Ciarán O'Mara
560a5cd8df
Check that EOF_BLOCK gets written
2023-05-02 14:56:48 +10:00
Ciarán O'Mara
10c1aacd4d
Improve Slack link
2023-05-01 11:31:55 +10:00
Ciarán O'Mara
cc5f21b854
Add doi to README
2023-02-28 21:23:26 +11:00
Ciarán O'Mara
9a9f2c1f5a
Fun with flags
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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
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Release v0.3.1
2022-10-14 22:09:50 +11:00
fe83a749d2
Update CHANGELOG for v0.3.1
2022-10-13 15:33:24 -05:00
1c57e9b0e2
Bump version number in Project.toml to 0.3.1
2022-10-13 15:26:59 -05:00
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
32e3213ee8
Update CHANGELOG
2022-10-10 16:48:49 -05:00
f7b9d9fa75
Update tests to use new AlignmentAnchor structure
2022-10-10 16:24:26 -05:00
9720fd0fcd
Bump BioAlignments version compat to 3
2022-10-10 16:24:25 -05:00
e6f542a368
Change alignment getter for BAM.Record to use existing cigar constructor
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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
946e77a734
Merge pull request #52 from BioJulia/release/0.3.0
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Release v0.3.0
2022-10-10 15:55:49 -05:00
0c4b3f5dd0
Update .github/workflows/TagBot.yml
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Co-authored-by: Ciarán O'Mara <Ciaran.OMara@utas.edu.au>
2022-10-10 13:06:28 +00:00
2e739e2d8d
Update .github/workflows/CompatHelper.yml
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Co-authored-by: Ciarán O'Mara <Ciaran.OMara@utas.edu.au>
2022-10-10 13:06:17 +00:00
8d9ccc91f2
Update .github/workflows/CompatHelper.yml
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Co-authored-by: Ciarán O'Mara <Ciaran.OMara@utas.edu.au>
2022-10-10 13:06:09 +00:00
a7a8e53e4d
Update .github/workflows/Documentation.yml
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Co-authored-by: Ciarán O'Mara <Ciaran.OMara@utas.edu.au>
2022-10-10 13:06:02 +00:00
46fcf71f96
Add CHANGELOG
2022-10-08 16:27:19 -05:00
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
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# 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
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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
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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
03d8e5e745
Update minimum Julia version to 1.6
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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
a7a76db3d4
Update BAM.sequence to return BioSequences.LongDNA{4}
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Same principles apply as updating SAM.sequence
2022-07-07 09:22:17 -05:00
1660a24a0f
Update SAM.sequence to return BioSequences.LongDNA{4}
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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
e560681afa
Update BioAlignments to v2.2 and BioSequences to v3
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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
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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
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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
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- 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