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ceca33998b
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add extensions fq in directory scanning
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2025-02-04 20:34:58 +01:00 |
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b9bee5f426
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Changes to be committed:
modified: go.mod
modified: go.sum
modified: pkg/obilua/obilib.go
modified: pkg/obilua/obiseq.go
modified: pkg/obilua/obiseqslice.go
new file: pkg/obilua/obitaxon.go
new file: pkg/obilua/obitaxonomy.go
modified: pkg/obioptions/version.go
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2025-02-02 16:52:52 +01:00 |
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c10df073a7
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Changes to be committed:
modified: pkg/obioptions/version.go
modified: pkg/obitax/iterator.go
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2025-02-01 12:06:19 +01:00 |
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d3dac1b21f
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Make obitag able to use the taxonomic path included in reference database as taxonomy
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2025-01-30 11:50:03 +01:00 |
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0df082da06
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Adds possibility to extract a taxonomy from taxonomic path included in sequence files
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2025-01-30 11:18:21 +01:00 |
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2452aef7a9
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patch multiple -Z options
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2025-01-29 21:35:28 +01:00 |
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337954592d
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add the --out option to the obitaxonomy
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2025-01-29 13:22:35 +01:00 |
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8a28c9ae7c
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add the --download-ncbi option to obitaxonomy
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2025-01-29 12:38:39 +01:00 |
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b6b18c0fa1
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Changes to be committed:
modified: pkg/obioptions/version.go
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2025-01-29 11:34:01 +01:00 |
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67e2758d63
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Switch to realease number 4.3.0
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2025-01-29 11:33:30 +01:00 |
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00f2dc2697
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Rename obifind obitaxonomy and introduce the new CSV format for taxonomy.
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2025-01-29 10:45:26 +01:00 |
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c50a0f409d
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break the import cyccle
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2025-01-27 17:23:07 +01:00 |
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7c4042df6b
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introduce obidefault
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2025-01-27 17:12:45 +01:00 |
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0a567f621c
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small changes
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2025-01-24 18:12:37 +01:00 |
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9acb4a85a8
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Refactoring of the default values
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2025-01-24 18:09:59 +01:00 |
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3137c1f841
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Adds the ability to read gzip-tar file for the taxonomy dump
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2025-01-24 11:47:59 +01:00 |
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ffd67252c3
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patch a bug in obimultiplex: change option -t into -s
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2025-01-23 13:50:24 +01:00 |
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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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