Ciarán O'Mara
560a5cd8df
Check that EOF_BLOCK gets written
1 year ago
Ciarán O'Mara
10c1aacd4d
Improve Slack link
1 year ago
Ciarán O'Mara
cc5f21b854
Add doi to README
1 year ago
Ciarán O'Mara
9a9f2c1f5a
Fun with flags
...
Implements flag queries.
1 year ago
Ciarán O'Mara
0d1eec3ed3
Subtype from XAMRecord
1 year ago
Ciarán O'Mara
8151d877e7
Subtype from XAMReader and XAMWriter
1 year ago
Ciarán O'Mara
50039e749f
Update CHANGELOG
2 years ago
Ciarán O'Mara
8272cea71e
Merge pull request #56 from jonathanBieler/bam_index_method
...
Added method for handling different bam index types.
2 years ago
Ciarán O'Mara
bda532e2ce
Merge branch 'master' into develop
2 years ago
Ciarán O'Mara
22f939ffbe
Merge pull request #57 from BioJulia/release/0.3.1
...
Release v0.3.1
2 years ago
Thomas A. Christensen II
fe83a749d2
Update CHANGELOG for v0.3.1
2 years ago
Thomas A. Christensen II
1c57e9b0e2
Bump version number in Project.toml to 0.3.1
2 years ago
Thomas A. Christensen II
e2b22becf4
Merge pull request #55 from MillironX/feature/bioalignments-3
2 years ago
Jonathan Bieler
286e271e91
update docstring
2 years ago
Jonathan Bieler
93a6b60d26
added method for handling different bam index types
2 years ago
Thomas A. Christensen II
32e3213ee8
Update CHANGELOG
2 years ago
Thomas A. Christensen II
f7b9d9fa75
Update tests to use new AlignmentAnchor structure
2 years ago
Thomas A. Christensen II
9720fd0fcd
Bump BioAlignments version compat to 3
2 years ago
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.
2 years ago
Thomas A. Christensen II
946e77a734
Merge pull request #52 from BioJulia/release/0.3.0
...
Release v0.3.0
2 years ago
Thomas A. Christensen II
0c4b3f5dd0
Update .github/workflows/TagBot.yml
...
Co-authored-by: Ciarán O'Mara <Ciaran.OMara@utas.edu.au>
2 years ago
Thomas A. Christensen II
2e739e2d8d
Update .github/workflows/CompatHelper.yml
...
Co-authored-by: Ciarán O'Mara <Ciaran.OMara@utas.edu.au>
2 years ago
Thomas A. Christensen II
8d9ccc91f2
Update .github/workflows/CompatHelper.yml
...
Co-authored-by: Ciarán O'Mara <Ciaran.OMara@utas.edu.au>
2 years ago
Thomas A. Christensen II
a7a8e53e4d
Update .github/workflows/Documentation.yml
...
Co-authored-by: Ciarán O'Mara <Ciaran.OMara@utas.edu.au>
2 years ago
Thomas A. Christensen II
46fcf71f96
Add CHANGELOG
2 years ago
Thomas A. Christensen II
5cbf9dfb1c
Bump version number to 0.3.0 in Project.toml
2 years ago
Ciarán O'Mara
5da017052b
Add messages to assertions
2 years ago
Ciarán O'Mara
8424757cc2
Merge branch 'master' into develop
...
# Conflicts:
# Project.toml
# test/runtests.jl
2 years ago
Ciarán O'Mara
4490e7c890
Merge branch 'hotfix/issue-31'
2 years ago
Ciarán O'Mara
d37e9a04d8
Merge pull request #48 from MillironX/feature/BioAlignmentsv2.2
...
Upgrade BioAlignments to v2.2 & BioSequences to v3
2 years ago
Ciarán O'Mara
0cc0405ca0
Increment BGZFStreams compatibility
2 years ago
Ciarán O'Mara
99aa013c2b
Add tests for issue #31
...
Test for expected results as described in https://github.com/BioJulia/XAM.jl/issues/31 .
2 years ago
Ciarán O'Mara
7609f6e24d
Increment version
2 years ago
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.
2 years ago
Ciarán O'Mara
675e5828b1
Correct docstring
2 years ago
Thomas A. Christensen II
a7a76db3d4
Update BAM.sequence to return BioSequences.LongDNA{4}
...
Same principles apply as updating SAM.sequence
2 years ago
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.
2 years ago
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.
2 years ago
Ciarán O’Mara
52d0ce21b0
Remove Gitter chat links
2 years ago
Ciarán O’Mara
dc0992ff54
Add LTS release to test matrix
2 years ago
Ciarán O'Mara
c7114bce16
Merge pull request #43 from jakobnissen/flagdocs
...
Improve documentation of flag function
2 years ago
Jakob Nybo Nissen
30d61bd79c
Remove mention of Gitter from README.md
3 years ago
Jakob Nybo Nissen
a72fcf47cb
Improve documentation of flag function
3 years ago
Ciarán O’Mara
18dae0d45d
Comments
3 years ago
Ciarán O’Mara
9d2a70531a
Return early
3 years ago
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)
).
3 years ago
Ciarán O’Mara
fa10f3bfcf
Readability
3 years ago
Ciarán O’Mara
c56eb0851a
Update Continuous Integration workflows
...
- Includes doctest in tests.
3 years ago
Ciarán O’Mara
22667dc7af
Merge branch 'hotfix/issue-34'
3 years ago
Ciarán O’Mara
5bd793bc5f
Merge branch 'master' into develop
3 years ago