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