..cbafd7f 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,5 +1,18 @@ # Changelog +## [0.5.0] - TBD + +### BREAKING + +- Fix uncertain bases and amino acids format of ins and delins because HGVS nomenclature was updated. + - DNA: `ins(10)` -> `insN[10]` + - RNA: `ins(10)` -> `insn[10]` + - Protein: `ins10` -> `insX[10]` + +### Fixed + +- Fix uncertain insertion. [#10](https://github.com/chrovis/clj-hgvs/pull/10) + ## [0.4.7] - 2023-04-25 ### Fixed @@ -126,7 +139,8 @@ ## 0.1.0 - 2017-04-17 -[Unreleased]: https://github.com/chrovis/clj-hgvs/compare/0.4.7...HEAD +[Unreleased]: https://github.com/chrovis/clj-hgvs/compare/0.5.0...HEAD +[0.5.0]: https://github.com/chrovis/clj-hgvs/compare/0.4.7...0.5.0 [0.4.7]: https://github.com/chrovis/clj-hgvs/compare/0.4.6...0.4.7 [0.4.6]: https://github.com/chrovis/clj-hgvs/compare/0.4.5...0.4.6 [0.4.5]: https://github.com/chrovis/clj-hgvs/compare/0.4.4...0.4.5 diff --git a/README.md b/README.md index bbce2dc..083df28 100644 --- a/README.md +++ b/README.md @@ -19,18 +19,25 @@ clj-hgvs provides: Clojure CLI/deps.edn: ```clojure -clj-hgvs {:mvn/version "0.4.7"} +clj-hgvs {:mvn/version "0.5.0"} ``` Leiningen/Boot: ```clojure -[clj-hgvs "0.4.7"] +[clj-hgvs "0.5.0"] ``` To use clj-hgvs with Clojure 1.8, you must include a dependency on [clojure-future-spec](https://github.com/tonsky/clojure-future-spec). +## Breaking Changes in 0.5.0 + +- Fix uncertain bases and amino acids format of ins and delins because HGVS nomenclature was updated. + - DNA: `ins(10)` -> `insN[10]` + - RNA: `ins(10)` -> `insn[10]` + - Protein: `ins10` -> `insX[10]` + ## Breaking Changes in 0.4.0 - HGVS data structure changes from map to record (`clj-hgvs.core/HGVS`). @@ -170,6 +177,6 @@ You may supply custom repair rules to the second argument: ## License -Copyright 2017-2023 [Xcoo, Inc.](https://xcoo.jp/) +Copyright 2017-2024 [Xcoo, Inc.](https://xcoo.jp/) Licensed under the [Apache License, Version 2.0](LICENSE). diff --git a/docs/clj-hgvs.coordinate.html b/docs/clj-hgvs.coordinate.html index 779fa0e..9ae3c0b 100644 --- a/docs/clj-hgvs.coordinate.html +++ b/docs/clj-hgvs.coordinate.html @@ -1,27 +1,27 @@ -clj-hgvs.coordinate documentation

Project

Namespaces

Public Vars

clj-hgvs.coordinate

Data structures and functions to handle HGVS coordinates.
-

->region-keyword

(->region-keyword s)
view source
->region-str
(->region-str k)
view source
Calculable
protocol
members
minus
(minus this n)
Subtracts n from the given coordinate and returns the new coordinate.
+clj-hgvs.coordinate documentation
Project
Namespaces
Public Vars
clj-hgvs.coordinate
Data structures and functions to handle HGVS coordinates.
+
->region-keyword
(->region-keyword s)
view source
->region-str
(->region-str k)
view source
Calculable
protocol
members
minus
(minus this n)
Subtracts n from the given coordinate and returns the new coordinate.
 
plus
(plus this n)
Adds n to the given coordinate and returns the new coordinate.
-
view source
circular-dna-coordinate
(circular-dna-coordinate position)
Returns CircularDNACoordinate instance having position. Throws an exception
-if position is illegal.
view source
coding-dna-coordinate
(coding-dna-coordinate position)(coding-dna-coordinate position offset region)
Returns CodingDNACoordinate instance having position, offset, and region.
-Throws an exception if any input is illegal.
view source
comparable-coordinates?
(comparable-coordinates? coord1 coord2)
Returns true if the two coordinates are comparable, else false.
-
view source
Coordinate
protocol
members
format
(format this)
Returns a string representing the given coordinate.
+
view source
circular-dna-coordinate
(circular-dna-coordinate position)
Returns CircularDNACoordinate instance having position. Throws an exception
+if position is illegal.
view source
coding-dna-coordinate
(coding-dna-coordinate position)(coding-dna-coordinate position offset region)
Returns CodingDNACoordinate instance having position, offset, and region.
+Throws an exception if any input is illegal.
view source
comparable-coordinates?
(comparable-coordinates? coord1 coord2)
Returns true if the two coordinates are comparable, else false.
+
view source
Coordinate
protocol
members
format
(format this)
Returns a string representing the given coordinate.
 
