github.com/BioJulia/FASTX.jl commits | Ecosyste.ms: OpenCollective

Update issue and PR template to match BioJulia guidelines

In BioJulia discussion 11, and BioJulia/Contributing, we've decided to make the
template less ve...

868d702ef8bb93c8e91f3d96507c8cfc4d7188c0 authored over 1 year ago

Bump TranscodingStreams to 0.10

e05e5ce4bcb3b10b6077ee6f58e6651b2ce80c00 authored over 1 year ago

Touch up documentation

* Mention the most important things first in the documentation: How to read and
write files.
* P...

53784f9d36e5c9591f18120f58a58b9a00df73b9 authored over 1 year ago

Add Base.print(::IO, ::Index)

This allows the user to turn an `Index` into a string easily, and also makes it
easier to test t...

d0eb7ea97ab06b41f41e01f1be770380e6ee502d authored over 1 year ago

Drop ReTest test dep

The reason to drop this is:
* To make it more in line with all other BioJulia packages
* To simp...

36e42cd24459ecfeebe5d0acb6f2cf7a1e5ddef6 authored over 1 year ago

Migrate to Automa v1

45854a40c6f6e8bcadd3b16ac5ed080c5fd809c9 authored over 1 year ago

Add short-form show for records

This makes them print somewhat nicer in e.g. arrays and dicts. It still does not
properly look a...

a98d262b63bc9e66d209255ab0b672ef7c0487f1 authored over 1 year ago

Fix: Allow non-PHRED quality scores e.g. Solexa

Solexa FASTQ reads are not PHRED scores, and as such can be negative.
Relax some of the checks r...

198d78ad96f3c8cca24d76b53cc39eeda70ed4d5 authored over 1 year ago

Bump ScanByte

ee0a192ea0a31390d413a51eadcfaa7736989a30 authored over 1 year ago

Fix doc examples for writer with do-syntax

ad95dd5b7337b71c422b72f2f023418b385d4893 authored over 1 year ago

Implement copy! for records

149d3a79bb62a22401f9da151e083b9faa467447 authored over 1 year ago

Migrate from SnoopPrecompile to PrecompileTools

4e2db69de4a0fa4111f6a381e1430ad1e71709b7 authored almost 2 years ago

Update files.md

Correct typo.

0f545b97d2e3143e8f9a76661c383df8adf87669 authored almost 2 years ago

Fix Base.read!(::Reader, ::Record) and add tests

These functions were not tested directly, and indeed did not work for FASTQ,
due to a typo.

26a43dda77ee19a5fc2824deaea311aa2ff22ae8 authored almost 2 years ago

Make BioSequences a weak dependency

In the upcoming Julia 1.9 release, Julia supports weak depencies which allow
deps to be supporte...

14a26ef332b3d8160eb7f516591b8660208c44c5 authored almost 2 years ago

Improve precompilation

Improve precompilation by operating on files instead of IOBuffers. This is more
representative o...

617e7c1ebf39896671979bf499137101804c2a28 authored about 2 years ago

Improve type stability slightly

29f386d2d82969ec14bccde5a47aff79692d0198 authored over 2 years ago

Add SnoopPrecompile

The small dependency SnoopPrecompile allows more efficient precompile statements
in packages. He...

f59007a884bc6ae4b4b2a57a9eb6ce494cbe8554 authored over 2 years ago

Merge pull request #86 from BioJulia/docs-preview

Try to get preview build to work

ac28dbbd4f2767c1e1db30b4ce541acb6dd66a8a authored over 2 years ago

try to get preview build

f1681919342c71b58945650bec755c8efed5b234 authored over 2 years ago

add newline

9dae22f30767937778973c959f6088e2cc9d9943 authored over 2 years ago

Rename seqlen to seqsize and export it

7bd3183f65feec35dd1f39dd93873ed36c026c85 authored over 2 years ago

Update README

* Remove reference to OpenCollective
* Remove reference to Gitter

8da41e7b1a06d4d711f60bbfd77f392947fd21db authored over 2 years ago

Fix printing of Records

76bdf567bb7f41ea109261778ae577c99832a20d authored over 2 years ago

Use ReTest (#84)

Use ReTest testing framework

5250a27bd7480225dca3f90d07f0881b78206050 authored over 2 years ago

Rewrite for v2 (#68)

Complete rewrite for v2.
See the changelog for more details.

f44c49832b5f736adf52a5fcffecfaa9118e63ae authored over 2 years ago

Fix missing character in docs example (#74)

f03bccfbafd4a76ec08bc616877a77e0dc7fcd95 authored almost 3 years ago

Clarify that streams take ownership of IO (#72)

Clarify that streams take ownership of IO

c3c802d4c3e18acffa520b16ef00ddf99ccb2840 authored almost 3 years ago

Update TagBot.yml (#67)

5e7efd6dc1e65a9783dd401ecef776b38c6732a4 authored almost 3 years ago

Bump BioSequences/BioSymbols to v3/v5 (#66)

