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Release_4.3.0

Release_4.4.0

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• 340579f6d7 New version of LCS computation, with abug on alignment length patched patched Eric Coissac 2022-11-15 08:21:46 +01:00
• 18be4becec Add some new packages Eric Coissac 2022-11-14 14:36:04 +01:00
• 0f99f9a6ba First trial of a fastest LCS implementation Eric Coissac 2022-11-14 07:42:15 +01:00
• 6429f24c57 Accellerate a bit LCS computation Eric Coissac 2022-10-27 17:30:55 +02:00
• f3ddac0f50 Small adjustment Eric Coissac 2022-10-27 11:18:44 +02:00
• 8aa323dad5 Add a first version of obitag the successor of ecotag Eric Coissac 2022-10-26 13:16:56 +02:00
• e17d1fbca6 Patch the error message stored in sequences by obimultiplex Eric Coissac 2022-10-17 21:32:24 +02:00
• f8df48338d Several bug in annotation management Eric Coissac 2022-10-12 23:01:47 +02:00
• aae3398701 Replace the CopyMap function by the MustFillMap and adds a InterfaceToIntMap function Eric Coissac 2022-10-12 22:56:38 +02:00
• 58dbdd8698 requires that father.count > son.count Eric Coissac 2022-10-05 09:53:56 +02:00
• d9c18ab0b5 Add a reverse complement worker Eric Coissac 2022-10-05 09:41:59 +02:00
• 935fc31982 Adds the new obicomplement command Eric Coissac 2022-10-05 09:40:09 +02:00
• 7873b90902 Patch a bug in obigrep... Eric Coissac 2022-10-02 20:52:26 +02:00
• 65210755cc Patch reading of annotation from stdin Eric Coissac 2022-09-29 14:48:05 +02:00
• d0f63fda56 add functionalities to the expression predicate evaluations Eric Coissac 2022-09-28 16:13:20 +02:00
• fe5d8e3340 Patch a bug in ngsfilter reading and sample matching Eric Coissac 2022-09-28 14:29:19 +02:00
• ebefa28cc0 Patch memory error related to []byte pool Eric Coissac 2022-09-28 14:28:37 +02:00
• 57ba460929 add the obi_mutation attribute to the sequences Eric Coissac 2022-09-20 22:03:44 +02:00
• da8e3fd7b7 Correct the orientation of the mutation pattern Eric Coissac 2022-09-20 22:03:01 +02:00
• 49b4d97803 Remove HTML escaping to json marshaling Eric Coissac 2022-09-20 22:01:52 +02:00
• 3cd8aabd83 Correct some misspelling in option helps Changes to be committed: modified: pkg/obitools/obiclean/options.go modified: pkg/obitools/obiconvert/options.go Eric Coissac 2022-09-20 21:59:38 +02:00
• f6735a634e Correctly patch the memory leak related to the apatsequence Eric Coissac 2022-09-12 15:19:46 +02:00
• 448f5f83fa Patch a bug in comparison of attibutes during sequence annotation merging Eric Coissac 2022-09-08 07:50:17 +02:00
• 6b8f4490cf Change obiclean algorithm for a better evaluation of ratio Eric Coissac 2022-08-31 20:38:03 +02:00
• 90ba980de6 correct the gml writer Eric Coissac 2022-08-30 10:28:05 +02:00
• cd202ba72e Adds of new modules Eric Coissac 2022-08-23 15:09:51 +02:00
• 91c2ce551d Add new modules Eric Coissac 2022-08-23 15:09:03 +02:00
• d04161a0fb small code refactoring Eric Coissac 2022-08-23 15:08:35 +02:00
• d2f4919bc8 comment out to option that need to be rethought Eric Coissac 2022-08-23 15:07:48 +02:00
• 989e678f6b refactor code and change algorithm used to read from many files Eric Coissac 2022-08-23 15:07:06 +02:00
• bdf317819b Code refactoring Eric Coissac 2022-08-23 11:12:00 +02:00