plain
(plain this)
Returns a plain map representing the given coordinate.
-
view source
genomic-coordinate
(genomic-coordinate position)
Returns GenomicCoordinate instance having position. Throws an exception if
-position is illegal.
view source
ICodingDNACoordinate
protocol
members
in-exon?
(in-exon? this)
Returns true if the coordinate is located in exon, else false.
-
view source
mitochondrial-coordinate
(mitochondrial-coordinate position)
Returns MitochondrialCoordinate instance having position. Throws an exception
-if position is illegal.
view source
non-coding-dna-coordinate
(non-coding-dna-coordinate position)
Returns NonCodingDNACoordinate instance having position. Throws an exception
-if position is illegal.
view source
parse-circular-dna-coordinate
(parse-circular-dna-coordinate s)
Parses a coordinate string used in circular-dna mutations, returning a
-CircularDNACoordinate or UnknownCoordinate.
view source
parse-coding-dna-coordinate
(parse-coding-dna-coordinate s)
Parses a coordinate string used in coding DNA mutations, returning a
-CodingDNACoordinate or UnknownCoordinate.
view source
parse-coordinate
(parse-coordinate s t)
view source
parse-genomic-coordinate
(parse-genomic-coordinate s)
Parses a coordinate string used in genomic mutations, returning a
-GenomicCoordinate or UnknownCoordinate.
view source
parse-mitochondrial-coordinate
(parse-mitochondrial-coordinate s)
Parses a coordinate string used in mitochondrial mutations, returning a
-MitochondrialCoordinate or UnknownCoordinate.
view source
parse-non-coding-dna-coordinate
(parse-non-coding-dna-coordinate s)
Parses a coordinate string used in non-coding DNA mutations, returning a
-NonCodingDNACoordinate or UnknownCoordinate.
view source
parse-protein-coordinate
(parse-protein-coordinate s)
Parses a coordinate string used in protein mutations, returning a
-ProteinCoordinate or UnknownCoordinate.
view source
parse-rna-coordinate
(parse-rna-coordinate s)
Parses a coordinate string used in RNA mutations, returning a RNACoordinate
-or UnknownCoordinate.
view source
parse-uncertain-coordinate
(parse-uncertain-coordinate s t)
view source
protein-coordinate
(protein-coordinate position)
Returns ProteinCoordinate instance having position. Throws an exception if
-position is illegal.
view source
restore
multimethod
(restore m)
Restores a plain map to a suitable coordinate record.
-
view source
rna-coordinate
(rna-coordinate position offset region)
Returns RNACoordinate instance having position, offset, and region. Throws an
-exception if any input is illegal.
view source
uncertain-coordinate
(uncertain-coordinate start end)
Returns UncertainCoordinate instance having start and end. Throws an
-exception if any input is illegal.
view source
unknown-coordinate
(unknown-coordinate)
Returns UnknownCoordinate instance.
-
view source

