46 commits

Author	SHA1	Message	Date
Thomas A. Christensen II	da2cbbd528	Add equals functionality to Deletion	2023-01-04 11:56:45 -06:00
Thomas A. Christensen II	f08d6eb991	Add length method for Substitution	2023-01-04 11:56:45 -06:00
Thomas A. Christensen II	3b2730b5c1	Add export for translate and reconstruct!	2023-01-04 11:56:45 -06:00
Thomas A. Christensen II	25c63906dc	Move exports to top of file ... Per Blue style, exports should be one per line, and appear immediately after using statements. Reorganize module file to comply	2023-01-04 11:56:45 -06:00
Thomas A. Christensen II	9f9d0899bd	Move Insertion-related code to edits/Insertion.jl	2023-01-04 11:56:45 -06:00
Thomas A. Christensen II	b36ab69c72	Move Deletion-related code to edits/Deletion.jl	2023-01-04 11:56:45 -06:00
Thomas A. Christensen II	ba9f0e8fb1	Move Substitution-related code to edits/Substitution.jl	2023-01-04 11:56:45 -06:00
Thomas A. Christensen II	8c2dd271f3	Move Variation-related code to Variation.jl	2023-01-04 11:56:45 -06:00
Thomas A. Christensen II	37965ac7eb	Move Variant-related code to Variant.jl	2023-01-04 11:56:45 -06:00
Thomas A. Christensen II	3f631ace8f	Move Edit-related code to Edit.jl	2023-01-04 11:56:45 -06:00
Thomas A. Christensen II	fb5b7dfacf	Remove commented-out code	2023-01-04 11:56:45 -06:00
Thomas A. Christensen II	128a5445ad	Switch alignment validation to after edit construction	2022-12-17 22:02:15 +00:00
Thomas A. Christensen II	f9058c5cb3	Update ranges to allow end position insertions	2022-12-17 22:02:15 +00:00
Thomas A. Christensen II	5be4dce200	Add check for soft clips when construction Variants from alignment	2022-12-17 22:02:15 +00:00
Thomas A. Christensen II	d8435be115	Add Variation-level validation for Variants ... Testing indicates that some Variants (particularly those with insertions and/or clips at the send of the query sequence) will validate fine as a Variant, but will fail validation as a Variation. This problem is particularly annoying when constructing Variants in the REPL, as the creation will complete successfully, but the show of the Variant will error out. To fix this, leverage the existing validation of Variation to check each Edit within a Variant upon construction.	2022-12-17 22:02:15 +00:00
Thomas A. Christensen II	91c3acc85e	Add equality function for Variant	2022-12-17 22:02:15 +00:00
Thomas A. Christensen II	3b33c85d00	Add type parameterization to variations getter ... I have encountered some cases where having a non-parameterized vector can crash a downstream process. I don't yet know how to make a MWE of that, but adding type parameters fixes my problem, and doesn't break any tests here.	2022-11-22 17:55:41 +00:00
Thomas A. Christensen II	f7278bd7d7	Remove unused AminoAcidSeq reference	2022-10-04 11:41:42 -05:00
Thomas A. Christensen II	1bbb85153c	Add constructor for Variant based on Variations ... A Variant is a collection of Variations, right? Unfortunately there was no way to convert a collection of Variations into a Variant, so I added one.	2022-07-21 12:33:35 +00:00
Thomas A. Christensen II	b8e44c7b81	Add public alternate base getter for Variation	2022-07-13 16:49:59 -05:00
Thomas A. Christensen II	cab314ec0b	Add public reference base getter for Variation	2022-07-13 16:49:58 -05:00
Thomas A. Christensen II	ccbe6eed62	Add private alternate base getter for Insertion	2022-07-13 16:49:57 -05:00
Thomas A. Christensen II	1b7c7f86d7	Add private reference base getter for Insertion	2022-07-13 16:49:56 -05:00
Thomas A. Christensen II	145e9e5f88	Add private alternate base getter for Deletion	2022-07-13 16:49:56 -05:00
Thomas A. Christensen II	bc073eaf20	Add private reference base getter for Deletion	2022-07-13 16:49:55 -05:00
Thomas A. Christensen II	c1f47c7b22	Add private alternate base getter for Substitution	2022-07-13 16:49:54 -05:00
Thomas A. Christensen II	73c2c2764f	Add private reference base getter for Substitution	2022-07-13 16:49:53 -05:00
Thomas A. Christensen II	a80ff869ce	Fix reference(::Variation) ... `reference(::Variation)` used the wrong field name. Fix that so I can use it downstream.	2022-07-13 16:49:52 -05:00
Thomas A. Christensen II	6d7a93604a	Add function to get variations from variant	2022-07-05 09:10:01 -05:00
Thomas A. Christensen II	dbdc575d75	Add accessor functions for Variant	2022-07-05 09:10:00 -05:00
Thomas A. Christensen II	89cad0120f	Add rightposition functions	2022-07-05 09:09:53 -05:00
Thomas A. Christensen II	fe1bbcc0f3	Add hash function for Variation	2022-06-30 16:48:37 -05:00
Thomas A. Christensen II	70965732cf	Add equality function for Variation	2022-06-30 16:48:24 -05:00
Thomas A. Christensen II	2d05b233a9	Add accessor functions for Variation properties	2022-06-14 16:24:05 -05:00
Thomas A. Christensen II	1e6f6ea075	Add accessor functions for Edit properties	2022-06-14 16:17:16 -05:00
Thomas A. Christensen II	76d5b6059e	Add Variation constructor based on edit parsing	2022-06-14 14:48:39 -05:00
Thomas A. Christensen II	ade9b7e41d	Fix inconsistent Variation positions (#4) ... * Change Variant constructor to use alignment positions Signed-off-by: Thomas A. Christensen II <25492070+MillironX@users.noreply.github.com> * Add test for positions of Variations Signed-off-by: Thomas A. Christensen II <25492070+MillironX@users.noreply.github.com>	2022-05-06 12:26:49 +02:00
Thomas A. Christensen II	d0f0f65d7f	Fix show function for Variations with Insertion edits (#3) ... Signed-off-by: Thomas A. Christensen II <25492070+MillironX@users.noreply.github.com>	2022-05-06 12:25:07 +02:00
Jakob Nybo Nissen	92a2d40553	Implement translate	2022-01-26 14:59:19 +01:00
Jakob Nybo Nissen	8024d50889	More stuff	2021-09-15 13:33:37 +02:00
Jakob Nybo Nissen	87277268f6	Full rewrite	2021-08-24 16:30:11 +02:00
Jakob Nybo Nissen	642658f592	Add parsing	2021-03-02 17:55:17 +01:00
Jakob Nybo Nissen	354f18e0e4	Switch to SumTypes	2021-03-02 15:50:37 +01:00
Jakob Nybo Nissen	40749eb6f5	Start fixing	2021-03-02 13:20:25 +01:00
Jakob Nybo Nissen	64ae3bc862	Rewrite	2020-10-20 15:26:27 +02:00
Jakob Nybo Nissen	ad3fe4303f	Initial commit	2020-10-01 17:03:01 +02:00