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69 Commits
Author SHA1 Message Date
Eric Coissac 3087c70daa Feature: Implement constrained k-mer generation and clique search 
This commit introduces core functionality for oligonucleotide family tagging, constrained k-mer generation, and clique finding. It also includes updates to the Go language version and refactors the logic for k-mer dissimilarity metrics.
 2026-11-03 09:25:34 +11:00
Eric Coissac 7542e33010 Several bugs dicoverd during the doc writing 2025-04-04 16:59:27 +02:00
Eric Coissac 7a9dc1ab3b update release notes 2025-03-12 14:06:20 +01:00
Eric Coissac 62e5a93492 update the compress option name 2025-03-11 17:14:40 +01:00
Eric Coissac b18c9b7ac6 add the --raw-taxid option 2025-03-08 09:40:06 +01:00
Eric Coissac 78df7db18d typos 2025-03-08 07:44:41 +01:00
Eric Coissac fc08c12ab0 update release notes 2025-03-08 07:42:20 +01:00
Eric Coissac 996ec69bd9 update the release notes for version 4.4.0 2025-03-01 12:56:39 +01:00
Eric Coissac 7b23314651 Some typos 2025-03-01 08:29:27 +01:00
Eric Coissac 1e541eac4c Last commit version 2025-03-01 08:24:26 +01:00
Eric Coissac 51b3e83d32 some cleaning 2025-02-24 11:31:49 +01:00
Eric Coissac 8671285d02 add the --min-sample-count option to obiclean. 2025-02-24 08:48:31 +01:00
Eric Coissac 00f2dc2697 Rename obifind obitaxonomy and introduce the new CSV format for taxonomy. 2025-01-29 10:45:26 +01:00
Eric Coissac 3137c1f841 Adds the ability to read gzip-tar file for the taxonomy dump 2025-01-24 11:47:59 +01:00
Eric Coissac ad2461a656 some minor improvements 2024-11-27 13:36:06 +01:00
Eric Coissac d29a56dcbf Changes to be committed: 
modified:   Release-notes.md
	modified:   pkg/obialign/pairedendalign.go
	modified:   pkg/obilua/obiseq.go
	modified:   pkg/obioptions/version.go
	modified:   pkg/obiseq/biosequence.go
	modified:   pkg/obitools/obipairing/pairing.go
 2024-11-27 09:56:22 +01:00
Eric Coissac 05bf2bfd6c Add option related to agrep match on obigrep and obiannotate 2024-09-09 16:52:13 +02:00
Eric Coissac c0c18030c8 Adds information on the new github address 2024-08-02 14:26:20 +02:00
Eric Coissac 242f4d8f56 Realease notes 2024-08-02 13:50:33 +02:00
Eric Coissac 1b1cd41fd3 Add some code refactoring from the blackboard branch 2024-08-02 12:35:46 +02:00
Eric Coissac c7ed47e110 first version of obidemerge, obijoin and a new filter for obicleandb but to be finnished 
Former-commit-id: 8a1ed26e5548c30db75644c294d478ec4d753f19
 2024-07-10 15:21:42 +02:00
Eric Coissac 2d4813614b Update the release Notes 
Former-commit-id: 5611fb13809c5cc45a515be5d62aac61e6fc51ad
 2024-06-07 09:11:06 +02:00
Eric Coissac 411124d1b3 Add automatic rules to manage version number 
Former-commit-id: f4fcc1927f4169025c1d8cc88c5f3abcdc76037c
 2024-06-01 17:26:16 +02:00
Eric Coissac 55ce36f329 Update of obipcr and homogenization of logging 
Former-commit-id: 46abf47c19ace5248042c02cf1f81d9f6c12eb10
 2024-05-16 15:18:30 +02:00
Eric Coissac cb35612a6c new --version option and qualities method in obiscript 
Former-commit-id: 7b0ce2901785d5c7494dec3a7a95d1fc5dc4a52b
 2024-04-13 12:40:43 +02:00
Eric Coissac 0a2ea962db obitag bug 
Former-commit-id: e6f8750d8db74c0b175c4a93d5b58bd84f293d52
 2024-04-03 16:28:06 +02:00
Eric Coissac d68210ef94 Tag version 4.2.0 