\ No newline at end of file
+
view source
genomic-coordinate
(genomic-coordinate position)
Returns GenomicCoordinate instance having position. Throws an exception if
+position is illegal.
view source
ICodingDNACoordinate
protocol
members
in-exon?
(in-exon? this)
Returns true if the coordinate is located in exon, else false.
+
view source
mitochondrial-coordinate
(mitochondrial-coordinate position)
Returns MitochondrialCoordinate instance having position. Throws an exception
+if position is illegal.
view source
non-coding-dna-coordinate
(non-coding-dna-coordinate position)
Returns NonCodingDNACoordinate instance having position. Throws an exception
+if position is illegal.
view source
parse-circular-dna-coordinate
(parse-circular-dna-coordinate s)
Parses a coordinate string used in circular-dna mutations, returning a
+CircularDNACoordinate or UnknownCoordinate.
view source
parse-coding-dna-coordinate
(parse-coding-dna-coordinate s)
Parses a coordinate string used in coding DNA mutations, returning a
+CodingDNACoordinate or UnknownCoordinate.
view source
parse-coordinate
(parse-coordinate s t)
view source
parse-genomic-coordinate
(parse-genomic-coordinate s)
Parses a coordinate string used in genomic mutations, returning a
+GenomicCoordinate or UnknownCoordinate.
view source
parse-mitochondrial-coordinate
(parse-mitochondrial-coordinate s)
Parses a coordinate string used in mitochondrial mutations, returning a
+MitochondrialCoordinate or UnknownCoordinate.
view source
parse-non-coding-dna-coordinate
(parse-non-coding-dna-coordinate s)
Parses a coordinate string used in non-coding DNA mutations, returning a
+NonCodingDNACoordinate or UnknownCoordinate.
view source
parse-protein-coordinate
(parse-protein-coordinate s)
Parses a coordinate string used in protein mutations, returning a
+ProteinCoordinate or UnknownCoordinate.
view source
parse-rna-coordinate
(parse-rna-coordinate s)
Parses a coordinate string used in RNA mutations, returning a RNACoordinate
+or UnknownCoordinate.
view source
parse-uncertain-coordinate
(parse-uncertain-coordinate s t)
view source
protein-coordinate
(protein-coordinate position)
Returns ProteinCoordinate instance having position. Throws an exception if
+position is illegal.
view source
restore
multimethod
(restore m)
Restores a plain map to a suitable coordinate record.
+
view source
rna-coordinate
(rna-coordinate position offset region)
Returns RNACoordinate instance having position, offset, and region. Throws an
+exception if any input is illegal.
view source
uncertain-coordinate
(uncertain-coordinate start end)
Returns UncertainCoordinate instance having start and end. Throws an
+exception if any input is illegal.
view source
unknown-coordinate
(unknown-coordinate)
Returns UnknownCoordinate instance.
+
view source

\ No newline at end of file
diff --git a/docs/clj-hgvs.core.html b/docs/clj-hgvs.core.html
index 192b408..5aeedc8 100644
--- a/docs/clj-hgvs.core.html
+++ b/docs/clj-hgvs.core.html
@@ -1,12 +1,12 @@
 
-clj-hgvs.core documentation
Project
Namespaces
Public Vars
clj-hgvs.core
Main functions for handling HGVS. See http://varnomen.hgvs.org/ for the
+clj-hgvs.core documentation
Project
Namespaces
Public Vars
clj-hgvs.core
Main functions for handling HGVS. See http://varnomen.hgvs.org/ for the
 detail HGVS nomenclature.
==
(== hgvs)(== hgvs1 hgvs2)(== hgvs1 hgvs2 & more)
Returns true if hgvs1 is equivalent to hgvs2, false otherwise.
 
 This function compares the fundamental equivalence of the given HGVS, ignoring
 the difference of the transcript version, the short/long amino acid style, and
-the description of the same mutation.
view source
data-readers
Tagged literal support if loader does not find "data_readers.clj".
-
view source
format
(format hgvs)(format hgvs opts)
Returns a HGVS string representing the given HGVS map.
+the description of the same mutation.
view source
data-readers
Tagged literal support if loader does not find "data_readers.clj".
+
view source
format
(format hgvs)(format hgvs opts)
Returns a HGVS string representing the given HGVS map.
 
 The second argument is an optional map to specify style:
 
@@ -25,7 +25,7 @@
                        default false.
 
    :ter-format         Ter codon style of protein frame shift and extension,
-                       default :long. <:long|:short>}
view source
hgvs
(hgvs transcript kind mutation)
Creates HGVS data represented as a record.
+                       default :long. <:long|:short>}
view source
hgvs
(hgvs transcript kind mutation)
Creates HGVS data represented as a record.
 
 transcript is nilable for conventional reasons, but you should supply it if
 possible.
@@ -34,13 +34,13 @@
 :circular-dna, :rna, and :protein.
 
 mutation must be a clj-hgvs.mutation record or string. The string mutation
-will be parsed by clj-hgvs.mutation/parse.
view source
normalize
(normalize s)
Reformats the HGVS string s, returning the normalized HGVS string.
+will be parsed by clj-hgvs.mutation/parse.
view source
normalize
(normalize s)
Reformats the HGVS string s, returning the normalized HGVS string.
 
