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github.com/BioJulia/GenomicFeatures.jl

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

Loosen type requirements for `coverage`

a4af60ab0947093ac30d70203997c87af9591827 authored over 1 year ago by Ciarán O'Mara <[email protected]>
Merge branch 'master' into develop

5d6c21ec064cde6a5f98761c1fec6fab02f5a843 authored over 1 year ago by Ciarán O'Mara <[email protected]>
Merge pull request #50 from BioJulia/release/v3.0.0

Release/v3.0.0

4f588ded4d210999b436e11ae37020f7a6258101 authored over 1 year ago by Ciarán O'Mara <[email protected]>
Apply suggestions from code review

Co-authored-by: Kevin Bonham <[email protected]>

865d5a9e42a67ac6a15aa8f92a0e4647db7e5c00 authored over 1 year ago by Ciarán O'Mara <[email protected]>
Benchmark fixes

91712bf4a162de9c5144dc01d83701b0314fcffc authored over 1 year ago by Ciarán O'Mara <[email protected]>
Update Documentation workflow

097a253279acff3f876bbecd1e442b48550c6f7b authored over 1 year ago by Ciarán O'Mara <[email protected]>
Add `baseintervaltype` methods

ebcbe23d9c1f0f5f044cbcb14d43ec834816ddb3 authored over 1 year ago by Ciarán O'Mara <[email protected]>
Increment compatibility

4ed213f9252388477499a24713f702fc2a5f1882 authored over 1 year ago by Ciarán O'Mara <[email protected]>
Move doctest to Documentation workflow

14e23a2a57656b4353e565e1178589ed3d47c533 authored over 1 year ago by Ciarán O'Mara <[email protected]>
Increment version

58db78e6931703b32dfd864d970fe79dd73bc610 authored over 1 year ago by Ciarán O'Mara <[email protected]>
Add `metadatatype` methods

9a611155061bb56092aa72ba5465272f33ab69b6 authored over 1 year ago by Ciarán O'Mara <[email protected]>
Expand `precedes` logic and test

84c72f9bf45d065de0bf526180994fd21cb33aa2 authored over 1 year ago by Ciarán O'Mara <[email protected]>
Use `groupname` instead of `seqname`

8bd1a9d201c1d1d4b2aee7d3a4edb3cfdc23bd08 authored over 1 year ago by Ciarán O'Mara <[email protected]>
Add `eltype` method for generators

798b6a1e31254de3f0f23ec23e31b7463d07e19d authored over 1 year ago by Ciarán O'Mara <[email protected]>
Add IterableGenomicCollection helper

857bf1d36fa33ab370590e9ade1b5c7d18a13302 authored over 1 year ago by Ciarán O'Mara <[email protected]>
Subtype from `AbstractGenomicCollection` type

46e596d5b641248b1b095cae53757be16765894e authored over 1 year ago by Ciarán O'Mara <[email protected]>
Add isless method for `AbstractGenomicInterval`

555d005cfdd04c98e16728779d6345fb9a0b91ac authored over 1 year ago by Ciarán O’Mara <[email protected]>
Add `GenomicPosition` type

4e65935489723157ba068b09474201584498534e authored over 1 year ago by Ciarán O'Mara <[email protected]>
Add metadata shortcut

c589dae3565cfbe30afe6b1cc19340096ecefa7a authored over 1 year ago by Ciarán O’Mara <[email protected]>
Test `GenomicIntervalCollection` constructors

81f9781a8c8c3bc7c55486c976f0d2e5509efc8a authored over 1 year ago by Ciarán O'Mara <[email protected]>
Shortcut with dispatch

761a9544ddecb391fdd60a4b60d99f3ce5469547 authored over 1 year ago by Ciarán O'Mara <[email protected]>
Add default `AbstractGenomicInterval` equivalency check

e1c088df12e310a7c638685f2934bc65c4d8bc52 authored over 1 year ago by Ciarán O'Mara <[email protected]>
Add show method for `AbstractGenomicInterval`

c29b04ffc87967b9a05a0bbd31009ba243cf56dd authored over 1 year ago by Ciarán O'Mara <[email protected]>
Add `groupname` methods

01e7d651ea00f51fe9b8ba042bf8c31d5fee20b6 authored over 1 year ago by Ciarán O'Mara <[email protected]>
Use `AbstractGenomicInterval` type

a874fe6b8de2114b15391abf5e338647915d8cc2 authored over 1 year ago by Ciarán O'Mara <[email protected]>
Subtype from `AbstractGenomicInterval` type

Allow users to develop their own custom concrete types.

b97e1c2792efec201b01988244e209ded3b837ef authored over 1 year ago by Ciarán O'Mara <[email protected]>
Un-Shadow `IntervalTrees.Interval` type

- Rename `Interval` to `GenomicInterval`.
- Rename `IntervalCollection` to `GenomicIntervalColle...

