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757448cb1e
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debug obigrep taxonomy options
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2025-01-15 20:48:34 +01:00 |
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4ae3336135
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obidemerge: set demerge on sample the default
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2025-01-10 17:09:44 +01:00 |
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d066bb6878
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Changes to be committed:
modified: .gitignore
modified: cmd/test/main.go
modified: pkg/obioptions/version.go
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2025-01-09 07:24:41 +01:00 |
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c58d9772ac
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Two small corrections on options
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2025-01-07 11:51:37 +01:00 |
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4fe0db63ff
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Patch CSV reader to use the new taxonomy system
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2024-12-20 21:30:00 +01:00 |
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ccd3b06532
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Merge branch 'master' into taxonomy
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2024-12-20 20:06:57 +01:00 |
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5d0f996625
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Patch a small bug on json write
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2024-12-20 19:42:03 +01:00 |
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abfa8f357a
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patch a bug in Taxid parsing
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2024-12-19 13:54:23 +01:00 |
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795df34d1a
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Changes to be committed:
modified: cmd/obitools/obitag/main.go
modified: cmd/obitools/obitag2/main.go
modified: go.mod
modified: go.sum
modified: pkg/obiformats/ncbitaxdump/read.go
modified: pkg/obioptions/version.go
modified: pkg/obiseq/attributes.go
modified: pkg/obiseq/taxonomy_lca.go
modified: pkg/obiseq/taxonomy_methods.go
modified: pkg/obiseq/taxonomy_predicate.go
modified: pkg/obitax/inner.go
modified: pkg/obitax/lca.go
new file: pkg/obitax/taxid.go
modified: pkg/obitax/taxon.go
modified: pkg/obitax/taxonomy.go
modified: pkg/obitax/taxonslice.go
modified: pkg/obitools/obicleandb/obicleandb.go
modified: pkg/obitools/obigrep/options.go
modified: pkg/obitools/obilandmark/obilandmark.go
modified: pkg/obitools/obilandmark/options.go
modified: pkg/obitools/obirefidx/famlilyindexing.go
modified: pkg/obitools/obirefidx/geomindexing.go
modified: pkg/obitools/obirefidx/obirefidx.go
modified: pkg/obitools/obirefidx/options.go
modified: pkg/obitools/obitag/obigeomtag.go
modified: pkg/obitools/obitag/obitag.go
modified: pkg/obitools/obitag/options.go
modified: pkg/obiutils/strings.go
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2024-12-19 13:36:59 +01:00 |
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f2525d7b07
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Changes to be committed:
modified: pkg/obilua/lua.go
modified: pkg/obioptions/version.go
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2024-12-04 11:42:05 +01:00 |
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39dd3e3ce8
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Add management of []interface{} to the LUA API.
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2024-12-04 10:58:17 +01:00 |
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f41a6fbb60
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Patch a small bug on json write
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2024-11-29 18:39:18 +01:00 |
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00b0edc15a
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refactoring of the file chunck writing
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2024-11-29 18:15:03 +01:00 |
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ad2461a656
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some minor improvements
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2024-11-27 13:36:06 +01:00 |
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40fb4e9767
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reduce the memory impact of obiuniq.
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2024-11-27 13:30:16 +01:00 |
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d29a56dcbf
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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
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2024-11-27 09:56:22 +01:00 |
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69ef1758a2
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obicsv debug
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2024-11-24 23:38:49 +01:00 |
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3d06978808
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a functional new version of obifind
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2024-11-24 19:33:24 +01:00 |
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7884a74f9c
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Patch a bug in obitagpcr
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2024-11-18 21:10:47 +01:00 |
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f3d8707c08
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Add default taxonomy
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2024-11-16 10:01:07 +01:00 |
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03f4e88a17
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Fisrt functional version
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2024-11-14 19:10:23 +01:00 |
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4b65bfce84
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Changes to be committed:
modified: pkg/obioptions/version.go
modified: pkg/obitools/obitagpcr/pcrtag.go
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2024-11-04 14:30:17 +01:00 |
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fc75974c68
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Changes to be committed:
modified: pkg/obioptions/version.go
modified: pkg/obitools/obitagpcr/options.go
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2024-11-04 13:25:52 +01:00 |
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fefc360f80
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Changes to be committed:
modified: pkg/obioptions/version.go
modified: pkg/obitools/obitagpcr/pcrtag.go
modified: pkg/obiutils/abs.go
new file: pkg/obiutils/abs_test.go
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2024-10-28 21:51:21 +01:00 |
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3e00d39d47
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In obimultiplex, patch a bug when no tag are associated to a primer.
