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github.com/BioJulia/GenomicFeatures.jl

Tools for genomic features in Julia.
https://github.com/BioJulia/GenomicFeatures.jl

Merge branch 'release/v2.0.0'

28f28a8f2a15fee7f19185f063f0f771e4a3de95 authored over 4 years ago by Ciarán O'Mara <[email protected]>
Merge branch 'master' into develop

4a95715904f3af1aefd18e95ddaf78b60b5b52f0 authored over 4 years ago by Ciarán O'Mara <[email protected]>
Wrap test sets

a99c0cc4dba4cea71da8f3caa9daba27528130db authored over 4 years ago by Ciarán O'Mara <[email protected]>
Rename LICENSE

d97ddb36f93e8e091f60be531ee1f4b647b0bb12 authored over 4 years ago by Ciarán O'Mara <[email protected]>
Update readme

90cbc27c7489c68948d423abffa1528fc7bb1a69 authored over 4 years ago by Ben J. Ward <[email protected]>
Edit manual index page

b319f6f77778aef05277a37ac38e81e07831a236 authored over 4 years ago by Ben J. Ward <[email protected]>
Add TagBot, update logo

c9776ccfdb6bda2a9d53858154302ca42e0f3c9e authored over 4 years ago by Ben J. Ward <[email protected]>
Generic constructor conversion tests

75d869830b598d864e7da7c065fbc6d284febc6a authored over 4 years ago by Ciarán O'Mara <[email protected]>
Generic IntervalCollection constructor

31dd794df38577fa0370ac8963336e2c4917ee1f authored over 4 years ago by Ciarán O'Mara <[email protected]>
Generic Interval constructor

aaa7e8912e6cf28dffe7298e678ef408bbdfcb77 authored over 4 years ago by Ciarán O'Mara <[email protected]>
Minor documentation tweaks/corrections

8d0a82d3506d7a5b38d6c936a57c409f17b3719a authored over 4 years ago by Ciarán O'Mara <[email protected]>
Add entries to change log

41770b42177fdde260f5c93c84be912c0f678186 authored over 4 years ago by Ciarán O'Mara <[email protected]>
Increment version

6674e992708447ef8a15f5cd7ff9911634808e54 authored over 4 years ago by Ciarán O'Mara <[email protected]>
Add entries to change log

35df83630324451f79f21010c8e5e35ca2837f39 authored almost 5 years ago by Ciarán O'Mara <[email protected]>
Migrate from BioCore to BioGenerics

5952f8927804b213d0d45453acacd56bbeb458d6 authored almost 5 years ago by Ciarán O'Mara <[email protected]>
Add BioJulia registry and drop support for older versions of Julia

- Drop versions of Julia incompatible with custom registries.
- CI preparation for BioJulia regi...

713f9ba1e328c9faf5207311560e709376d3b07d authored almost 5 years ago by Ciarán O'Mara <[email protected]>
Remove reference to GFF3

This detail would be included in the documentation of the GFF3 package.

e022a5569f09f8afe55015460a9eb9f9c8ced4a9 authored almost 5 years ago by Ciarán O'Mara <[email protected]>
Temporarily remove Interval Streams documentation

92158d7e33d7b6de0eba4100d7da7917122e41ef authored almost 5 years ago by Ciarán O'Mara <[email protected]>
Add links to BioJulia packages

9bbb9b021f18f7e2e52474d081336988df13f451 authored almost 5 years ago by Ciarán O'Mara <[email protected]>
Remove IO from documentation

e376570837a5c2a8adffbbf9e241cd8120c8fb7b authored almost 5 years ago by Ciarán O'Mara <[email protected]>
Remove unused function

b4194adee5084c46bf65bd2211c1c06269b368f1 authored almost 5 years ago by Ciarán O'Mara <[email protected]>
Extract parsers

- Removes all IO submodules.
- Prunes Project.toml

365b9f19c6195b9cd35e295e956bc5bb07f97442 authored almost 5 years ago by Ciarán O'Mara <[email protected]>
Merge branch 'release/v1.0.4'

e7ce4e36210407fb9f05e36c303c562aad30d9c0 authored almost 5 years ago by Ciarán O'Mara <[email protected]>
Merge branch 'master' into develop

99a208497b11478a95f948726aa1efcf70b71c2f authored almost 5 years ago by Ciarán O'Mara <[email protected]>
Increment version

