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

Merge branch 'master' into develop

629b1f306122e619482ecbae35c73df79225af5e authored 12 months ago

Merge pull request #67 from BioJulia/hotfix/CompatHelper

Correct YML whitespace.

f865c26835614294e4f3a2d1fac2d27c79dc57f8 authored 12 months ago

Correct YML whitespace

0db336ba177543e6514d4a312d1e46a48d22fc7f authored 12 months ago

Merge branch 'master' into develop

c9f2e64852359cca815daafcc7ac93f10a238e9b authored 12 months ago

Merge branch 'release/v0.4.0'

beefc452d2eff8847267966b4719724abac6a92f authored 12 months ago

Better align `flags.jl` nomenclature with the SAMv1 specification

456d820866f88efdff6ea1d3962fd5c91f6cb825 authored 12 months ago

Pluralise flag

1d1d9c483606cba9c5eaa5b5e525c12463dde92f authored almost 1 year ago

Update TagBot workflow

671f522be541dc4fd8922b7e82124e04eab63c50 authored about 1 year ago

Update Documentation workflow

afaa3636b8a92b7a29444a3d4c0704cd20eae56c authored about 1 year ago

Update UnitTests badge

38bc47da4e6731569ed3ab60063e27b370c746fe authored about 1 year ago

Update UnitTests workflow

- Add GitHub "annotations"
- Update codecov-action

95d470d85b7cc2a0df9f007e8be0a57839c612df authored about 1 year ago

Increment version

aca2471faaec6e6911278c7b013123b0977c4231 authored about 1 year ago

Update CHANGELOG

6a31ffa343cd5d558094947fcef4cc2fe53113c6 authored about 1 year ago

Update Automa to v1

5079f1b6b8aacddc4bd0ae99778493692ea8b761 authored about 1 year ago

Merge pull request #62 from jonathanBieler/patch-1

Fix deprecated find in header docs

d2921847a8272d68f6439883de12e6abededefcc authored over 1 year ago

Update hts-files.md

Fix find -> findall for headers

4a64cda57743ad2b24c14fd3c3f85abd2554498e authored over 1 year ago

Check that EOF_BLOCK gets written

560a5cd8dfb5d6c732c4e37ecc6c2c30f9986a0d authored over 1 year ago

Improve Slack link

10c1aacd4da057d51c2110c3256192d73571b5b2 authored over 1 year ago

Add doi to README

cc5f21b8548d34010e388a8d43379a9240a07ee6 authored almost 2 years ago

Fun with flags

Implements flag queries.

9a9f2c1f5ad7ad7765475e744c8dc9a958458c08 authored almost 2 years ago

Subtype from XAMRecord

0d1eec3ed3e9ba65a118e6b86a6a8c80779de153 authored almost 2 years ago

Subtype from XAMReader and XAMWriter

8151d877e79eda65808f16a968db3e488afa3380 authored almost 2 years ago

Update CHANGELOG

50039e749f39bb7b29d28ccd808331493767eec7 authored over 2 years ago

Merge pull request #56 from jonathanBieler/bam_index_method

Added method for handling different bam index types.

8272cea71efba979b544c9f54a55cc6f26591d9e authored over 2 years ago

Merge branch 'master' into develop

bda532e2ceb92e1dce80194d78cab6a25288213b authored over 2 years ago

Merge pull request #57 from BioJulia/release/0.3.1

Release v0.3.1

22f939ffbe3b3b765a3b47c43fd7b795fe433b54 authored over 2 years ago

Update CHANGELOG for v0.3.1

fe83a749d20132b7805e611917817b91c28a00e7 authored over 2 years ago

Bump version number in Project.toml to 0.3.1

1c57e9b0e2e8b0f87edc39387fd436ddc374a185 authored over 2 years ago

Merge pull request #55 from MillironX/feature/bioalignments-3

e2b22becf463acdef1fcfbfd19d2b54411f8a1f0 authored over 2 years ago

update docstring

286e271e9135b4379996e69deb0c6726eb4c5a01 authored over 2 years ago

added method for handling different bam index types

93a6b60d26e2b0c70ea8755d5b0913c1df7bb88d authored over 2 years ago

Update CHANGELOG

32e3213ee8dc008084e0e3b60a51e3993f8a71dc authored over 2 years ago

Update tests to use new AlignmentAnchor structure

f7b9d9fa75ca686c6412fdecd6a012f1dfaa7fcc authored over 2 years ago

Bump BioAlignments version compat to 3

9720fd0fcd342c10791c7e1b620653d2362845ee authored over 2 years ago

Change alignment getter for BAM.Record to use existing cigar constructor

Rather than keep a copy of the BioAlignments cigar constructor embedded in
this function, have i...

