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Author	SHA1	Message	Date
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
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
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