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4844b20770
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Merge branch 'master' of https://git.metabarcoding.org/obitools/obitools3
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2024-01-12 15:36:58 +13:00 |
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0d98a4f717
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Switch to version 3.0.1b26
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2024-01-10 16:40:08 +13:00 |
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837ff1a1ba
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Taxonomy: fixed an issue related to StopIteration behaviour in new
versions of python
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2024-01-10 15:53:15 +13:00 |
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aeed42456a
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export: columns are now in alphabetical order when exporting to tab
format
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2024-01-10 15:52:28 +13:00 |
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fb6e27bb5d
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Revert "Testing RAM instead of mmap for blob alignment"
This reverts commit 6d94cdcc0d
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2023-11-29 04:22:31 +01:00 |
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6d94cdcc0d
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Testing RAM instead of mmap for blob alignment
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2023-11-29 16:19:34 +13:00 |
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8a1f844645
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obi import: fixed bug caused by new behaviour of StopIteration
exceptions in Python>=3.7
v3.0.1b25
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2023-09-21 17:47:40 +12:00 |
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791ccfb92e
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Fixed include bug in previous version and switch to version 3.0.1b24
v3.0.1b24
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2023-05-15 11:35:42 +12:00 |
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1c9a906f5b
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ngsfilter and ecopcr: now check for primers too long for apat library to
handle (31bp max) and switch to version 3.0.1b23
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2023-05-12 17:04:21 +12:00 |
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55b2679b23
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New command obi rm and switch to version 3.0.1b22
v3.0.1b22
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2023-05-08 17:48:50 +12:00 |
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9ea2124adc
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Switch to version 3.0.1b21
v3.0.1b21
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2023-02-13 11:00:01 +13:00 |
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2130a949c7
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New command: obi taxonomy to add local taxa (closes #64)
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2023-02-13 10:59:20 +13:00 |
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eeb93afa7d
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import: now automatically renames scientific_name tag to
`SCIENTIFIC_NAME`, and suggests using `--input-na-string` when a
sequence import fails
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2023-02-13 10:40:38 +13:00 |
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755ce179ad
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head: added output format options
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2023-02-13 10:31:26 +13:00 |
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7e492578b3
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Switch to version 3.0.1b20
v3.0.1b20
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2022-09-21 11:33:03 +12:00 |
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02e9df3ad1
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alignpairedend and ngsfilter: ids of original sequences are now kept
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2022-09-21 11:32:19 +12:00 |
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55ada80500
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import: made ngsfilter file parsing more resilient and switching to
version 3.0.1b19
v3.0.1b19
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2022-07-15 16:02:21 +12:00 |
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ef9d9674b0
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obi import: added SINTAX format import and switch to version 3.0.1b18
v3.0.1b18
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2022-05-17 09:36:33 +12:00 |
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4f39bb2418
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switch to version 3.0.1b17
v3.0.1b17
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2022-05-03 10:55:36 +12:00 |
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0a2b8adb50
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import: added import of UNITE fasta format
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2022-05-03 10:54:41 +12:00 |
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f9b99a9397
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annotate: fixed a bug where a column type could be wrongly guessed and
switch to version 3.0.1b16
v3.0.1b16
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2022-03-30 16:32:07 +13:00 |
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ce2833c04b
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switch to version v3.0.1b15
v3.0.1b15
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2022-02-25 17:48:44 +13:00 |
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f64b3da30b
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split command
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2022-02-25 17:44:18 +13:00 |
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388b3e0410
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removed a trace
v3.0.1b14
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2021-11-11 15:53:27 +13:00 |
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c9db990b83
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switch to version 3.0.1b14
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2021-11-11 15:28:00 +13:00 |
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3f253feb5e
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Cython: View: fixed keys method to get list of view keys
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2021-11-11 15:27:32 +13:00 |
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85d2bab607
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small fix
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2021-11-11 15:26:48 +13:00 |
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53b3d81137
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small fixes and improvements
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2021-11-11 15:26:09 +13:00 |
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f6353fbf28
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obi export: added options to export to metabaR compatible format
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2021-11-11 15:24:12 +13:00 |
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5a8b9dca5d
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goes with previous commit
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2021-11-11 15:12:04 +13:00 |
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8bd6d6c8e9
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Python: URI decoding: now properly checking that paths can be encoded in
ASCII (issue #89)
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2021-11-02 11:17:59 +13:00 |
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405e6ef420
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Python: URI decoding: added metabaR output
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2021-11-02 11:16:29 +13:00 |
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fedacfafe7
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switch to version 3.0.1b13
v3.0.1b13
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2021-09-13 11:46:17 +12:00 |
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2d66e0e965
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python: genbank parser: better handling of white spaces
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2021-09-13 11:44:38 +12:00 |
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f43856b712
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switch to version 3.0.1b12
v3.0.1b12
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2021-09-08 10:56:55 +12:00 |
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9e0c319806
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Cython: fixed rewriting of column when rewriting a 1 element dict column
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2021-09-08 10:54:23 +12:00 |
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58b42cd977
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C: views: now correctly parses view names containing '.' when cleaning
unfinished views. Closes #115
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2021-09-08 10:52:42 +12:00 |
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34de90bce6
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ngsfilter: checks better if there is an associated sequencing quality
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2021-09-08 10:30:11 +12:00 |
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4be9f36f99
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stats: fixed the computation of variance when it is equal to 0
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2021-08-05 11:32:16 +12:00 |
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f10e78ba3c
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C: fixed the printing of view informations from a DMS (fixes #114)
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2021-08-05 11:31:24 +12:00 |
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88c8463ed7
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Cython: taxonomy: improved logging
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2021-08-05 11:29:20 +12:00 |
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89168271ef
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ecopcr: now accepting taxonomy from a different DMS than the reference
sequences
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2021-08-05 11:28:57 +12:00 |
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82d2642000
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Switch to version 3.0.1b11
v3.0.1b11
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2021-07-22 09:25:39 +12:00 |
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99c1cd60d6
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export: now exports header for tabular files by default and added option
to only export specific columns
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2021-07-22 09:23:18 +12:00 |
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ce7ae4ac55
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export: fixed 'only' option printing one too many if printing header
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2021-07-21 15:23:04 +12:00 |
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0b4283bb58
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cat: improved error handling
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2021-07-21 15:22:08 +12:00 |
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747f3efbb2
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Improved taxonomy reading information display
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2021-07-21 15:20:44 +12:00 |
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6c1a3aff47
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Fixed the handling of sample names that are numbers (forcing conversion)
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2021-07-21 15:19:24 +12:00 |
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e2932b05f2
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Implements #108 export integer missing values as 0 for tables by default
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2021-07-21 14:41:54 +12:00 |
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32345b9ec4
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Addresses #111
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2021-07-19 15:55:25 +12:00 |
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