e6f542a368c368e85c3cc411fb4fb84fa694d441 authored over 2 years ago

Merge pull request #52 from BioJulia/release/0.3.0

Release v0.3.0

946e77a7343bff28da35360820655e9960236b0f authored over 2 years ago

Update .github/workflows/TagBot.yml

Co-authored-by: Ciarán O'Mara <[email protected]>

0c4b3f5dd00de71a96d92031db0cdf14534352ce authored over 2 years ago

Update .github/workflows/CompatHelper.yml

Co-authored-by: Ciarán O'Mara <[email protected]>

2e739e2d8d0181b5e3fb1e1c8c6b1ecb4f2d7848 authored over 2 years ago

Update .github/workflows/CompatHelper.yml

Co-authored-by: Ciarán O'Mara <[email protected]>

8d9ccc91f2953ab82b5ceb5131776ecd0da071a2 authored over 2 years ago

Update .github/workflows/Documentation.yml

Co-authored-by: Ciarán O'Mara <[email protected]>

a7a8e53e4d211f45594213c5fbf5ef2f27286184 authored over 2 years ago

Add CHANGELOG

46fcf71f96ef03de906ea7f7ae7fea9a1801e098 authored over 2 years ago

Bump version number to 0.3.0 in Project.toml

5cbf9dfb1cec668f6dcaefdef8a4d9d58736743a authored over 2 years ago

Add messages to assertions

5da017052b32433ecbd41042600271e7e0c4a387 authored over 2 years ago

Merge branch 'master' into develop

# Conflicts:
# Project.toml
# test/runtests.jl

8424757cc21cf46e2cec58d9aa501b17931125f7 authored over 2 years ago

Merge branch 'hotfix/issue-31'

4490e7c890bb32ba9068c4e06e8a3f731f023454 authored over 2 years ago

Merge pull request #48 from MillironX/feature/BioAlignmentsv2.2

Upgrade BioAlignments to v2.2 & BioSequences to v3

d37e9a04d8b7b1f2b67ffa6202336c19500163eb authored over 2 years ago

Increment BGZFStreams compatibility

0cc0405ca02a7087c7b157665570152eda6562fe authored over 2 years ago

Add tests for issue #31

Test for expected results as described in https://github.com/BioJulia/XAM.jl/issues/31.

99aa013c2b6687ab466a92a694a5e13cd1ff7dd9 authored over 2 years ago

Increment version

7609f6e24dedfcdb573bfab462ec7ffeed381bf3 authored over 2 years ago

Update minimum Julia version to 1.6

BioSymbols v3 requires Julia 1.6+, so update the "julia" compat entry and
remove unit testing ag...

03d8e5e7456da6e4149f44b299e1181a9d5c8ea8 authored over 2 years ago

Correct docstring

675e5828b198bc997a76d60ea3a125d46897a4ba authored over 2 years ago

Update BAM.sequence to return BioSequences.LongDNA{4}

Same principles apply as updating SAM.sequence

a7a76db3d454353af8a83434e3492ac355fe3ea7 authored over 2 years ago

Update SAM.sequence to return BioSequences.LongDNA{4}

BioSequences v3 changed LongDNASeq to LongDNA{N}. We can't assume that
there aren't ambiguous nu...

1660a24a0fe9283a1d38631e39644e51a506b7c1 authored over 2 years ago

Update BioAlignments to v2.2 and BioSequences to v3

Ok, so this isn't atomic, but we can't upgrade these separately.

e560681afa7c441584bbc26fac0cf0f04f6ef931 authored over 2 years ago

Remove Gitter chat links

52d0ce21b0930fde1f97e781c3839670f8ee2cc7 authored almost 3 years ago

Add LTS release to test matrix

dc0992ff540ffff13c54d2647052ddabcebcad86 authored about 3 years ago

Merge pull request #43 from jakobnissen/flagdocs

Improve documentation of flag function

c7114bce16c331804b748cbbede224d4c35b906f authored about 3 years ago

Remove mention of Gitter from README.md

30d61bd79c4254138b21bf19299e8a664291de12 authored about 3 years ago

Improve documentation of flag function

a72fcf47cbfef82ee296ca28dff95e2a8ef7ad2b authored about 3 years ago

Comments

18dae0d45dc9432930fb7f880837d844c0b7ea9e authored over 3 years ago

Return early

9d2a70531a32ee11770aca2f4397b2a00e8a9c9b authored over 3 years ago

Tidy state machines and improve error messages

Makes better use of the existing flow in [Automa.jl](https://github.com/BioJulia/Automa.jl/blob/...

