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Author	SHA1	Message	Date
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