4da88a93118ac7e4935e193fcadd39736ef8226f authored over 1 year ago by Ciarán O'Mara <[email protected]>
Test shorthand and longhand bulk insertion

7c0fbaff23ff2d52a3830d57e17186ee24fd1618 authored over 1 year ago by Ciarán O'Mara <[email protected]>
Remove focus from Interval metadata

Develops `intervaltype` methods.

c96a9df7dbf9f0b575ee2dfec50c1d019ed34331 authored over 1 year ago by Ciarán O'Mara <[email protected]>
Rename `OverlapIterator` fields

9351dcae625c459bdb7ed1495fb6bb94e89d8502 authored over 1 year ago by Ciarán O’Mara <[email protected]>
Adjust focus of `IntervalCollection` element type

This commit makes the `IntervalCollection` element type generic, which is a breaking change.

a4b7a7ebfd8ea02a653219dc2fdc73b7ccc5268e authored over 1 year ago by Ciarán O’Mara <[email protected]>
Merge branch 'release/v2.1.0'

b99efced1167938254f76db46b5813752e662ed1 authored over 1 year ago by Ciarán O'Mara <[email protected]>
Merge branch 'master' into develop

8f49a18a319a261983da663e491dd648151a2270 authored over 1 year ago by Ciarán O'Mara <[email protected]>
Update CompatHelper workflow

751cbd916c84c4d04266bf246934806c15c8c107 authored over 1 year ago by Ciarán O'Mara <[email protected]>
Update Documentation workflow

ea7d2ea0abcf8b28273e8275a2bd928d2a89b026 authored over 1 year ago by Ciarán O'Mara <[email protected]>
Improve slack link

c7f2cb6bbd1d672f9c1db3a0141d8a70f9e43f43 authored over 1 year ago by Ciarán O'Mara <[email protected]>
Update UnitTests workflow

Reduces the number of OS tested as there is no need to check third-party software or integrations.

cd9395b0a4f665a761ed874b9bafab4b44a29729 authored over 1 year ago by Ciarán O'Mara <[email protected]>
Update TagBot workflow

84b2d6ef0509a247d55c00fb0db6c2136ff8ef21 authored over 1 year ago by Ciarán O'Mara <[email protected]>
Update authors

8f2e96928af36609c049aeeff08c63e718629fd3 authored over 1 year ago by Ciarán O'Mara <[email protected]>
Increment version

9a96ce5b88ca97cc7d6ac12500c0b66707ada96c authored over 1 year ago by Ciarán O'Mara <[email protected]>
Add `hasintersection` methods

9761d57ccce77e7323272deaa60601ebecccfb27 authored over 1 year ago by Ciarán O'Mara <[email protected]>
Provide an `eachoverlap` iterator that accepts reversed parameters

d64824aa78007e06c74e578fe09f616af732600a authored over 1 year ago by Ciarán O'Mara <[email protected]>
Add `volume` method

14ca3d32770b96b8036a3fd3da149cf2cf6d728e authored over 1 year ago by Ciarán O'Mara <[email protected]>
Use `leftposition` and `rightposition` in `coverage`

78204adb8a71dcd142ed7a77aefdb027a2e8651e authored over 1 year ago by Ciarán O'Mara <[email protected]>
Remove redundant method

0c5f40d2f346267831408ead996c41273f1b744f authored over 1 year ago by Ciarán O'Mara <[email protected]>
Simplify codecov

7c9866555c699cfd248dd451818dcb307cf71b48 authored over 1 year ago by Ciarán O'Mara <[email protected]>
Add `span` method

78398581988085122a31cd3630eb5751c3cf9761 authored over 1 year ago by Ciarán O'Mara <[email protected]>
Add doi to README

b2787f3bca854e9275bb5180b38e05c7e1325808 authored almost 2 years ago by Ciarán O'Mara <[email protected]>
Loosen types

This commit contains breaking changes.