8f26bbf4a728761de812dbfd296a286c988d7bbc authored over 3 years ago

Update Continuous Integration workflows

- Includes doctest in tests.

c56eb0851a0876156656a002a119a311d596fe4e authored over 3 years ago

Readability

fa10f3bfcfa0e0dec43d2059a57dcdd7d7939ea3 authored over 3 years ago

Merge branch 'hotfix/issue-34'

22667dc7afe68a76cd5cdbc22c65b77c0ddf15b3 authored almost 4 years ago

Merge branch 'master' into develop

5bd793bc5fe388b09008fde9f0c2dc25187d4684 authored almost 4 years ago

Cater for blank sam files

c423694f296075e11317f961561744bb60ec664a authored almost 4 years ago

Adjust for Automa 0.8.1

Defines an unambiguous state machine.
https://github.com/BioJulia/Automa.jl/pull/49.

64f371e1e479b07d7d14621b0bd23ad040087842 authored almost 4 years ago

Increment version

aaf3710fbed304f7c8bb843ca6151bcdf8d12b84 authored almost 4 years ago

Make BAM record layout match BAM specs

b086fefbd5db44b68ac5945af3c28fbccb3ee30e authored over 4 years ago

Merge pull request #29 from CiaranOMara/feature/crosscheck

Begin crosschecks

8836b4dbb66e3d0e58c0243b02948542944aef26 authored over 4 years ago

Minimal adjustements

d38c2becf0dc15b27bd40237f313db74cae593b8 authored over 4 years ago

Begin crosschecks

433b8d14e8e11735d4196b71bf29f83482cd3ebd authored over 4 years ago

improve BAM.quality performance

dde235fbc8313432dc7b16f94310128074d875e4 authored over 4 years ago

Tidy

dce44b3f558d06cc1b9f7e425d67bc0f03d7f7b1 authored over 4 years ago

Note

69e77a234c47a5762572bb1a6787001e35e4580e authored over 4 years ago

Merge branch 'hotfix/isnextmapped'

a51e91141fe967a920228f6e6077f7a38e0451b5 authored over 4 years ago

Merge branch 'master' into develop

149d2cd898327925cbedcd1eb6bbc6050ea5ea17 authored over 4 years ago

Correct scope

639b8238c7bcad70c49e26884dcd02e0c1d09850 authored over 4 years ago

Increment version

eb11106b01be1b9e781ac3bedd4f83a40afc2898 authored over 4 years ago

Merge branch 'release/v0.2.5'

dfa5a3217f67f7efbdb41770cb73f65edb6c922d authored over 4 years ago

Merge branch 'master' into develop

b97c97e90fb7660f5e9dc5958b8bfcd84b941c98 authored over 4 years ago

Increment version

bde477d54fe8d6d5d8f5bbcc158b7af3f02bacd2 authored over 4 years ago

Use `copyto!`

https://github.com/BioJulia/BioSequences.jl/pull/95

6141d679e8f30a269e9aa2d940f38bef2a503da7 authored over 4 years ago

Simplify use of `appendfrom!`

946068b2f3d2e907ff5eeec1f77e49907aa32f1a authored over 4 years ago

Use @info

436cfd84baf799b4c35ddeee5835d94114814db0 authored over 4 years ago

Move imports

73de48e2325443c228f69b2c7407de2be83137c5 authored over 4 years ago

Isolate testsets

0ac352f1d24eff2d70dbda63d44e2dcb1e6a2f3c authored over 4 years ago

Update CI and documentation for the general registry

- Update documentation workflow.
- Update CompatHelper workflow.
- Update TagBot workflow.
- Upd...

eaf5c73eb5af325ac97a46c18dd3d539fa9cb41a authored over 4 years ago

Merge branch 'master' into develop

81dbf417989b4815f233a4710b663cdb9c201096 authored over 4 years ago

Merge pull request #12 from BioJulia/hotfix/iterate

hotfix/iterate

551a5906c5593e3d1d1a4011f389cd319a14e12a authored over 4 years ago

Correct not found check

8b7a2ecc2b80ca7717b65d1489c99f50a0bf0d10 authored over 4 years ago

Increment version

cc183115399e87bdf4709d29d91bdf2da23e1414 authored over 4 years ago

Merge branch 'master' into develop

32a2b129e1d473860668b5820bee18ae02a7f333 authored almost 5 years ago

Merge branch 'hotfix/iteration'

060349bd2be1320d360d5892802513696324736a authored almost 5 years ago

Update documentation

b440bc3c4d3b77d2f062d422387a7337557f3a76 authored almost 5 years ago

Empty records during iteration

f00547177f8aac5168a5c8178012b1f51bd571e4 authored almost 5 years ago

Record equivalency functions

300158dbef8b23e122f258bf22a08a331efd6892 authored almost 5 years ago

Tests for in-place-reading pattern

5fa8c5bd2eb31d56b2bec67a8634e596ff43ec38 authored almost 5 years ago

Increment version

bb13a38cf70b3eab70eccde534098466b5a5b2ec authored almost 5 years ago