* Bump BioSequences/BioSymbols to v3/v5

* Bump Julia version

b1537390930d319e41ea37f1f14defe66bf66b6d authored almost 3 years ago

Update authors (#61)

0093974d36022bf6606f49fb54f47bd4e2979091 authored about 3 years ago

Merge pull request #58 from jakobnissen/master

Export all user-facing functions

f6e82ec1a717996102c19beb3d4cf12c3ec1ef85 authored about 3 years ago

Remove mention of Gitter on README.md

eb0bda0c80969800ccced725c919a99ed247e58b authored over 3 years ago

Merge branch 'exports'

38878439351f08ec63a0c4057d39688b426fe7fd authored over 3 years ago

Export all user-facing functions

fba10715a74c184071074a136a7071d7e92de682 authored over 3 years ago

Translate between FASTQ & FASTA files (#53)

c7079979e8a6a83ac2a3860baea929498835cdf9 authored over 3 years ago

Merge pull request #52 from jakobnissen/master

Allow trailing whitespace in sequences

0d81f163d41eadb8e907a3471d1ab532402ddcff authored over 3 years ago

Allow trailing whitespace in sequences

af6b19ae667644055b919cd53d2a53b60f4119b7 authored over 3 years ago

Update Project.toml

c4f9fb81704908bb68a330c4c93a49f477e8eea9 authored over 3 years ago

Add changelog for 1.2.0

d69c33b976bc14a04c7184b5ddac472f354c97f9 authored over 3 years ago

Merge pull request #49 from jakobnissen/newlineend

Allow trailing newlines for FASTQ files

215360d88ca3c32fa6b6304eaf85c4a15d385c85 authored over 3 years ago

Fix ambiguity

ab3a1b58fa88c551368fcbd65323d2cf88996b66 authored over 3 years ago

Allow trailing newlines for FASTQ files

8c4bfc3e49c406d1a3287cd54669be0c51ee47b6 authored over 3 years ago

Merge pull request #45 from jakobnissen/fixheader

Fix header code

e9202ba134e05070a047b916e02e77b0df1a1696 authored almost 4 years ago

Fix header code

7d98cbcd20f3c7421fae8d1a900eb807b4d8f0ff authored almost 4 years ago

Merge pull request #44 from BioTurboNick/patch-2

FASTQ example added

be4082269bff2a797afe54dd3cd94051ca6affce authored almost 4 years ago

Merge branch 'master' into patch-2

e9f59467b08c0f5074319c6f5b0893f1c774b7ca authored almost 4 years ago

Merge pull request #43 from BioTurboNick/patch-1

Model good behavior with do block syntax

364c75c26eb7790ab870395dbae50e2503065b4e authored almost 4 years ago

Added example

bc07e72779dc16dd176d34e7b0b6727ddd10b8b7 authored almost 4 years ago

Model good behavior

3f84b0fc3f7c2548d8c3809f16176470f95cb811 authored almost 4 years ago

fix

dfcfd801bc5b773120bcbc73f4f0c89fa0beb802 authored almost 4 years ago

Model good behavior

53a4735542f7dd0ceacd0ab0cb6fb0a4882327d0 authored almost 4 years ago

Merge pull request #41 from jakobnissen/qualityiter

Add quality and sequence iterator

e72dcfe3053533a022db3adb4c3cb5fcc23c3dbd authored almost 4 years ago

Add sequence iterator

6b0f588dfdcd760627574074ae38b22966c1a0b4 authored almost 4 years ago

Add quality iterator

0754245539ce65850bc35d26b32fcd208c6a11e1 authored almost 4 years ago

Merge pull request #38 from jakobnissen/fixdescrparse

Fix description newline bug

b1a8ecb1ab02121910f63e17a3d20eb62cb9b6e4 authored almost 4 years ago

Merge pull request #39 from jakobnissen/fixlinecount

Fix FASTQ line counting bug

ff646a06cd535fb50269171d977f43507b2f6faf authored almost 4 years ago

Fix line counting

7c80fb9753ed9bd0c813506678d458fb8ee77d11 authored about 4 years ago

Fix description newline bug

ced3d8b6fdcd79d104130c5e7c9fd8f4c1458ce6 authored about 4 years ago

Subset fastq record using string syntax (#35)

* Subset fastq record using string syntax

* fix code coverage

* start adding fastqRead

...

b0c50a4ede503a7e7df590953886835b537a3a6b authored over 4 years ago

Make writers parametric and buffered (#26)

b3076c2ab10d328360d17fe91ff761fc26815634 authored over 4 years ago

Add constant time fasta index seeking [NEED REVIEW] (#31)

* Add constant time fasta index seeking

* Add index seeking tests and comments

* Add windo...

bb8c980e5cd312e0e7201d8b71b38d84980cd65d authored over 4 years ago

Simplify seekrecord (#30)

d5b23c103ec3c8c48bd3527458ee9bf1c8bdf902 authored over 4 years ago

Fix windows newline bug (issue 25) (#28)