 The default style will be used for reformatting. See clj-hgvs.core/format
-document for further details of the style options.
view source
parse
(parse s)
Parses a HGVS string s, returning a map representing the HGVS.
-
view source
plain
(plain hgvs)
Returns a plain map representing the given HGVS. This function is useful for
+document for further details of the style options.
view source
parse
(parse s)
Parses a HGVS string s, returning a map representing the HGVS.
+
view source
plain
(plain hgvs)
Returns a plain map representing the given HGVS. This function is useful for
 sending data through another codec. Use clj-hgvs.core/restore to retrieve
-original HGVS data.
view source
repair-hgvs-str
(repair-hgvs-str s)(repair-hgvs-str s repairers)
Attempts to repair an invalid HGVS string, returning a correct HGVS string.
+original HGVS data.
view source
repair-hgvs-str
(repair-hgvs-str s)(repair-hgvs-str s repairers)
Attempts to repair an invalid HGVS string, returning a correct HGVS string.
 
 The repair rules are based on frequent mistakes in popular public-domain
 databases such as dbSNP and ClinVar. See clj-hgvs.repairer/built-in-repairers
@@ -58,9 +58,9 @@
                           lower-case-ext))
 
   (repair-hgvs-str "p.*833EXT*?" my-repairers)
-  => "p.*833ext*?"
view source
restore
(restore m)
Restores a plain map to a suitable HGVS data structure. This function is
-useful for sending data through another codec.
view source
with-validation-disabled
macro
(with-validation-disabled & body)
Disables validation within a scope.
+  => "p.*833ext*?"
view source
restore
(restore m)
Restores a plain map to a suitable HGVS data structure. This function is
+useful for sending data through another codec.
view source
with-validation-disabled
macro
(with-validation-disabled & body)
Disables validation within a scope.
 
 HGVS data are checked upon interpretation phases by default, but in the scope,
 all validations will be skipped. This macro may improve the performance on
-handling HGVS which validity is already known.
view source

\ No newline at end of file
+handling HGVS which validity is already known.
view source

\ No newline at end of file
diff --git a/docs/clj-hgvs.mutation.html b/docs/clj-hgvs.mutation.html
index ae4e0f5..49915c7 100644
--- a/docs/clj-hgvs.mutation.html
+++ b/docs/clj-hgvs.mutation.html
@@ -1,41 +1,41 @@
 
-clj-hgvs.mutation documentation
Project
Namespaces
Public Vars
clj-hgvs.mutation
Data structures and functions to handle HGVS mutations.
+clj-hgvs.mutation documentation
Project
Namespaces
Public Vars
clj-hgvs.mutation
Data structures and functions to handle HGVS mutations.
 