2543d77f7328696358f6ef5271a4ba621af04c84 authored almost 5 years ago by Ciarán O'Mara <[email protected]>
Add dates to changelog

f31784d0ab8952055ccce763e57309a1a8638b37 authored almost 5 years ago by Ciarán O'Mara <[email protected]>
Merge branch 'master' into develop

7ab6c618f9696c443d9bdfdeee5411d733ad8ee9 authored almost 5 years ago by Ciarán O'Mara <[email protected]>
Merge branch 'compat'

d4a5c80e065719ee3582c957078442fb05f9f6af authored almost 5 years ago by Ciarán O'Mara <[email protected]>
Increment version

e5ebf2c30a3096b65bce91e63db9419b9ba7168f authored almost 5 years ago by Ciarán O'Mara <[email protected]>
Correct CompatHelper configuration

8c823a1f47ac0149e91e1cad78a6f04891d3acc5 authored almost 5 years ago by Ciarán O'Mara <[email protected]>
Merge branch 'compathelper/new_version/2020-01-07-04-02-45-709-383418431' into compat

5891a4f34cd037ac7722ee6fe4f129f548887456 authored almost 5 years ago by Ciarán O'Mara <[email protected]>
Merge branch 'compathelper/new_version/2020-01-07-04-02-51-483-4171759597' into compat

0809a828f8b1578572dc9cc2d0c08fee4ff5da95 authored almost 5 years ago by Ciarán O'Mara <[email protected]>
CompatHelper: bump compat for "ColorTypes" to "0.9"

1fb75ac8e73495acaedd36ee57e7bf001e554e84 authored almost 5 years ago by github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
CompatHelper: bump compat for "FixedPointNumbers" to "0.7"

0c9b40dfae3549c10e1895a9d7fb8f188b877577 authored almost 5 years ago by github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
Merge branch 'master' into develop

32e6c0f8b02c60832f3fa8cf65e907cd2860f8c6 authored almost 5 years ago by Ciarán O'Mara <[email protected]>
Merge branch 'hotfix/strand'

e0783f58869a890662da752953551996a99469ff authored almost 5 years ago by Ciarán O'Mara <[email protected]>
Increment version

ee7244d1db246a82244fe51bfe703a8ec2c8229c authored almost 5 years ago by Ciarán O'Mara <[email protected]>
Correct typo in Strand constructor

e74110eaeabe88e7ccb1fafb527ed8df28fcc381 authored almost 5 years ago by Ciarán O'Mara <[email protected]>
Flatten isordered method

2944cc80c32196a16b6b860c7918ff72bfad885e authored almost 5 years ago by Ciarán O'Mara <[email protected]>
Flatten isless method

ae16fa9ed2965918028936f9efb67614c1738321 authored almost 5 years ago by Ciarán O'Mara <[email protected]>
Flatten strand conversion

e1a9c96ce2dfd9e0c95d17f8949d58f3e5bbc736 authored almost 5 years ago by Ciarán O'Mara <[email protected]>
Remove conversion

c8751c94b89094a1bd2b958c6618f02f47fbeb7d authored almost 5 years ago by Ciarán O'Mara <[email protected]>
Flatten compare_overlap

146425b358f3f5275be30ec700686b228fde2d4a authored almost 5 years ago by Ciarán O'Mara <[email protected]>
Remove hard wraps (code)

ef89542c826b5e69413b7b30708616eddca6b165 authored almost 5 years ago by Ciarán O'Mara <[email protected]>
Elucidate function return

f105032327c66f0367b4d6071b893bce5438a34d authored almost 5 years ago by Ciarán O'Mara <[email protected]>
Add parameter type to bulk insertion sort flag

289a2edd4585177f97c92bc30b22a6983ef15ba8 authored almost 5 years ago by Ciarán O'Mara <[email protected]>
Update changelog

11fcb379b9eb0ac901c4053644cacecd6fa1cc1e authored almost 5 years ago by Ciarán O'Mara <[email protected]>
Merge branch 'master' into develop

b62ad35a1a51f5898e99436ca467ee8f7d22b08b authored almost 5 years ago by Ciarán O'Mara <[email protected]>
Fix package UUID

4014c57348689e1a07a1588bfe15faf6b9bd2b17 authored almost 5 years ago by Ben J. Ward <[email protected]>
Merge pull request #22 from BioJulia/release/v1.0.1

release/v1.0.1

028580e85bbc11f546c8eee76f638f61e3fafc7a authored almost 5 years ago by Ciarán O'Mara <[email protected]>
Set CompatHelper to generate PRs against master

c724b7895c7475691b33195486633ec553ec530b authored about 5 years ago by Ciarán O'Mara <[email protected]>
Allow Windows 32bit to fail

c5da00fbaf318099c7e4d73f8e10f5f7eb4493fd authored about 5 years ago by Ciarán O'Mara <[email protected]>
Compatibility bounds