06f73422ffe134422e503fb0bc37ee75ca529d63 authored about 3 years ago by Ciarán O'Mara <[email protected]>
Merge branch 'master' into develop

30437841b2905c7421fd18bcad7ba81578aebf71 authored about 3 years ago by Ciarán O'Mara <[email protected]>
Merge pull request #47 from BioJulia/release/v2.0.5

Release/v2.0.5

483a38eeed7d63fd1ae47c0a3d0d04a78ab45fe1 authored about 3 years ago by Ciarán O'Mara <[email protected]>
Update badges to show the status of the default branch

18f7d4dbab93d6cce343ae52a78bd260d562515c authored about 3 years ago by Ciarán O'Mara <[email protected]>
Add badge for downstream tests

a612b6471085e6d6f9c0bf34d21fcd80347da0cd authored about 3 years ago by Ciarán O'Mara <[email protected]>
Tweak strand definition

2d881022d8369aad6731e0d4e77829e8fa0cf2ae authored about 3 years ago by Ciarán O’Mara <[email protected]>
Drop changelog in favour of GitHub features

22e66217bb6c38a0badbc22e43b2f7316f27ed9b authored about 3 years ago by Ciarán O'Mara <[email protected]>
Filtering example

551028de1f95298a76793c8d3cdb99ea6076c18f authored about 3 years ago by Ciarán O’Mara <[email protected]>
Increment version

0932d2f723715c4507187bce1eaa3f8f2bccdcd3 authored about 3 years ago by Ciarán O'Mara <[email protected]>
Tidy method signature types

6870d9f6c8e5a266115a81c6165300f276d17a14 authored about 3 years ago by Ciarán O'Mara <[email protected]>
Use argument types

44b4f9fbcbfb7e42b34881ebae666d9bf0a3be0d authored about 3 years ago by Ciarán O'Mara <[email protected]>
Add workflow for downstream tests

cd0052aa08c6a02205a7a8e21494214215b4783a authored about 3 years ago by Ciarán O'Mara <[email protected]>
Use accessor functions when handling intervals

ce5d26ec038adff79c4f1f65bd908c3750407399 authored about 3 years ago by Ciarán O'Mara <[email protected]>
Update chat links

f8895bbe5894eaa411744a2efa5d4a8f543063ba authored about 3 years ago by Ciarán O'Mara <[email protected]>
Workflow maintenance

2d731eac84bdb7bfb2876858f7d13757a12922a6 authored about 3 years ago by Ciarán O'Mara <[email protected]>
Rename `OverlapIterator` types

343e8b72f77172be3cc911294b4d34eb344fadbe authored about 3 years ago by Ciarán O'Mara <[email protected]>
Tweak push! method

Use get! method with default.

86c12e93101f3cfe8b54c98266a26200c3b79170 authored about 3 years ago by Ciarán O’Mara <[email protected]>
Tweak IntervalCollection equivalency method

e0e933d7be303bda55a00b352d6f6706ca4fdd14 authored about 3 years ago by Ciarán O’Mara <[email protected]>
Merge branch 'master' into develop

5a2e8484ba8d34d86db049ed7d636263156ad9c6 authored over 3 years ago by Ciarán O’Mara <[email protected]>
Merge branch 'compat'

d6de934ee755c169b483d16c43ee09f346c1c8e2 authored almost 4 years ago by Ciarán O’Mara <[email protected]>
Increment version

abc519ab0b8be6486707bcb50423ed24b138828c authored almost 4 years ago by Ciarán O’Mara <[email protected]>
Merge pull request #37 from BioJulia/compathelper/new_version/2020-08-18-00-08-49-930-4249727338

CompatHelper: bump compat for "DataStructures" to "0.18"

0aafa30284b2a478deeaf04ee0b41d610221e06c authored almost 4 years ago by Ciarán O'Mara <[email protected]>
CompatHelper: bump compat for "DataStructures" to "0.18"

114c5172e0e8c8f9773fef6e9cfc170de5fcad82 authored over 4 years ago by github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
Merge branch 'master' into develop

d885bc9bb12ad2cdd308932cee85c084d69d761e authored over 4 years ago by Ciarán O'Mara <[email protected]>
Merge branch 'release/v2.0.3'

99632a32b437e32625b3df23e78ea2cc271625d7 authored over 4 years ago by Ciarán O'Mara <[email protected]>
Add changelog entries

d63fea96ef95da39038b95f7979d83bb403b637d authored over 4 years ago by Ciarán O'Mara <[email protected]>
Coverage example