Former-commit-id: 9315e463fcf9c654ff34738d0fb93c94538600a1
 2024-04-03 12:57:00 +02:00
Eric Coissac bf41d16e67 Patch a bug in obitag on the identification of the best match 
Former-commit-id: e551b3b83e79a517dd5409ea8112fb005c39c2ee
 2024-04-03 12:30:40 +02:00
Eric Coissac e25c3b7365 Bug in the json parsing 
Former-commit-id: e652b04b9fa7e11124eb5930c7bec4613c808758
 2024-03-19 13:50:13 +01:00
coissac 0f3871d203 Change the API of workers 
Former-commit-id: 9b07306edd8cf28266f86f95823948fa99d39ea9
 2024-03-02 16:03:46 -04:00
coissac 1542ce4c63 Work on EMBL and Genbank parser efficienct 
Former-commit-id: 309cc9ce4eea4c8085d7d4451a66a81710532f07
 2024-02-20 13:23:07 +01:00
coissac c1d9bea6bb Release 4.1.2 
Former-commit-id: 68a0f5c50b7a33e31b76c0c0994e17dc8321963b
 2024-02-16 18:05:08 +01:00
coissac 23758b00f6 Patch a bug in the embl reader and adds some doc 
Former-commit-id: 9b5f75fb14bcc3043da1647055279987a295d271
 2024-01-31 15:43:02 +01:00
coissac e3938c7ba0 Update release date 
Former-commit-id: 773ca2e8938c10cdf24911598d56708a5a80fbc2
 2023-12-20 10:06:17 +01:00
coissac 1a0ca8c847 Tags release 4.1.1 
Former-commit-id: 31c11305f9301615bdc1c9dfd0c7270777b6a096
 2023-12-20 10:02:40 +01:00
coissac 2caaa62485 Implements the kmeans++ algo to select the landmarks in the geometric method 
Former-commit-id: 732404a0dc6d7276e4e479dd2481aa4bd42d4ce5
 2023-12-11 16:07:03 +01:00
coissac 03bef6461d Complement to the documentation 
Former-commit-id: 89952a6f3bb261a6aaec24430906e635914ffce4
 2023-12-04 13:16:34 +01:00
coissac 72ad84c2d4 remove a forgotten debug log 
Former-commit-id: 9fe06483b0dabc9d618f4f1d752ae9e472a07904
 2023-11-25 14:04:22 +01:00
coissac db6de58548 Patch bug in ngsfilter reader 
Former-commit-id: 77a1c39bf9c023bf4a3f58167e1e8a4d5d82e7c9
 2023-11-25 13:55:43 +01:00
coissac 5d24522aa6 update the release notes 
Former-commit-id: 71ffb326302e5f108a52a41853e1c7dc6ee76136
 2023-11-24 17:45:13 +01:00
coissac 72e5855ee9 Adds changes 
Former-commit-id: 85e9faa305c918618cef5d8ea5e2eca8956213d4
 2023-11-22 14:58:21 +01:00
coissac 9384876416 Push version 4.1.0 
Former-commit-id: 87a36bc61d99557fa4539ff44417ae1cdd2b2317
 2023-11-16 07:51:43 +01:00
coissac 4017e213e9 release note 
Former-commit-id: 55acaae2d107ab19dcd5b1765ac866030e9ea143
 2023-11-10 00:45:11 +01:00
coissac dedf125f6e Patch a bug in Subsequence and adds few unit tests. 
Former-commit-id: caddc9ad6523e4ef02899bfe83cc8681ef674383
 2023-11-08 10:16:34 +02:00
coissac 8f96517f3c small changes 
Former-commit-id: 1fee30445f03ff627dab1c335e75c3f278621f6e
 2023-11-07 21:20:45 +02:00
coissac aa0443e484 correction to release notes 
Former-commit-id: 424819230f26bccd6f5ef26684f50e9ff477a7de
 2023-11-07 12:20:40 +02:00
coissac 185b974d13 Adds a JSON output format 
Former-commit-id: 26f07460772c0f735bf705d473f892878d3e57f0
 2023-11-07 11:56:49 +02:00
coissac 61c30f9b6a Patch rev complement and first implementation of --auto in obicsv 
Former-commit-id: f3020e81283b1073c4d1c2d2ff0887e3998e6764
 2023-11-07 09:37:07 +02:00
coissac ddf0f2cede Add the -D (--delta) option to obipcr 
Former-commit-id: 753079807faaddb23e03fd6350125bfa67f98c7f
 2023-10-13 17:04:10 +02:00
coissac c2533667b2 Tag a Fatal bug release 4.0.5 
Former-commit-id: 10b27c6d3867756d3159ef22eefd75db3fab84d0
 2023-08-29 18:32:00 +02:00