902c63956ffa1d08bb1d3bfe3ff3c56c3366e072 authored about 5 years ago by Ciarán O'Mara <[email protected]>
Add documentation workflow

Use DOCUMENTER_KEY

Add push_preview to deploydocs

d012df91a1c5c8612ee60152f7b130128cc8f8c6 authored about 5 years ago by Ciarán O'Mara <[email protected]>
Dev links

c49f1100351845b324ddd8704ca8e874c9b4708c authored about 5 years ago by Ciarán O'Mara <[email protected]>
Correct typo

5940a1be02428b1dae4530f3286dc54ecb55029f authored about 5 years ago by Ciarán O'Mara <[email protected]>
Update change log

fdd977ed265e4efd09c4cdfcea87a719c11f1b95 authored about 5 years ago by Ciarán O'Mara <[email protected]>
Increment version

f84103de7003d67d1cfb43668cf76a5aff8977ef authored about 5 years ago by Ciarán O'Mara <[email protected]>
Header capitalisation

f2cd3ed4de69f059bab65799364a8bac0e3b18b9 authored about 5 years ago by Ciarán O'Mara <[email protected]>
Move Interval documentation

93822344e38895c8c572e4ec94225293c3de69fb authored about 5 years ago by Ciarán O'Mara <[email protected]>
Add API References section to documentation

99d0aabff84c3e1bc2c4a92f79f38f988efede6d authored about 5 years ago by Ciarán O'Mara <[email protected]>
Add IntervalTrees link

e411553792432366b5666e12da5d574261c8ab36 authored about 5 years ago by Ciarán O'Mara <[email protected]>
Add CompatHelper workflow

96a8a4cee431e8617f672334c4b9bb03fc8258f1 authored about 5 years ago by Ciarán O'Mara <[email protected]>
Align readme sections with branding

2e530610c667e1d9713444e296d896c847fb3b91 authored about 5 years ago by Ciarán O'Mara <[email protected]>
Match descriptions

a4fae798c2a65e5bb53102756d4d9ff76f516542 authored about 5 years ago by Ciarán O'Mara <[email protected]>
Remove obsolete house keeping files

Code of conduct and contributing files are now under https://github.com/BioJulia/Contributing.

83cf4a6115562ee1fbc714e2b46ebef71adfa88c authored about 5 years ago by Ciarán O'Mara <[email protected]>
Update installation instructions

00674317c7fa573f718e85fd1385f017f5c55743 authored about 5 years ago by Ciarán O'Mara <[email protected]>
Move sticker

e23aedfb9230920aedcef7800fdc5d133ba283a0 authored about 5 years ago by Ciarán O'Mara <[email protected]>
Migrate from Discord to Gitter

2a40c480a45881a6af62cc682f575dd8b35d7eb7 authored about 5 years ago by Ciarán O'Mara <[email protected]>
Use default icon style

23c40b39c7b795727acbab4d3ada41d9cc309ada authored about 5 years ago by Ciarán O'Mara <[email protected]>
Update documented types

Closes #17.

798c560bd7117eaaa2c5813adf193ba62f3ed77b authored about 5 years ago by Ciarán O'Mara <[email protected]>
Use # for headers

cbaf46cb713e390eebc63d1580d0cddcf019bfad authored about 5 years ago by Ciarán O'Mara <[email protected]>
Remove hard wraps (documentation)

2ad09eb8bbe7485b0c60462dc19e701e88970baa authored about 5 years ago by Ciarán O'Mara <[email protected]>
Add change log

a694df358acc1607ca869606cc5a2fbf1b8ba80d authored about 5 years ago by Ciarán O'Mara <[email protected]>
Update CI

- Add Julia v1.1
- Add Julia v1.2
- Add Julia v1.3

2c4d6fb41410c57345055ac58c60cb4be39c5409 authored about 5 years ago by Ciarán O'Mara <[email protected]>
Update Documenter

ee66a2d949ef8da0ec0f190f3b83994c5d7f1d92 authored about 5 years ago by Ciarán O'Mara <[email protected]>
Update coverage

Coverage

9bcbf14a7c9a400924a6644acc0c383aa060cc68 authored about 5 years ago by Ciarán O'Mara <[email protected]>
Project.toml