• 57e0966d35 Adds some documentation Eric Coissac 2022-08-23 11:11:36 +02:00
• 4df99cec5b Chang log package Eric Coissac 2022-08-23 11:10:04 +02:00
• abaede48b5 Refactoring of some code Eric Coissac 2022-08-23 11:07:39 +02:00
• 62968aaa26 patch the Taxid method Eric Coissac 2022-08-23 11:06:51 +02:00
• 1e58c92086 Adds a function to test that a list contains at least one occurrence of an element Eric Coissac 2022-08-23 11:06:28 +02:00
• 5a81525e46 Adds a genbank parser Eric Coissac 2022-08-23 11:04:57 +02:00
• a71e65963b Modify the .gitignore Eric Coissac 2022-08-21 17:53:51 +02:00
• 31c45bf46f Adds documentation and few methods to the BioSequences Eric Coissac 2022-08-21 17:53:19 +02:00
• eca1af9957 Patch a bug on the FilterOn method Eric Coissac 2022-08-21 15:05:14 +02:00
• ad4a861261 Change some comments Eric Coissac 2022-08-21 14:47:22 +02:00
• 10663bf79c Patch an algorithm error on th Annotation Classifier Eric Coissac 2022-08-21 14:45:53 +02:00
• f1e3a68dc4 improved performance Eric Coissac 2022-08-21 13:44:09 +02:00
• 02f445f02f same as previous commit Eric Coissac 2022-08-21 13:43:27 +02:00
• 34e957d3fb Add an option alowwing to use the pool method instead of the concat method when several input files are specified Eric Coissac 2022-08-21 13:43:00 +02:00
• 844e24b818 Add information on the number of workers in the log Eric Coissac 2022-08-21 13:41:58 +02:00
• f00456fcf3 Add a second way to merge several batch iterators using the pool method. Eric Coissac 2022-08-21 13:41:15 +02:00
• 3e40ae9d52 Patch a memory leak in apat sequence Eric Coissac 2022-08-21 13:40:20 +02:00
• 9677f531c4 Improved performance and ability to read very long sequences. Eric Coissac 2022-08-21 13:38:13 +02:00
• 5dd835d3e7 A first functional version of obiclean Eric Coissac 2022-08-20 18:01:07 +02:00
• a07d348aea small change Eric Coissac 2022-07-31 21:52:04 +02:00
• 821abb1395 package obistat debut Eric Coissac 2022-07-28 16:52:27 +02:00
• b4cabf31fc Correctly print StatsOn values in obiformat style Eric Coissac 2022-06-14 10:00:45 +02:00
• f0de4d8f28 Finalize the correct merging of statistic of occurrences, in I expect every situation Eric Coissac 2022-06-14 09:54:33 +02:00
• 6b13729eba Adds a test for not pushing empty batch on the output Eric Coissac 2022-06-14 09:53:35 +02:00
• cf5b4baa54 Small bug in sequence counting on merge Eric Coissac 2022-05-30 16:28:59 +02:00
• f14860a486 Patch header parting and formatiing Eric Coissac 2022-05-27 11:53:29 +03:00
• 656eda1f73 A fiirst version of LCS score function Eric Coissac 2022-03-07 16:37:21 +01:00
• 62cd1c44dc Corrects some bug in building the sequence filter Eric Coissac 2022-02-25 10:36:01 +01:00
• 011898bd9d A first version of obigrep. Normally fully functionnal, but not fully tested Eric Coissac 2022-02-25 07:29:52 +01:00
• 0a36447e2a Adds the log module Eric Coissac 2022-02-24 12:15:36 +01:00
• a18745a34d Modify the gitignore Eric Coissac 2022-02-24 12:15:09 +01:00
• abcf02e488 Start to use leveled log Eric Coissac 2022-02-24 12:14:52 +01:00
• f18cc034bb add an option alias -O for the old obi format Eric Coissac 2022-02-24 07:26:55 +01:00
• f5b278f5ec edit .gitignore Eric Coissac 2022-02-24 07:09:35 +01:00
