millironx/XAM.jl
1
0
Fork 0
mirror of https://github.com/MillironX/XAM.jl.git synced 2024-12-22 12:58:19 +00:00
Code Issues Releases Packages Activity
116 commits 21 branches 10 tags 2.5 MiB
Commit graph

116 commits

This branch
This branch
All branches
Author SHA1 Message Date
Thomas A. Christensen II
a7a8e53e4d
Update .github/workflows/Documentation.yml 
Co-authored-by: Ciarán O'Mara <Ciaran.OMara@utas.edu.au>
 2022-10-10 13:06:02 +00:00
Thomas A. Christensen II
46fcf71f96
Add CHANGELOG 2022-10-08 16:27:19 -05:00
Thomas A. Christensen II
5cbf9dfb1c
Bump version number to 0.3.0 in Project.toml 2022-10-08 15:21:06 -05:00
Ciarán O'Mara
5da017052b Add messages to assertions 2022-08-15 21:28:38 +10:00
Ciarán O'Mara
8424757cc2 Merge branch 'master' into develop 
# Conflicts:
#	Project.toml
#	test/runtests.jl
 2022-08-15 15:34:24 +10:00
Ciarán O'Mara
4490e7c890 Merge branch 'hotfix/issue-31' 2022-08-15 15:32:07 +10:00
Ciarán O'Mara
d37e9a04d8
Merge pull request #48 from MillironX/feature/BioAlignmentsv2.2 
Upgrade BioAlignments to v2.2 & BioSequences to v3
 2022-08-15 15:30:19 +10:00
Ciarán O'Mara
0cc0405ca0 Increment BGZFStreams compatibility 2022-08-15 12:30:29 +10:00
Ciarán O'Mara
99aa013c2b Add tests for issue #31 
Test for expected results as described in https://github.com/BioJulia/XAM.jl/issues/31.
 2022-08-15 12:30:27 +10:00
Ciarán O'Mara
7609f6e24d Increment version 2022-08-15 09:43:35 +10:00
Thomas A. Christensen II
03d8e5e745
Update minimum Julia version to 1.6 
BioSymbols v3 requires Julia 1.6+, so update the "julia" compat entry and
remove unit testing against Julia 1.0.
 2022-07-11 07:29:08 -05:00
Ciarán O'Mara
675e5828b1
Correct docstring 2022-07-09 13:37:21 +10:00
Thomas A. Christensen II
a7a76db3d4
Update BAM.sequence to return BioSequences.LongDNA{4} 
Same principles apply as updating SAM.sequence
 2022-07-07 09:22:17 -05:00
Thomas A. Christensen II
1660a24a0f
Update SAM.sequence to return BioSequences.LongDNA{4} 
BioSequences v3 changed LongDNASeq to LongDNA{N}. We can't assume that
there aren't ambiguous nucleotides in a SAM file, so use the larger
LongDNA variant. The method signatures are also simplified, so simplify
their calls, accordingly.
 2022-07-07 09:22:16 -05:00
Thomas A. Christensen II
e560681afa
Update BioAlignments to v2.2 and BioSequences to v3 
Ok, so this isn't atomic, but we can't upgrade these separately.
 2022-07-07 09:22:15 -05:00
Ciarán O’Mara
52d0ce21b0 Remove Gitter chat links 2022-03-22 22:44:09 +11:00
Ciarán O’Mara
dc0992ff54 Add LTS release to test matrix 2021-12-31 13:24:30 +11:00
Ciarán O'Mara
c7114bce16
Merge pull request #43 from jakobnissen/flagdocs 
Improve documentation of flag function
 2021-11-27 12:35:13 +11:00
Jakob Nybo Nissen
30d61bd79c Remove mention of Gitter from README.md 2021-10-22 15:24:03 +02:00
Jakob Nybo Nissen
a72fcf47cb Improve documentation of flag function 2021-10-22 10:48:07 +02:00
Ciarán O’Mara
18dae0d45d Comments 2021-07-06 14:47:43 +10:00
Ciarán O’Mara
9d2a70531a Return early 2021-07-06 14:47:43 +10:00
Ciarán O’Mara
8f26bbf4a7 Tidy state machines and improve error messages 
Makes better use of the existing flow in [Automa.jl](b6997f7415/src/Stream.jl (L124-L127)).
