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Author	SHA1	Message	Date
Thomas A. Christensen II	6b2bd018e2	docs: Add examples of alignment getters	2023-04-08 20:44:21 -05:00
Thomas A. Christensen II	341faa45e3	docs: Add autodocs for cigar	2023-04-08 20:43:50 -05:00
Thomas A. Christensen II	8458f74053	docs: Add autodocs for alignment	2023-04-08 20:43:30 -05:00
Thomas A. Christensen II	2d16c0b7b6	docs: Rename 'Variants' header to 'Haplotypes'	2023-04-08 20:40:17 -05:00
Thomas A. Christensen II	db170730f0	test: Add test for alignment(::Haplotype)	2023-04-08 20:24:39 -05:00
Thomas A. Christensen II	4817c8016a	feat: Add alignment(::Haplotype) function	2023-04-08 20:24:35 -05:00
Thomas A. Christensen II	95ef4fdc62	test: Add tests for cigar(::Haplotype)	2023-04-08 20:23:39 -05:00
Thomas A. Christensen II	719a123992	feat: Add cigar(::Haplotype) function	2023-04-08 20:23:34 -05:00
Thomas A. Christensen II	e84f765357	feat: Add _cigar_between(::Variation, ::Variation) function ... Add a function that can calculate the matching bases between two (non-matching) Variations and return a matching (M) CIGAR operation	2023-04-08 20:19:49 -05:00
Thomas A. Christensen II	c3a7788dbd	feat: Add _cigar(::Variation) function ... Add a function that can convert the information contained in an Insertion or a Deletion into a CIGAR operator.	2023-04-08 20:19:46 -05:00
Thomas A. Christensen II	011651857f	Bump version number in Project.toml to 0.2.2	2023-01-28 20:07:48 +00:00
Thomas A. Christensen II	4f39d9c822	Update CHANGELOG for v0.2.2	2023-01-28 20:07:48 +00:00
Thomas A. Christensen II	4f046fef9f	Update CHANGELOG	2023-01-28 19:57:10 +00:00
Thomas A. Christensen II	282050d442	Fix validation code for Haplotype	2023-01-28 19:57:10 +00:00
Thomas A. Christensen II	7bd39b1d54	Add tests for _is_valid(::Haplotype)	2023-01-28 19:57:10 +00:00
Thomas A. Christensen II	57ebe391bf	Fix tests for _is_valid(::Haplotype)	2023-01-28 19:57:10 +00:00
Thomas A. Christensen II	2a5a5389ec	Add tests for _is_valid(::Haplotype)	2023-01-28 19:57:10 +00:00
Thomas A. Christensen II	9776d5a31e	Bump version number in Project.toml to 0.2.1	2023-01-11 17:32:15 -06:00
Thomas A. Christensen II	d53acf0df9	Update CHANGELOG for v0.2.1	2023-01-11 17:32:15 -06:00
Thomas A. Christensen II	b7d4831cf2	Update CHANGELOG	2023-01-11 17:17:10 -06:00
Thomas A. Christensen II	2fa5782719	Add more informative errors to _is_valid	2023-01-11 17:17:10 -06:00
Thomas A. Christensen II	4e6c781c60	Update CHANGELOG	2023-01-11 15:01:43 -06:00
Thomas A. Christensen II	d0f55742d6	Add documentation for haplotype reference switching	2023-01-11 15:01:43 -06:00
Thomas A. Christensen II	ecaa995d2b	Update API documentation for different translate methods	2023-01-11 15:01:43 -06:00
Thomas A. Christensen II	6a4a39c859	Add tests for translate(::Haplotype)	2023-01-11 15:01:43 -06:00
Thomas A. Christensen II	a61a80d586	Add translate function for Haplotypes	2023-01-11 15:01:43 -06:00
Thomas A. Christensen II	e251b292a7	Fix tests for translate(::Variation)	2023-01-11 15:01:43 -06:00
Thomas A. Christensen II	239b366a1c	Add tests for translate(::Variation)	2023-01-11 15:01:43 -06:00
Thomas A. Christensen II	f38f0edb00	Bump version number to 0.2.0 in Project.toml	2023-01-10 12:29:04 -06:00
Thomas A. Christensen II	a437409afc	Update test information in READMEs	2023-01-10 12:29:04 -06:00
Thomas A. Christensen II	52d401d623	Update CHANGELOG for v0.2.0	2023-01-10 12:29:04 -06:00
Thomas A. Christensen II	381e4f9736	Add Zenodo badge	2023-01-10 18:12:03 +00:00
Thomas A. Christensen II	e621983dd5	Update CHANGELOG	2023-01-10 12:00:50 -06:00
Thomas A. Christensen II	c360caf9bd	Add tests for Variation sorting	2023-01-10 12:00:50 -06:00
Thomas A. Christensen II	0b2879b78c	Add isless function for Variation	2023-01-10 12:00:50 -06:00
Thomas A. Christensen II	6119368af3	Add tests for Edit sorting	2023-01-10 12:00:50 -06:00
Thomas A. Christensen II	860ce56b34	Add isless function for Edit	2023-01-10 12:00:50 -06:00
Thomas A. Christensen II	2ff4181dd8	Fix deletion equality function ... Fixes: da2cbbd528 ("Add equals functionality to Deletion") Signed-off-by: Thomas A. Christensen II <25492070+MillironX@users.noreply.github.com>	2023-01-10 11:41:08 -06:00
Thomas A. Christensen II	5bd939a15c	Update CHANGELOG	2023-01-10 11:22:06 -06:00
Thomas A. Christensen II	6c86782a2c	Update documentation to reflect new reconstruct syntax	2023-01-10 11:22:06 -06:00
Thomas A. Christensen II	b870007826	Add test for reconstruct function	2023-01-10 11:22:06 -06:00
Thomas A. Christensen II	b80dd8c950	Rename reconstruct! function to reconstruct ... The exclamation mark is conventionally used to mark mutating functions, but reconstruct is no longer mutating, so change the notation.	2023-01-10 11:22:06 -06:00
Thomas A. Christensen II	adbf0ce7f1	Refactor reconstruct! to use the built-in reference sequence ... reconstruct! previously allow changing of _any_ sequence to match a haplotype, with no check to see if that sequence is compatible with the reference sequence the haplotype is based on. Change that to only allow reconstructing sequences from the reference sequence itself, making this a non-mutating function.	2023-01-10 11:22:06 -06:00
Thomas A. Christensen II	8a71715cd9	Change v::Haplotype function arguments to h::Haplotype ... `v` made sense for a `Variant`, but doesn't for a `Haplotype`, so pretty things up.	2023-01-05 11:58:29 -06:00
Thomas A. Christensen II	4e0d88039d	Update CHANGELOG	2023-01-05 11:58:29 -06:00
Thomas A. Christensen II	1384783fcc	Update documentation wording to reflect new type names	2023-01-05 11:58:29 -06:00
Thomas A. Christensen II	46c84b06bb	Rename variants.md to haplotypes.md	2023-01-05 11:58:29 -06:00
Thomas A. Christensen II	5839de3ce1	Rename Variant type to Haplotype	2023-01-05 11:58:29 -06:00
Thomas A. Christensen II	44aa41e628	Rename Variant.jl to Haplotype.jl	2023-01-05 11:58:29 -06:00
Thomas A. Christensen II	3ef4a92ba2	Update CHANGELOG	2023-01-04 11:56:45 -06:00