8f8218b2e100bf49f67267b59c136efe17a7b3e8 authored over 4 years ago

Add header function (#33)

492275622cbae654de861b8a241ff16c9548b078 authored over 4 years ago

Update README.md

db4caae947daf7e68fafbd3183324e05f5a21c24 authored over 4 years ago

Update Project.toml

2f977b1abc90e481ad1948695de65e943e31162a authored over 4 years ago

Fix zero-length copy (#24)

078000d57d0c793ffb1b3589bfe76ed08506a2f8 authored over 4 years ago

Update Project.toml

345e3e935eb5795a28b43157211567dbc851fff1 authored over 4 years ago

Update index.md

0f02681389bacc743833d9fabf111350c2e2b6ea authored over 4 years ago

Update README.md

4c570fbf6bc37588c714d7083f526112d1b7e267 authored over 4 years ago

Support Julia LTS (#21)

9c7285163ddec678a1b04ed612fc3761560649b2 authored over 4 years ago

Change from encode_copy! to copyto! as per change in BioSequences (#18)

9a69972da599ffac513e8d10afd4c7dfabc2dcb0 authored over 4 years ago

Inbounds FASTQ parser (#20)

4a0c465b9a364cd70b80506785b50b4ad11cdafd authored over 4 years ago

Update .travis.yml

2729dc00f4346672edef381e5248c8aa19d07541 authored over 4 years ago

Update appveyor.yml

400bf6dcc14216b3c56c5db48ccd7a48bc790cd6 authored over 4 years ago

add notes on reading gzipped files (#17)

31061cdf3749baf62b40ef50cdc99a07672c1701 authored over 4 years ago

Update CompatHelper.yml

4c99e033bbfdf7db0bb745fa9232b1256aa1fb6d authored over 4 years ago

Update docs

9a5de4d57060984afd7f9bcb57d03bfe0ca783fb authored over 4 years ago

Update README.md

738619d570927252febd30329dfbc5be5298d082 authored over 4 years ago

Merge branch 'tsbugfix'

3b0a452d311dbb62ef203f4132fb424e9a68996a authored almost 5 years ago

Add julia 1.3 to travis

30f4dda1b12d2cfd7b63699068969664fdf78683 authored almost 5 years ago

Add TagBot

8ba5c816c2d109f18e6025918addae6a7bf2e3fc authored almost 5 years ago

Update Project.toml version number

03c04ce512cfece0540a64259d0931589e1edbba authored almost 5 years ago

Implement generic methods for commonly used functions and export them (#11)

* Implement generic methods for commonly used functions and export them

* Remove generic meth...

c7ca87cbfab14c0f08085402bdc33e380a379169 authored about 5 years ago

CompatHelper: bump compat for "Automa" to "0.8" (#16)

db1a910d3e0932fe8f00838cb26bf02d9ac4a4d4 authored about 5 years ago

Merge branch 'master' of github.com:BioJulia/FASTX.jl

6d48e3904c9e4e7f154e0868d578b2d737bfa57f authored about 5 years ago

Add CompatHelper

808a0b45c79e56cd37f3747382c5659d2dafa0f4 authored about 5 years ago

quick FASTA.identifier(record) example (#15)

to save 30mins of pain

6485a52ca5479aa64ca35a001534b210f8128fc4 authored about 5 years ago

Implement hashing and equality for Records (#10)

* Implement == for FASTQ.Record

* Implement hashing for FASTA and FASTQ Record

* Add hashi...

fd093197f96cbc373433684e2d454f918eab072c authored over 5 years ago

Handle case where input is a TranscodingStream. (#9)

d718b47f1f1938972d2012ccacedc90a525def4b authored over 5 years ago

Update changelog

6ce757a7337f71e7b8d9270f861db179b6afc0b5 authored over 5 years ago

Add copyto! methods for copying record data to BioSequences (#6)

- Add copyto! methods for copying record data to BioSequences.
- Updates BioSequences and BioSy...

55c6b783824bafa1eb51eaf2c6211d49d335ed8e authored over 5 years ago

Get coverage working again

eb149bc546d43c247157b4acfb29d8cf1da9f865 authored over 5 years ago

Get documentation working again

ba9bd86b18f13e60f9939d6a5af0dc16488aba84 authored over 5 years ago

Accessor methods now return `nothing` rather than throw an exception.

f376618e82275a2622a7880d7254e60f927cadf9 authored over 5 years ago

Update readme

e50d3228b755e23e2d3c1ab95ca5c71b63aa6594 authored almost 6 years ago

Use TranscodingStreams

ab25467a35dcde230d30bb5eab5d00b7e8e95d8d authored almost 6 years ago

Remove reference part of site, all methods are documented in manual already

8aefc15379ab4ffffb9676ecc0ffcac7e9ea2dad authored about 6 years ago

Update the indes page of the gh-pages site

0e3826af98404dc719666680c6a919920de035f8 authored about 6 years ago