1cea1a76898e5a28653564041f38b941635e3592 authored about 5 years ago by Ciarán O'Mara <[email protected]>
Update .gitignore

c9314c423522aab6d30c159e0c3892c1d12694b8 authored about 5 years ago by Ciarán O'Mara <[email protected]>
Small fix in docs

9e256b25148ebbeb6fa3e2c17896c50dcfd26d2c authored about 5 years ago by Diego Javier Zea <[email protected]>
Version 1.0 updates (#15)

8fc34ff680f5e742e25d2bd3d4722cb33fbe3cd5 authored over 6 years ago by Ben J. Ward <[email protected]>
Fix julia deprecations (#12)

This PR fixes many of the deprecations from julia v0.6, which
will become errors in v0.7 and be...

4acbbd6d4950c0d822b435c47781e290f198ae32 authored over 6 years ago by femtocleaner[bot] <femtocleaner[bot]@users.noreply.github.com>
Contributing files rollout (#11)

* Rollout file CONTRIBUTING.md

* Rollout file CODE_OF_CONDUCT.md

* Rollout file .github/PU...

823297b1e0af50711f440f146a0e52340f4e4c22 authored over 6 years ago by Ben J. Ward <[email protected]>
Drop Julia 0.5 (#9)

* drop Compat.jl

* replace immutable with struct

* replace type with mutable struct

* f...

ce551969d9dabaf535cfd8edc4719c522ca16294 authored over 7 years ago by Kenta Sato (佐藤 建太) <[email protected]>
make index types immutable (#6)

3d55c41cacc6cd9221535c34545946c5aa22f81a authored over 7 years ago by Kenta Sato (佐藤 建太) <[email protected]>
support tabix (#5)

* support tabix for GFF3

* fix a typo

* merge GFF3 tests

* make the overlap iterator ge...

5381331535866cbbac1c9a50b736513bdcf80f4e authored over 7 years ago by Kenta Sato (佐藤 建太) <[email protected]>
add read and write methods for Strand (#4)

Since these are needed for multi-process parallelism.

a2e54222240a0b06d52074a216b0f09ce3d2ba68 authored over 7 years ago by Kenta Sato (佐藤 建太) <[email protected]>
Merge pull request #3 from BioJulia/dcj/filter

Add optional filter functions to eachoverlap, and a findfirst function.

baecd090de80b241c981ec4e195708abf1ed3c2f authored over 7 years ago by Daniel C. Jones <[email protected]>
Update IntervalTrees require. Make filter keyword arg in findfilter.

8aacb699a1e7905157b0d77bdbfcfb23bdb9de9c authored over 7 years ago by Daniel C. Jones <[email protected]>
Add optional filter functions to eachoverlap, and a findfirst function.

4c4e1e89865816fa5e7c617940a4338e498ccf4b authored over 7 years ago by Daniel C. Jones <[email protected]>
merge chunks more aggressively

57944d338ffd333716a8b1c8605e83622e2eaa02 authored over 7 years ago by Kenta Sato <[email protected]>
use a specific commit when testing on specimens

3619443128a09774fb6583f6d2ab651eb60245e3 authored over 7 years ago by Kenta Sato <[email protected]>
replace type aliases with constants

0dd37f4ec87682fbf8982bd2c5c0571e052e9e18 authored over 7 years ago by Kenta Sato <[email protected]>
print compactly when showing an interval collection

a80a64791d540a2195e47d7c9ebc496cfa955f0c authored over 7 years ago by Kenta Sato <[email protected]>
fix the link to docs [ci skip]

471e7f0700e4c1084d4798158eb05ecf158f8523 authored over 7 years ago by Kenta Sato <[email protected]>
add Indexes

77bf7daab777f78b451b2cc7fccb4ca13cf4aaec authored over 7 years ago by Kenta Sato <[email protected]>
support Julia v0.6 (#1)

* use heappop!/heappush! in DataStructures.jl

* use primitive type

* replace typealias wit...

fa6e3293f0786c2a2bbd3dc63adb881ac7a53f0a authored over 7 years ago by Kenta Sato (佐藤 建太) <[email protected]>
add more tests on GFF3

c3a3f9b616484a6d3be4323af92ccaf5c9533f09 authored over 7 years ago by Kenta Sato <[email protected]>
replace Bio with BioCore

c93c774795af2484b6ac334058f702000bedd88b authored over 7 years ago by Kenta Sato <[email protected]>
tidy up docs of IO and add examples

40f2e3ea1cce127cf8a3bbbcc082827dc6c7fb45 authored over 7 years ago by Kenta Sato <[email protected]>