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8620ea1637
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First version of obimatrix
Former-commit-id: 6e09eb0dd75bc688a6c83ef40dd88658fb1b296e
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2023-11-12 20:40:56 +01:00 |
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5ea2b8afcf
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a first version of obisummary
Former-commit-id: cca1019d82a14a322f46a20890b996b5c7491d41
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2023-11-09 22:33:06 +02:00 |
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45ea4dacf7
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Every small changes to include into Release 4.0.4
Former-commit-id: b2a48c5b5c471f072785e02d4bb0f149a09cdf6f
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2023-08-27 17:22:51 +02:00 |
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be47ec909c
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add the --skip-empty option
Former-commit-id: ec9cb0ecaf90a61bf9289cf4c089b5cc2fcb65a5
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2023-07-17 14:24:02 +02:00 |
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49fa1a76cb
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correction in obitag to save partially indexed reference db
Former-commit-id: ba1e5ce42ac77b143d20fd8903a6e157d83c09f5
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2023-06-07 17:48:38 +02:00 |
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71023423e6
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Add a new command obitagpcr able to tag reads according to their corresponding pcr samples
Former-commit-id: 1f34bf0a27d55afc3556efd64f6ccee6d2329aff
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2023-04-07 17:45:22 +02:00 |
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d70bb45f3f
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Small change in parallelisation tuning
Former-commit-id: 3fe2495b7fd86a0ba47dd87907323a457bae481a
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2023-04-05 14:15:47 +02:00 |
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84b3e4d097
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Reduce memomry inprint of obipcr
Former-commit-id: bd25be2d454f083c729346a828e27f07ad1a216e
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2023-03-31 10:53:53 +02:00 |
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4bf041be62
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Add some option to the obiconsensus command
Former-commit-id: cf30a404a4943e4527106c977b01712ef454e028
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2023-03-28 21:23:27 +07:00 |
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e863dc456a
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Add an option --pprof
Former-commit-id: 3ca1280e8daddbf1075e3189f9851211ce8882ae
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2023-03-28 20:07:26 +07:00 |
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245230ae12
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A small correction
Former-commit-id: 2616ea6bc0e288312326bfb2542e24da22876965
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2023-03-27 19:51:38 +07:00 |
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a33e471b39
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First attempt for obiconsensus... The graph traversing algorithm is too simple
Former-commit-id: 0456e6c7fd55d6d0fcf9856c40386b976b912cba
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2023-03-27 19:51:10 +07:00 |
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b3922c3896
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Produce less weird crash on non existing files
Former-commit-id: 74bb27bd53c685be530632994bd2ba24c1f362e1
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2023-03-07 17:34:25 +07:00 |
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9811e440b8
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Takes into account the option parsing errors
Former-commit-id: d0b3ed0b96a72f79f887df8fbc325427e63d7a73
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2023-03-07 11:06:08 +07:00 |
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ebb05fcdf7
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code refactoring. Prefix function name having behaviour depending on command line option by the prefix CLI
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2023-02-23 23:32:59 +01:00 |
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a0ab14c205
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Complete the documentation and add a Release note file
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2023-02-18 19:54:21 +01:00 |
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6e36b22040
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Normalise the managment of speed measure
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2023-02-16 13:31:49 +01:00 |
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08521c74e2
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Adds Aho-Corasick matching to obiannotate
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2023-02-09 15:59:11 +01:00 |
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526bf79c7f
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Patch for some lost of data during sequence writing
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2023-02-08 13:14:26 +01:00 |
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e3d4da2859
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small things...
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2023-02-01 08:14:29 +01:00 |
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fa6853fca1
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Comment profiling code
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2023-01-31 22:39:34 +01:00 |
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f74c0bd517
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First prelease of obiannotate
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2023-01-27 11:35:39 +01:00 |
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2d375df94f
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move the worker class to the obiseq package
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2023-01-22 22:39:13 +01:00 |
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20b16c0ba1
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Force sequence reading to produce lowercase sequences.
Adds two columns to the obiclean ratio csv file
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2022-11-22 15:06:09 +01:00 |
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09fc426b67
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Refactoring related to iterators
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2022-11-16 17:13:03 +01:00 |
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340579f6d7
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New version of LCS computation, with abug on alignment length patched patched
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2022-11-15 08:21:46 +01:00 |
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f3ddac0f50
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Small adjustment
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2022-10-27 11:18:44 +02:00 |
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8aa323dad5
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Add a first version of obitag the successor of ecotag
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2022-10-26 13:16:56 +02:00 |
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935fc31982
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Adds the new obicomplement command
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2022-10-05 09:40:09 +02:00 |
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bdf317819b
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Code refactoring
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2022-08-23 11:12:00 +02:00 |
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f1e3a68dc4
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improved performance
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2022-08-21 13:44:09 +02:00 |
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5dd835d3e7
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A first functional version of obiclean
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2022-08-20 18:01:07 +02:00 |
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f14860a486
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Patch header parting and formatiing
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2022-05-27 11:53:29 +03:00 |
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656eda1f73
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A fiirst version of LCS score function
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2022-03-07 16:37:21 +01:00 |
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011898bd9d
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A first version of obigrep. Normally fully functionnal, but not fully tested
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2022-02-25 07:29:52 +01:00 |
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abcf02e488
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Start to use leveled log
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2022-02-24 12:14:52 +01:00 |
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eaf65fbcce
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Some code refactoring, a new version of obiuniq more efficient in memory and a first make file allowing to build obitools
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2022-02-24 07:08:40 +01:00 |
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2e7c1834b0
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Big change iin the data model, and a first version of obiuniq
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2022-02-21 19:00:23 +01:00 |
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9737f97084
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before big changes
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2022-02-18 22:53:09 +01:00 |
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3586ecc483
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second version of obidistribute and a first buggy version of obiuniq
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2022-02-15 00:47:02 +01:00 |
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eb32620bb3
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Adds a first version of a new obidistribute command
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2022-02-14 00:01:01 +01:00 |
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38e4655f38
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Correct for a strange bug...
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2022-02-07 11:51:35 +01:00 |
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98a4363d22
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obimultiplex saves unassigned sequence
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2022-02-01 23:25:19 +01:00 |
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8dbda68746
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Adds the command obimultiplex
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2022-02-01 17:31:28 +01:00 |
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251d3be923
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Add automatic garbage collection on ApatPattern
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2022-01-24 17:26:30 +01:00 |
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4551df08b1
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Adds a reader for NGS filter files and change some API for the apat library
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2022-01-18 13:09:32 +01:00 |
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6571296bb2
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Add some documentation
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2022-01-16 19:53:39 +01:00 |
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64676db3f4
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Connect the command line options to the algorithm of obipairing
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2022-01-16 17:30:30 +01:00 |
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576a9f4d2d
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A global version of a Slice pool
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2022-01-16 00:21:42 +01:00 |
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e1b7e1761c
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Change the memory management for thee BuildAlignment function
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2022-01-15 19:10:16 +01:00 |
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