 2021-06-29 13:25:30 +10:00
Ciarán O’Mara
fa10f3bfcf Readability 2021-06-29 13:23:00 +10:00
Ciarán O’Mara
c56eb0851a Update Continuous Integration workflows 
- Includes doctest in tests.
 2021-06-29 13:23:00 +10:00
Ciarán O’Mara
22667dc7af Merge branch 'hotfix/issue-34' 2021-04-01 12:37:54 +11:00
Ciarán O’Mara
5bd793bc5f Merge branch 'master' into develop 2021-04-01 12:37:54 +11:00
Ciarán O’Mara
c423694f29 Cater for blank sam files 2021-04-01 12:37:35 +11:00
Ciarán O’Mara
64f371e1e4 Adjust for Automa 0.8.1 
Defines an unambiguous state machine.
https://github.com/BioJulia/Automa.jl/pull/49.
 2021-04-01 12:37:35 +11:00
Ciarán O’Mara
aaf3710fbe Increment version 2021-03-27 00:28:44 +11:00
Jakob Nissen
b086fefbd5 Make BAM record layout match BAM specs 2020-10-20 01:52:31 +11:00
Ciarán O'Mara
8836b4dbb6
Merge pull request #29 from CiaranOMara/feature/crosscheck 
Begin crosschecks
 2020-10-20 01:50:13 +11:00
Ciarán O'Mara
d38c2becf0 Minimal adjustements 2020-08-13 16:45:53 +10:00
Ciarán O'Mara
433b8d14e8 Begin crosschecks 2020-08-13 16:45:51 +10:00
Jonathan Bieler
dde235fbc8 improve BAM.quality performance 2020-08-02 17:40:52 +10:00
Ciarán O'Mara
dce44b3f55 Tidy 2020-07-08 23:30:44 +10:00
Ciarán O'Mara
69e77a234c Note 2020-07-08 23:30:44 +10:00
Ciarán O'Mara
a51e91141f Merge branch 'hotfix/isnextmapped' 2020-07-08 23:06:44 +10:00
Ciarán O'Mara
149d2cd898 Merge branch 'master' into develop 2020-07-08 23:06:44 +10:00
Diego Alvarez
639b8238c7 Correct scope 2020-07-08 11:57:31 +10:00
Ciarán O'Mara
eb11106b01 Increment version 2020-07-08 11:03:10 +10:00
Ciarán O'Mara
dfa5a3217f Merge branch 'release/v0.2.5' 2020-06-22 10:48:03 +10:00
Ciarán O'Mara
b97c97e90f Merge branch 'master' into develop 2020-06-22 10:48:03 +10:00
Ciarán O'Mara
bde477d54f Increment version 2020-06-22 10:35:34 +10:00
Ciarán O'Mara
6141d679e8 Use copyto! 
https://github.com/BioJulia/BioSequences.jl/pull/95
 2020-06-22 10:30:51 +10:00
Ciarán O'Mara
946068b2f3 Simplify use of appendfrom! 2020-06-22 10:30:51 +10:00
Ciarán O'Mara
436cfd84ba Use @info 2020-06-20 23:32:01 +10:00
Ciarán O'Mara
73de48e232 Move imports 2020-06-20 23:31:53 +10:00
Ciarán O'Mara
0ac352f1d2 Isolate testsets 2020-06-20 23:31:45 +10:00
Ciarán O'Mara
eaf5c73eb5 Update CI and documentation for the general registry 
- Update documentation workflow.
- Update CompatHelper workflow.
- Update TagBot workflow.
- Update unit test workflow.
- Update codecov.
 2020-06-20 23:31:02 +10:00