->long-amino-acid
(->long-amino-acid s)
Converts a single-letter amino acid into a three-letter one. s must be String
-or Character. Returns nil if s is not present in amino acid list.
view source
->short-amino-acid
(->short-amino-acid s)
Converts a three-letter amino acid into a single-letter one. s must be String
-or Character. Returns nil if s is not present in amino acid list.
view source
dna-alleles
(dna-alleles mutations1 mutations2)
view source
dna-conversion
(dna-conversion coord-start coord-end alt)
Constructor of DNAConversion. Throws an exception if any input is illegal.
-
view source
dna-deletion
(dna-deletion coord-start coord-end)(dna-deletion coord-start coord-end ref)
Constructor of DNADeletion. Throws an exception if any input is illegal.
-
view source
dna-duplication
(dna-duplication coord-start coord-end)(dna-duplication coord-start coord-end ref)
Constructor of DNADuplication. Throws an exception if any input is illegal.
-
view source
dna-indel
(dna-indel coord-start coord-end ref alt)
Constructor of DNAIndel. Throws an exception if any input is illegal.
-
view source
dna-insertion
(dna-insertion coord-start coord-end alt)
Constructor of DNAInsertion. Throws an exception if any input is illegal.
-
view source
dna-inversion
(dna-inversion coord-start coord-end)
Constructor of DNAInversion. Throws an exception if any input is illegal.
-
view source
dna-repeated-seqs
(dna-repeated-seqs coord-start coord-end ref ncopy)
Constructor of DNARepeatedSeqs. Throws an exception if any input is illegal.
-
view source
dna-substitution
(dna-substitution coord ref typ)(dna-substitution coord ref typ alt)
Constructor of DNASubstitution. Throws an exception if any input is illegal.
-
view source
equiv
(equiv mutation1 mutation2)
view source
Equivalence
protocol
members
equiv*
(equiv* this o)
view source
long-amino-acids
A list of three-letter amino acids.
-
view source
Mutation
protocol
members
format
(format this)(format this opts)
Returns a string representing the given mutation. The second argument is an
+or Character. Returns nil if s is not present in amino acid list.
view source
->short-amino-acid
(->short-amino-acid s)
Converts a three-letter amino acid into a single-letter one. s must be String
+or Character. Returns nil if s is not present in amino acid list.
view source
dna-alleles
(dna-alleles mutations1 mutations2)
view source
dna-conversion
(dna-conversion coord-start coord-end alt)
Constructor of DNAConversion. Throws an exception if any input is illegal.
+
view source
dna-deletion
(dna-deletion coord-start coord-end)(dna-deletion coord-start coord-end ref)
Constructor of DNADeletion. Throws an exception if any input is illegal.
+
view source
dna-duplication
(dna-duplication coord-start coord-end)(dna-duplication coord-start coord-end ref)
Constructor of DNADuplication. Throws an exception if any input is illegal.
+
view source
dna-indel
(dna-indel coord-start coord-end ref alt)
Constructor of DNAIndel. Throws an exception if any input is illegal.
+
view source
dna-insertion
(dna-insertion coord-start coord-end alt)
Constructor of DNAInsertion. Throws an exception if any input is illegal.
+
view source
dna-inversion
(dna-inversion coord-start coord-end)
Constructor of DNAInversion. Throws an exception if any input is illegal.
+
view source
dna-repeated-seqs
(dna-repeated-seqs coord-start coord-end ref ncopy)
Constructor of DNARepeatedSeqs. Throws an exception if any input is illegal.
+
view source
dna-substitution
(dna-substitution coord ref typ)(dna-substitution coord ref typ alt)
Constructor of DNASubstitution. Throws an exception if any input is illegal.
+
view source
equiv
(equiv mutation1 mutation2)
view source
Equivalence
protocol
members
equiv*
(equiv* this o)
view source
long-amino-acids
A list of three-letter amino acids.
+
view source
Mutation
protocol
members
format
(format this)(format this opts)
Returns a string representing the given mutation. The second argument is an
 optional map to specify style. See document of clj-hgvs.core/format for
 details of the option.
plain
(plain this)
Returns a plain map representing the given mutation.
-
view source
no-protein
(no-protein)
view source
no-rna
(no-rna)
view source
parse
(parse s kind)
view source
parse-dna
(parse-dna s kind)
Parses a DNA mutation string s, returning a record implementing Mutation
+
view source
no-protein
(no-protein)
view source
no-rna
(no-rna)
view source
parse
(parse s kind)
view source
parse-dna
(parse-dna s kind)
Parses a DNA mutation string s, returning a record implementing Mutation
 protocol. kind must be selected from :genome, :mitochondria, :coding-dna, or
-:non-coding-dna.
view source
parse-dna-alleles
(parse-dna-alleles s kind)
view source
parse-dna-conversion
(parse-dna-conversion s kind)
view source
parse-dna-deletion
(parse-dna-deletion s kind)
view source
parse-dna-duplication
(parse-dna-duplication s kind)
view source
parse-dna-indel
(parse-dna-indel s kind)
view source
parse-dna-insertion
(parse-dna-insertion s kind)
view source
parse-dna-inversion
(parse-dna-inversion s kind)