• eaf65fbcce Some code refactoring, a new version of obiuniq more efficient in memory and a first make file allowing to build obitools Eric Coissac 2022-02-24 07:08:40 +01:00
• 2e7c1834b0 Big change iin the data model, and a first version of obiuniq Eric Coissac 2022-02-21 19:00:23 +01:00
• 9737f97084 before big changes Eric Coissac 2022-02-18 22:53:09 +01:00
• 37ce3536e1 New more functionnal version of obiuniq. But it has a memory leak Eric Coissac 2022-02-18 10:01:23 +01:00
• 6067b92e2f Adds the notioon of NA value Eric Coissac 2022-02-18 10:00:42 +01:00
• aef546dae3 Patch a bug in the recycle method Eric Coissac 2022-02-18 10:00:15 +01:00
• 94457f5116 Creare a reorder method Eric Coissac 2022-02-18 09:59:47 +01:00
• cb125bb2a4 Adds an error message when no sample can be associated Eric Coissac 2022-02-18 09:58:56 +01:00
• 2636882f9f big bug on subschunk Eric Coissac 2022-02-18 09:58:08 +01:00
• ce226acac0 Few debug on obidistribute and some progresses on obiunique, but -c and -m options are still not working Eric Coissac 2022-02-15 10:49:01 +01:00
• 3586ecc483 second version of obidistribute and a first buggy version of obiuniq Eric Coissac 2022-02-15 00:47:02 +01:00
• b931321ba1 Adds the hash option to obidistribute Eric Coissac 2022-02-14 09:12:57 +01:00
• eb32620bb3 Adds a first version of a new obidistribute command Eric Coissac 2022-02-14 00:01:01 +01:00
• 1544bafde1 Updates modules Eric Coissac 2022-02-09 22:03:38 +01:00
• bd630ea512 Forget the binary writer Eric Coissac 2022-02-09 22:00:38 +01:00
• 27556ce81f Start of implementing binary file format Eric Coissac 2022-02-07 11:57:08 +01:00
• d5a1a191f8 update go.sum Eric Coissac 2022-02-07 11:54:47 +01:00
• b193c3edfe adds the obifind command to gitignore Eric Coissac 2022-02-07 11:52:56 +01:00
• 79fcd98e43 updated go.mod Eric Coissac 2022-02-07 11:52:06 +01:00
• 38e4655f38 Correct for a strange bug... Eric Coissac 2022-02-07 11:51:35 +01:00
• 30d80db02d All an option to limit number of CPU Eric Coissac 2022-02-06 18:52:53 +01:00
• 98a4363d22 obimultiplex saves unassigned sequence Eric Coissac 2022-02-01 23:25:19 +01:00
• e9cdfd7e03 Make subseq method dealing with qualities Eric Coissac 2022-02-01 18:49:32 +01:00
• bc1d7b26a9 adds missing file Eric Coissac 2022-02-01 18:04:11 +01:00
• 8dbda68746 Adds the command obimultiplex Eric Coissac 2022-02-01 17:31:28 +01:00
• 76d9309508 Remame PCR struct to PCRSim Eric Coissac 2022-01-27 12:13:27 +01:00
• b9da72d379 Adds finalizer to ApatSequence Eric Coissac 2022-01-24 22:54:41 +01:00
• 251d3be923 Add automatic garbage collection on ApatPattern Eric Coissac 2022-01-24 17:26:30 +01:00
• 703eb62819 Adds elements to .gitignore Eric Coissac 2022-01-18 13:10:56 +01:00
• 4551df08b1 Adds a reader for NGS filter files and change some API for the apat library Eric Coissac 2022-01-18 13:09:32 +01:00
• 6571296bb2 Add some documentation Eric Coissac 2022-01-16 19:53:39 +01:00
• 64676db3f4 Connect the command line options to the algorithm of obipairing Eric Coissac 2022-01-16 17:30:30 +01:00
• 576a9f4d2d A global version of a Slice pool Eric Coissac 2022-01-16 00:21:42 +01:00
• e1b7e1761c Change the memory management for thee BuildAlignment function Eric Coissac 2022-01-15 19:10:16 +01:00
• e8fff6477b Work on iterators and recycling of biosequences Eric Coissac 2022-01-14 23:11:36 +01:00