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2024-10-22 14:12:20 +02:00 |
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9e8a7fd9be
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Patch a bug in fastq reader
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2024-10-20 16:07:43 +02:00 |
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7255c71576
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commit version
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2024-09-24 16:36:59 +02:00 |
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2b4a633c30
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EndGapFree alignments
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2024-09-24 15:52:12 +02:00 |
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05bf2bfd6c
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Add option related to agrep match on obigrep and obiannotate
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2024-09-09 16:52:13 +02:00 |
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65ae82622e
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correction of several small bugs
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2024-09-03 06:08:07 -03:00 |
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373464cb06
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On development genome skim tools
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2024-08-30 11:17:33 +02:00 |
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31bfc88eb9
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Patch a bug on writing to stdout, and add clearer error on openning data files
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2024-08-13 09:45:28 +02:00 |
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bdb96dda94
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Adds the obimicrosat command
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2024-08-05 15:31:20 +02:00 |
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3f57935328
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Adjust the size of the genbank and embl buffer size
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2024-08-05 11:32:37 +02:00 |
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886b5d9a96
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Optimize memory for readers and writers
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2024-08-05 10:48:28 +02:00 |
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f83032e643
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Tag version
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2024-08-02 14:30:53 +02:00 |
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242f4d8f56
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Realease notes
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2024-08-02 13:50:33 +02:00 |
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1b1cd41fd3
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Add some code refactoring from the blackboard branch
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2024-08-02 12:35:46 +02:00 |
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bc1aaaf7d9
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New install script updated for github
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2024-07-29 14:35:21 +02:00 |
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67665a6b40
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Xprize update
Former-commit-id: d38919a897961e4d40da3b844057c3fb94fdb6d7
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2024-07-25 18:09:03 -04:00 |
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4e4fac491f
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Fisrt versin of the two levels indexing
Former-commit-id: 4d86483bc120e27cb6f5d2c216596d410274fc69
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2024-07-12 15:17:48 +02:00 |
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42c5881ddc
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some cleanning on the new tools
Former-commit-id: f265a3910d2872c56af81c9b873669f2cb627781
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2024-07-11 10:46:11 +02:00 |
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c7ed47e110
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first version of obidemerge, obijoin and a new filter for obicleandb but to be finnished
Former-commit-id: 8a1ed26e5548c30db75644c294d478ec4d753f19
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2024-07-10 15:21:42 +02:00 |
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bd855c4965
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Adds CSV as an input format
Former-commit-id: a365bb6947064adc2709d66df05fa54c6fe47fad
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2024-07-03 21:04:27 +02:00 |
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5d9ac261ff
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correct an attribute name
Former-commit-id: 2bc540dc3863aef4f8745666047c2a7d94405343
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2024-07-01 17:44:18 +02:00 |
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fd663357b5
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First version of obicleandb...
Former-commit-id: e60b61d015abbf029a555b51de99b4252c50ab59
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2024-07-01 17:12:42 +02:00 |
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0187a82c5f
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Patch a bug in obimultiplex loosing sequence with primer dimer
Former-commit-id: ea14e1aa2e4670c19fe8ee7ec61565bd21cc25b0
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2024-06-30 17:42:28 +02:00 |
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154753de90
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Same bug but for fastq sequence writing only
Former-commit-id: 86d208fe66828da9943c559df80ff095b07eaf7a
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2024-06-26 18:46:47 +02:00 |
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e40d0bfbe7
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Debug fasta and fastq writer when the first sequence is hudge
Former-commit-id: d208ff838abb7e19e117067f6243298492d60f14
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2024-06-26 18:39:42 +02:00 |
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1835cb2cf3
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remove sonic which only works on AMD64
Former-commit-id: 5073957b4706b68896006ee0f7bc30e49ff72c3b
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2024-06-24 14:53:18 +02:00 |
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