view source
parse-dna-repeated-seqs
(parse-dna-repeated-seqs s kind)
view source
parse-dna-substitution
(parse-dna-substitution s kind)
view source
parse-protein
(parse-protein s)
Parses a protein mutation string s, returning a record implementing Mutation
-protocol.
view source
parse-protein-alleles
(parse-protein-alleles s)
view source
parse-protein-deletion
(parse-protein-deletion s)
view source
parse-protein-duplication
(parse-protein-duplication s)
view source
parse-protein-extension
(parse-protein-extension s)
view source
parse-protein-frame-shift
(parse-protein-frame-shift s)
view source
parse-protein-indel
(parse-protein-indel s)
view source
parse-protein-insertion
(parse-protein-insertion s)
view source
parse-protein-repeated-seqs
(parse-protein-repeated-seqs s)
view source
parse-protein-substitution
(parse-protein-substitution s)
view source
parse-rna
(parse-rna s)
Parses a RNA mutation string s, returning a record implementing Mutation
-protocol.
view source
parse-rna-alleles
(parse-rna-alleles s)
view source
parse-rna-conversion
(parse-rna-conversion s)
view source
parse-rna-deletion
(parse-rna-deletion s)
view source
parse-rna-duplication
(parse-rna-duplication s)
view source
parse-rna-indel
(parse-rna-indel s)
view source
parse-rna-insertion
(parse-rna-insertion s)
view source
parse-rna-inversion
(parse-rna-inversion s)
view source
parse-rna-repeated-seqs
(parse-rna-repeated-seqs s)
view source
parse-rna-substitution
(parse-rna-substitution s)
view source
parse-uncertain-mutation
(parse-uncertain-mutation s kind)
view source
protein-alleles
(protein-alleles mutations1 mutations2)
view source
protein-deletion
(protein-deletion ref-start coord-start)(protein-deletion ref-start coord-start ref-end coord-end)
Constructor of ProteinDeletion. Throws an exception if any input is illegal.
-
view source
protein-duplication
(protein-duplication ref-start coord-start)(protein-duplication ref-start coord-start ref-end coord-end)
Constructor of ProteinDuplication. Throws an exception if any input is illegal.
-
view source
protein-extension
(protein-extension ref coord alt region new-site)
Constructor of ProteinExtension. Throws an exception if any input is illegal.
-
view source
protein-frame-shift
(protein-frame-shift ref coord alt new-ter-site)
Constructor of ProteinFrameShift. Throws an exception if any input is illegal.
-
view source
protein-indel
(protein-indel ref-start coord-start ref-end coord-end alts)
Constructor of ProteinIndel. Throws an exception if any input is illegal.
-
view source
protein-insertion
(protein-insertion ref-start coord-start ref-end coord-end alts)
Constructor of ProteinInsertion. Throws an exception if any input is illegal.
-
view source
protein-no-effect
(protein-no-effect)
view source
protein-repeated-seqs
(protein-repeated-seqs ref-start coord-start ref-end coord-end ncopy)
Constructor of ProteinRepeatedSeqs. Throws an exception if any input is illegal.
-
view source
protein-substitution
(protein-substitution ref coord alt)
Constructor of ProteinSubstitution. Throws an exception if any input is illegal.
-
view source
protein-unknown-mutation
(protein-unknown-mutation)
view source
restore
multimethod
(restore m)
Restores a plain map to a suitable mutation record.
-
view source
rna-alleles
(rna-alleles mutations1 mutations2)
view source
rna-conversion
(rna-conversion coord-start coord-end alt)
Constructor of RNAConversion. Throws an exception if any input is illegal.
-
view source
rna-deletion
(rna-deletion coord-start coord-end)(rna-deletion coord-start coord-end ref)
Constructor of DNAdeletion. Throws an exception if any input is illegal.
-
view source
rna-duplication
(rna-duplication coord-start coord-end)(rna-duplication coord-start coord-end ref)
Constructor of RNADuplication. Throws an exception if any input is illegal.
-
view source
rna-indel
(rna-indel coord-start coord-end ref alt)
Constructor of RNAIndel. Throws an exception if any input is illegal.
-
view source
rna-insertion
(rna-insertion coord-start coord-end alt)
Constructor of RNAInsertion. Throws an exception if any input is illegal.
-
view source
rna-inversion
(rna-inversion coord-start coord-end)
Constructor of RNAInversion. Throws an exception if any input is illegal.
-
view source
rna-no-effect
(rna-no-effect)
view source
rna-repeated-seqs
(rna-repeated-seqs coord-start coord-end ref ncopy)
Constructor of RNARepeatedSeqs. Throws an exception if any input is illegal.
-
view source
rna-splice-affected
(rna-splice-affected)
view source
rna-substitution
(rna-substitution coord ref alt)
Constructor of RNASubstitution. Throws an exception if any input is illegal.
-
view source
rna-unknown-mutation
(rna-unknown-mutation)
view source
SeparatelyFormat
protocol
members
format-common
(format-common this opts)
format-unique
(format-unique this opts)
view source
short-amino-acids
A list of single-letter amino acids.
-
view source
uncertain-mutation
(uncertain-mutation mutation)
Constructor of UncertainMutation. Throws an exception if any input is
-illegal.
view source

