Changelog.md

Changelog

All notable changes to this project will be documented in this file. Dates are displayed in UTC.

Generated by auto-changelog.

v9.3.6

• publishing new patch d110080
• exporting top level jbeiXmlToJson fbfbe52

v9.3.5

6 April 2023

• adding support for jbei .seq/.xml files 586edf8
• publishing new patch 127dae9

v9.3.4

5 April 2023

• exporting searchWholeObjByName ad4f472
• publishing new patch bf9c059

v9.3.2

7 March 2023

• adding .prot snapgene file parsing d9e86d7
• publishing new patch 64da55c
• tiny copy fix 2b6c8aa

v9.3.1

24 February 2023

• publishing new minor edec4f5
• updating gp|genpep parsing logic 2bf2372

v9.3.0

13 February 2023

• adding geneious parsing 0a88d06
• publishing new patch 9df36e3

v9.2.1

27 January 2023

• Added json to json function from OVE #238
• added json to json function f564e38
• Updated jsonToJsonString naming and fixed export 4857492
• improved jsonToJson tests a1bf50b

v9.2.0

18 January 2023

• Adds digest part fields to genbank notes #237
• stripping URLs from fasta/json files by default, adding option to mangleUrls or to not do any stripping/mangling 9a65171
• moves global var outta fn f71f466
• avois custom formatting 15ab7cd

v9.1.0

6 January 2023

• adding mangling and unmangling to URLs by default when converting to/from fasta/gb 023fc1b
• publishing new patch af5e959

v9.0.1

14 November 2022

• publishing new major a21fe72
• updating validateSequence to also set falsy feature types to misc_feature 114a80a

v9.0.0

14 November 2022

• updating to add a new coerceFeatureTypes flag bc7811a
• publishing new patch 4e4aded

v8.3.32

27 September 2022

• 'n' should be a string before call n.toLowerCase() #231
• add test 5fc05eb
• publishing new patch 97aa93b
• Update validateSequence.js 8aedc4f

v8.3.31

16 August 2022

• updating anyToJson to handle auto parsing in of teselagen JSON files 43cbdef
• publishing new patch 95d0e45

v8.3.30

4 August 2022

• updating to remove xml2Js with fast-xml-parser 5b3a51e
• publishing new patch e754d97
• tiny e9b4ed5

v8.3.29

29 July 2022

• adding an arrowheadType value to hold genbank 'direction' information dd24abe
• publishing new patch 76adb12

v8.3.28

14 July 2022

• update more codes c87c22e
• treat circularityExplicitlyDefined as an option to the parser 08ace7c
• minor tweaks bbc71bb

v8.3.27

17 June 2022

• package.json and nvmrc #227
• Add accession in genbankToJson and in test 833e4cd
• updating yarn lock 9c4b6a9
• Update README.md ddd81d8

v8.3.25

10 March 2022

• Add support for unparsed names (close #185) #224
• Merge pull request #224 from Benjamin-Lee/master #185
• Add support for unparsed names (close #185) #185
• publishing new patch f7de14d
• removing prepublishOnly in favor of prepare 37c6a80

v8.3.24

4 March 2022

• publishing new patch 877bed5
• trying to fix non-updating releases 04e493c

v8.3.23

4 March 2022

• publishing new patch 0bff809
• trying to fix non-updating releases ac05f96

v8.3.22

23 February 2022

• adding support for .bases and .primerBindsOn properties on primers 675f8f2
• publishing new patch 9820009

v8.3.21

25 January 2022

• updating jsonToGenbank to make sure there is always a space at the 68 position 9a9ba5b
• publishing new patch b3ddd77
• updating repo path 8a3f7bb

v8.3.20

9 November 2021

• publishing new patch 1290f23
• exporting convertBasePosTraceToPerBpTrace as a top level function 81520f2

v8.3.19

3 November 2021

• updating ab1 parser to include a per base pair trace 22ac977
• publishing new patch d36b49b

v8.3.18

13 October 2021

• updating npmignore cb5e479
• publishing new patch 6ddfad4

v8.3.17

12 October 2021

• updating ab1ToJson to remove qualNums if that data is missing/corrupted f046dea
• publishing new patch 9b501d5

v8.3.16

16 August 2021

• publishing new patch 174d529
• adding support for import/export of annotations with overlapsSelf=true 541412b

v8.3.15

16 August 2021

• adding support for import/export of annotations with overlapsSelf=true 15ed418
• Merge pull request #216 from TeselaGen/dependabot/npm_and_yarn/tar-4.4.15 1dc4980
• [Security] Bump tar from 4.4.10 to 4.4.15 6cb660f