997132f94e654077a38c29f9c97570010cb2bfcf authored over 4 years ago by Ciarán O'Mara <[email protected]>
Add docstrings, jdoctests, and references

- Strand docstrings
- IntervalCollection docstrings
- Interval docstring

8a6c44c2ecbba7595f00b841cb0cf3d47bfdb9d5 authored over 4 years ago by Ciarán O'Mara <[email protected]>
Increment version

4729ada47d2568d13c96d9402ba998a308e290d6 authored over 4 years ago by Ciarán O'Mara <[email protected]>
Documentation tweaks

b95741edb7271fb568391ee1163b2b3e34fd636f authored over 4 years ago by Ciarán O'Mara <[email protected]>
Move code common used for benchmarks and tests into Utilities.jl

c10623f6a97f89e964bdc1d19c8f388dbdf362f2 authored over 4 years ago by Ciarán O'Mara <[email protected]>
Benchmark workflow

Conditionally posts benchmark results.

481fe0d10669e168379b11d156cdca621e48aa4c authored over 4 years ago by Ciarán O'Mara <[email protected]>
Update CI and documentation for the general registry

- Julia LTS
- Name tweaks

101e7927329fb075cfe7fcb91f97694036a73509 authored over 4 years ago by Ciarán O'Mara <[email protected]>
Add Benchmarks

- Local benchmark script

20f418019af2e0d5af65c918a9dc291e6a9c3d36 authored over 4 years ago by Ciarán O'Mara <[email protected]>
Merge branch 'hotfix/eachoverlap'

b99be3f27849f4c07545f10c1deff1d310989632 authored over 4 years ago by Ciarán O'Mara <[email protected]>
Merge branch 'master' into develop

7e06779527ea95a3bbbfd4fb10a465664d95ea56 authored over 4 years ago by Ciarán O'Mara <[email protected]>
Add changelog entries and increment version

83002657c9ac7f4d5694d1cb213e1934d8a24249 authored over 4 years ago by Ciarán O'Mara <[email protected]>
Correct non-overlapping query

c35a6559fbd8dbb857884ef9a863fe52f3181364 authored over 4 years ago by Ciarán O'Mara <[email protected]>
Merge branch 'release/v2.0.1'

5104b11e442e044ad8c32b0e1b713504bacea834 authored over 4 years ago by Ciarán O'Mara <[email protected]>
Merge branch 'master' into develop

9fc0551497579c738b343e72f677a05aebd62a80 authored over 4 years ago by Ciarán O'Mara <[email protected]>
Add entries to change log

57b9561aae9f75eeeca80fd43e0246484a0b78aa authored over 4 years ago by Ciarán O'Mara <[email protected]>
Increment version

85558c4542ed92a0022c8bac97e472c0c63976fd authored over 4 years ago by Ciarán O'Mara <[email protected]>
Update latest documentation link

d3c0c18b31be2da8f1c96060131fb7411fc3eb0c authored over 4 years ago by Ciarán O'Mara <[email protected]>
Update CompatHelper workflow

b4609599f463c42278727c9dcbbcf5bb5e5ca51b authored over 4 years ago by Ciarán O'Mara <[email protected]>
Minor documentation tweaks

ef8380ee0f63ed3c6fb933a56939929a5879e62e authored over 4 years ago by Ciarán O'Mara <[email protected]>
Update lifecycle status

ba049fdf16162717aa3cbf52c841e1c330ddc849 authored over 4 years ago by Ciarán O'Mara <[email protected]>
Update documentation workflow

1943f1d6358f6f077b3e410cb9a4b2b4c7cc2f50 authored over 4 years ago by Ciarán O'Mara <[email protected]>
Change subheading

0a9484e0a19b3af22896d6d772dc8de84e198c8d authored over 4 years ago by Ciarán O'Mara <[email protected]>
Add documentation badge

583ac07bf9e02ad7f0f84d4d3dc2b28f6a9f0648 authored over 4 years ago by Ciarán O'Mara <[email protected]>
Clarify origin of AbstractInterval

42d5b34b6ba16d84dfdbb225bb97b06cb2836c96 authored over 4 years ago by Ciarán O'Mara <[email protected]>
Use UnitTests workflow

3498d6f04213950148707f19d9293868a274f9be authored over 4 years ago by Ciarán O'Mara <[email protected]>
Correct change log entries

7cd623465fa0a2b4a419cba71e06c6b6828e637c authored over 4 years ago by Ciarán O'Mara <[email protected]>