\ No newline at end of file
+:non-coding-dna.
view source
parse-dna-alleles
(parse-dna-alleles s kind)
view source
parse-dna-conversion
(parse-dna-conversion s kind)
view source
parse-dna-deletion
(parse-dna-deletion s kind)
view source
parse-dna-duplication
(parse-dna-duplication s kind)
view source
parse-dna-indel
(parse-dna-indel s kind)
view source
parse-dna-insertion
(parse-dna-insertion s kind)
view source
parse-dna-inversion
(parse-dna-inversion s kind)
view source
parse-dna-repeated-seqs
(parse-dna-repeated-seqs s kind)
view source
parse-dna-substitution
(parse-dna-substitution s kind)
view source
parse-protein
(parse-protein s)
Parses a protein mutation string s, returning a record implementing Mutation
+protocol.
view source
parse-protein-alleles
(parse-protein-alleles s)
view source
parse-protein-deletion
(parse-protein-deletion s)
view source
parse-protein-duplication
(parse-protein-duplication s)
view source
parse-protein-extension
(parse-protein-extension s)
view source
parse-protein-frame-shift
(parse-protein-frame-shift s)
view source
parse-protein-indel
(parse-protein-indel s)
view source
parse-protein-insertion
(parse-protein-insertion s)
view source
parse-protein-repeated-seqs
(parse-protein-repeated-seqs s)
view source
parse-protein-substitution
(parse-protein-substitution s)
view source
parse-rna
(parse-rna s)
Parses a RNA mutation string s, returning a record implementing Mutation
+protocol.
view source
parse-rna-alleles
(parse-rna-alleles s)
view source
parse-rna-conversion
(parse-rna-conversion s)
view source
parse-rna-deletion
(parse-rna-deletion s)
view source
parse-rna-duplication
(parse-rna-duplication s)
view source
parse-rna-indel
(parse-rna-indel s)
view source
parse-rna-insertion
(parse-rna-insertion s)
view source
parse-rna-inversion
(parse-rna-inversion s)
view source
parse-rna-repeated-seqs
(parse-rna-repeated-seqs s)
view source
parse-rna-substitution
(parse-rna-substitution s)
view source
parse-uncertain-mutation
(parse-uncertain-mutation s kind)
view source
protein-alleles
(protein-alleles mutations1 mutations2)
view source
protein-deletion
(protein-deletion ref-start coord-start)(protein-deletion ref-start coord-start ref-end coord-end)
Constructor of ProteinDeletion. Throws an exception if any input is illegal.
+
view source
protein-duplication
(protein-duplication ref-start coord-start)(protein-duplication ref-start coord-start ref-end coord-end)
Constructor of ProteinDuplication. Throws an exception if any input is illegal.
+
view source
protein-extension
(protein-extension ref coord alt region new-site)
Constructor of ProteinExtension. Throws an exception if any input is illegal.
+
view source
protein-frame-shift
(protein-frame-shift ref coord alt new-ter-site)
Constructor of ProteinFrameShift. Throws an exception if any input is illegal.
+
view source
protein-indel
(protein-indel ref-start coord-start ref-end coord-end alts)
Constructor of ProteinIndel. Throws an exception if any input is illegal.
+
view source
protein-insertion
(protein-insertion ref-start coord-start ref-end coord-end alts)
Constructor of ProteinInsertion. Throws an exception if any input is illegal.
+
view source
protein-no-effect
(protein-no-effect)
view source
protein-repeated-seqs
(protein-repeated-seqs ref-start coord-start ref-end coord-end ncopy)
Constructor of ProteinRepeatedSeqs. Throws an exception if any input is illegal.
+
view source
protein-substitution
(protein-substitution ref coord alt)
Constructor of ProteinSubstitution. Throws an exception if any input is illegal.
+
view source
protein-unknown-mutation
(protein-unknown-mutation)
view source
restore
multimethod
(restore m)
Restores a plain map to a suitable mutation record.
+
view source
rna-alleles
(rna-alleles mutations1 mutations2)
view source
rna-conversion
(rna-conversion coord-start coord-end alt)
Constructor of RNAConversion. Throws an exception if any input is illegal.
+
view source
rna-deletion
(rna-deletion coord-start coord-end)(rna-deletion coord-start coord-end ref)
Constructor of DNAdeletion. Throws an exception if any input is illegal.
+
view source
rna-duplication
(rna-duplication coord-start coord-end)(rna-duplication coord-start coord-end ref)
Constructor of RNADuplication. Throws an exception if any input is illegal.
+
view source
rna-indel
(rna-indel coord-start coord-end ref alt)
Constructor of RNAIndel. Throws an exception if any input is illegal.
+
view source
rna-insertion
(rna-insertion coord-start coord-end alt)
Constructor of RNAInsertion. Throws an exception if any input is illegal.
+
view source
rna-inversion
(rna-inversion coord-start coord-end)
Constructor of RNAInversion. Throws an exception if any input is illegal.
+
view source
rna-no-effect
(rna-no-effect)
view source
rna-repeated-seqs
(rna-repeated-seqs coord-start coord-end ref ncopy)
Constructor of RNARepeatedSeqs. Throws an exception if any input is illegal.
+
view source
rna-splice-affected
(rna-splice-affected)
view source
rna-substitution
(rna-substitution coord ref alt)
Constructor of RNASubstitution. Throws an exception if any input is illegal.
+
view source
rna-unknown-mutation
(rna-unknown-mutation)
view source
SeparatelyFormat
protocol
members
format-common
(format-common this opts)
format-unique
(format-unique this opts)
view source
short-amino-acids
A list of single-letter amino acids.
+
view source
uncertain-mutation
(uncertain-mutation mutation)
Constructor of UncertainMutation. Throws an exception if any input is
+illegal.
view source