v8.3.14

22 July 2021

• Pr/thomas1664/105 #188
• adding an allowOverflowAnnotations to parsers b2b11f7
• Merge pull request #209 from TeselaGen/dependabot/npm_and_yarn/elliptic-6.5.4 6f46387
• [Security] Bump elliptic from 6.5.1 to 6.5.4 0d0b7f7

v8.3.13

10 June 2021

• updating end of line gb parsing and adding test case from #162 901ef57
• refactor: improved previous fix and added tests c69eebf
• refactor: removed redundant test 4d1ff15

v8.3.12

9 June 2021

• adding a umd example to the readme and updating the validation function slightly 849b802

v8.3.11

1 June 2021

• removing errant console 5de90ab

v8.3.10

28 May 2021

• keep casing, add back in oligo option 791bb96
• fix genbank DEFINITION parsing to handle new lines + test ac7ffa2
• Do not create uracil features. Always change u's to t's 6cc7c0f

v8.3.6

10 May 2021

• updating jsonToFasta to better handle isProtein option a733821
• Merge pull request #178 from TeselaGen/dependabot/npm_and_yarn/hosted-git-info-2.8.9 b41cfec
• [Security] Bump hosted-git-info from 2.8.4 to 2.8.9 ab7424e

v8.3.5

13 April 2021

• fixing logical error in longestFeatureTypeLength calculation 6b7a624

v8.3.4

13 April 2021

• fixing jsonToGenbank to coerce primers with type 'primer' to type 'primer_bind' 06e5424

v8.3.3

13 April 2021

• Rename primer features to primer_bind on export ebc286e
• Fix isBrowser logic 51e1e9d

v8.3.0

2 April 2021

• making getUtf8StringFromFile work in a node env; removing ability to be able to parse gff or sbol without specifying a fileName (for the file extension) 4771a20

v8.2.0

1 April 2021

• improving robustness of nodejs arraybuffer parsing 1d461d7

v8.1.0

31 March 2021

• updating snapgeneToJson to follow same format as other parsers and not throw an error but instead just return a non-successful result 6039a3d

v8.0.0

31 March 2021

• removing callback style functions; only async/await and promises supported now c04762f

v7.0.13

30 March 2021

• fixing regression that removed the ability to pass a string to anyToJson while in a browser context a590278
• Merge pull request #172 from TeselaGen/dependabot/npm_and_yarn/y18n-3.2.2 f2491ed
• [Security] Bump y18n from 3.2.1 to 3.2.2 d73a5a5

v7.0.12

12 March 2021

• removing /test files from npm 9bb1eaf

v7.0.11

12 March 2021

• removing /test files from npm 696823e

v7.0.10

12 March 2021

• removing /test files from npm ea95cf5

v7.0.9

12 March 2021

• removing /test files from npm 37fc1c9

v7.0.8

12 March 2021

• removing /test files from npm 2458f0f

v7.0.7

12 March 2021

• updating snapgene parser to pull off custom names and description 5839422

v7.0.6

3 March 2021

• removing waldojs as a dependency 4ab66a8
• Merge pull request #163 from TeselaGen/dependabot/npm_and_yarn/lodash-4.17.21 409f026
• [Security] Bump lodash from 4.17.15 to 4.17.21 fe18b24

v7.0.5

17 February 2021

• Fixed typos concerning xxxxToJson #102
• Fixed typos #101
• [Security] Bump merge from 1.2.0 to 1.2.1 #27
• [Security] Bump stringstream from 0.0.5 to 0.0.6 #30
• [Security] Bump tar from 2.2.1 to 2.2.2 #31
• [Security] Bump lodash from 4.17.11 to 4.17.13 #32
• [Security] Bump fstream from 1.0.11 to 1.0.12 #22
• [Security] Bump extend from 3.0.1 to 3.0.2 #21
• Added gff sequence parser #19
• Remove dot at .dna check for snapgene extension #18
• added more GenBank feature types #10
• Updated fasta protein validation message #11
• not replace spaces for _ on proteins #3
• adding a UMD build and removing es and lib from github b90db4f
• updating readme and adding built files 89d3a8c
• publishing new patch 7c74ddd

1.0.3

1 March 2016

• updating package.json c100ace

1.0.2

24 February 2016

• removing try/catch that was eating errors in xml parser 7758d09

1.0.0

23 February 2016

• updating travis #2
• fixing tests #1
• setting up repo ce75a1f
• updating parsers to limit length of feature names 1cfcf09
• updating interface to all parsers to follow: 'string, callback, [options]' style signature 8ab1c1a