millironx/XAM.jl
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Author SHA1 Message Date
Ciarán O'Mara
9a9f2c1f5a Fun with flags 
Implements flag queries.
 2023-02-28 12:57:52 +11:00
Ciarán O'Mara
0d1eec3ed3 Subtype from XAMRecord 2023-02-28 12:57:52 +11:00
Ciarán O'Mara
8151d877e7 Subtype from XAMReader and XAMWriter 2023-02-28 12:54:59 +11:00
Ciarán O'Mara
50039e749f Update CHANGELOG 2022-10-14 22:24:41 +11:00
Ciarán O'Mara
8272cea71e
Merge pull request #56 from jonathanBieler/bam_index_method 
Added method for handling different bam index types.
 2022-10-14 22:15:31 +11:00
Ciarán O'Mara
bda532e2ce Merge branch 'master' into develop 2022-10-14 22:12:10 +11:00
Ciarán O'Mara
22f939ffbe
Merge pull request #57 from BioJulia/release/0.3.1 
Release v0.3.1
 2022-10-14 22:09:50 +11:00
Thomas A. Christensen II
fe83a749d2
Update CHANGELOG for v0.3.1 2022-10-13 15:33:24 -05:00
Thomas A. Christensen II
1c57e9b0e2
Bump version number in Project.toml to 0.3.1 2022-10-13 15:26:59 -05:00
Thomas A. Christensen II
e2b22becf4
Merge pull request #55 from MillironX/feature/bioalignments-3 2022-10-13 14:15:58 -05:00
Jonathan Bieler
286e271e91 update docstring 2022-10-13 15:17:20 +02:00
Jonathan Bieler
93a6b60d26 added method for handling different bam index types 2022-10-13 15:06:39 +02:00
Thomas A. Christensen II
32e3213ee8
Update CHANGELOG 2022-10-10 16:48:49 -05:00
Thomas A. Christensen II
f7b9d9fa75
Update tests to use new AlignmentAnchor structure 2022-10-10 16:24:26 -05:00
Thomas A. Christensen II
9720fd0fcd
Bump BioAlignments version compat to 3 2022-10-10 16:24:25 -05:00
Thomas A. Christensen II
e6f542a368
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 it call the existing constructor. There may be
performance implications for using `cigar` instead of `cigar_rle`, but
having a second copy of the constructor here is an antipattern if I've ever
seen one, so prioritise stable code over performant code.
 2022-10-10 16:24:11 -05:00
Thomas A. Christensen II
946e77a734
Merge pull request #52 from BioJulia/release/0.3.0 
Release v0.3.0
 2022-10-10 15:55:49 -05:00
Thomas A. Christensen II
0c4b3f5dd0
Update .github/workflows/TagBot.yml 
Co-authored-by: Ciarán O'Mara <Ciaran.OMara@utas.edu.au>
 2022-10-10 13:06:28 +00:00
Thomas A. Christensen II
2e739e2d8d
Update .github/workflows/CompatHelper.yml 
Co-authored-by: Ciarán O'Mara <Ciaran.OMara@utas.edu.au>
 2022-10-10 13:06:17 +00:00
Thomas A. Christensen II
8d9ccc91f2
Update .github/workflows/CompatHelper.yml 
Co-authored-by: Ciarán O'Mara <Ciaran.OMara@utas.edu.au>
 2022-10-10 13:06:09 +00:00
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