\ No newline at end of file
diff --git a/docs/clj-hgvs.repairer.html b/docs/clj-hgvs.repairer.html
index 5bdaa34..f705671 100644
--- a/docs/clj-hgvs.repairer.html
+++ b/docs/clj-hgvs.repairer.html
@@ -1,6 +1,6 @@
 
-clj-hgvs.repairer documentation
Project
Namespaces
Public Vars
clj-hgvs.repairer
HGVS repair functions.
+clj-hgvs.repairer documentation
Project
Namespaces
Public Vars
clj-hgvs.repairer
HGVS repair functions.
 
built-in-repairers
The built-in repair functions.
 
 A repair fn must take a HGVS string and an inferred kind, and return a
@@ -13,5 +13,5 @@
       s))
 
 The built-in rules are based on frequent mistakes in popular public-domain
-databases such as dbSNP and ClinVar.
view source
infer-kind
(infer-kind s)
Infers a kind from the provided string, returning the kind keyword.
-
view source

\ No newline at end of file
+databases such as dbSNP and ClinVar.
view source
infer-kind
(infer-kind s)
Infers a kind from the provided string, returning the kind keyword.
+
view source

\ No newline at end of file
diff --git a/docs/index.html b/docs/index.html
index 44dd367..b6229dd 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -1,4 +1,4 @@
 
-clj-hgvs 0.4.7
Project
Namespaces
clj-hgvs 0.4.7
Released under the Apache License, Version 2.0
Clojure(Script) library for handling HGVS.
Installation
To install, add the following dependency to your project or build file:
[clj-hgvs "0.4.7"]
Namespaces
clj-hgvs.coordinate
Data structures and functions to handle HGVS coordinates.
Public variables and functions:
clj-hgvs.core
Main functions for handling HGVS. See http://varnomen.hgvs.org/ for the
+clj-hgvs 0.5.0
Project
Namespaces
clj-hgvs 0.5.0
Released under the Apache License, Version 2.0
Clojure(Script) library for handling HGVS.
Installation
To install, add the following dependency to your project or build file:
[clj-hgvs "0.5.0"]
Namespaces
clj-hgvs.coordinate
Data structures and functions to handle HGVS coordinates.
Public variables and functions:
clj-hgvs.core
Main functions for handling HGVS. See http://varnomen.hgvs.org/ for the
 detail HGVS nomenclature.
Public variables and functions:
clj-hgvs.mutation
Data structures and functions to handle HGVS mutations.
Public variables and functions:
clj-hgvs.repairer
HGVS repair functions.
Public variables and functions:

\ No newline at end of file
diff --git a/project.clj b/project.clj
index d0d6315..92ddb46 100644
--- a/project.clj
+++ b/project.clj
@@ -1,4 +1,4 @@
-(defproject clj-hgvs "0.5.0-SNAPSHOT"
+(defproject clj-hgvs "0.5.0"
   :description "Clojure(Script) library for handling HGVS"
   :url "https://github.com/chrovis/clj-hgvs"
   :license {:name "Apache License, Version 2.0"