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b0b96ac37a0580496224ff194a0a8bc95002046f
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Author SHA1 Message Date
Celine Mercier b0b96ac37a version 3.0.0b23a 2020-06-05 16:10:24 +02:00
Celine Mercier 687e42ad22 C: kmer alignment: fixed a bug where scores of 0 were at 
(0+kmer_length-1) (and now setting alignment direction to None if score
is 0
 2020-06-05 16:09:33 +02:00
Celine Mercier 5fbbb6d304 alignpairedend: fixed a bug when rebuilding joined (unaligned) sequences 
where only the forward sequence was kept
 2020-06-05 16:06:43 +02:00
Celine Mercier 359a9fe237 Switch to version 3.0.0b23 2020-06-04 15:35:03 +02:00
Celine Mercier f9b6851f75 Python: correctly flagged some mandatory options as required 2020-06-04 15:34:24 +02:00
Celine Mercier 2a2c233936 obi import: fixed a bug when skipping an entry 2020-05-29 21:19:42 +02:00
Celine Mercier faf8ea9d86 Switch to version 3.0.0b21 2020-05-28 20:42:09 +02:00
Celine Mercier ffe2485e94 Genbank parser: now reading ORIGIN lines with comments without 
triggering error
 2020-05-28 20:41:34 +02:00
Celine Mercier 6094ce2bbc obi import: skip on error more robust 2020-05-28 20:40:36 +02:00
Celine Mercier a7dcf16c06 Minor changes for pip release 2020-05-20 15:59:04 +02:00
Celine Mercier f13f8f6165 obi import: minor doc/display improvements 2020-05-20 11:46:29 +02:00
Celine Mercier b5a29ac413 Switch to version 3.0.0b19 2020-05-20 10:29:36 +02:00
Celine Mercier efd2b9d338 Cleaner installation 2020-05-20 10:29:12 +02:00
Celine Mercier ca6e3e7aad obi import: fixed to work with seq genbank extension 2020-05-20 10:28:14 +02:00
Celine Mercier 76ed8e18e5 Switch to version 3.0.0b18 with version formatting that fits setuptools 2020-05-18 17:08:55 +02:00
Celine Mercier 1d17f28aec setup: now using setuptools instead of distutils to work with pip 2020-05-18 17:08:09 +02:00
Celine Mercier fa834e4b8b obi import: small bug fix 2020-05-18 17:06:58 +02:00
Celine Mercier a72fea3cc9 Python: fasta parser: fixed a bug stopping the program when the last 
line contained a single nucleotide
 2020-05-12 11:24:12 +02:00
Celine Mercier e9a37d8a6e Switch to version 3.0.0-beta16 2020-05-07 17:09:26 +02:00
Celine Mercier ef074f8455 typo 2020-05-07 17:08:59 +02:00
Celine Mercier aec5e69f2c C, views: no more automatic COUNT column if MERGED_sample column exists 2020-05-07 17:08:07 +02:00
Celine Mercier 170ef3f1ba Views: added obi prefix to commands in bash history 2020-05-07 17:07:01 +02:00
Celine Mercier f999946582 obi uniq: fixed the remerging of already merged informations, and 
efficiency improvements
 2020-05-07 17:05:54 +02:00
Celine Mercier 773b36ec37 obi import: fixed the import of old obitools files with premerged 
informations, and other minor improvements
 2020-05-07 17:03:04 +02:00
Celine Mercier 69cb434a6c version 3.0.0-beta15c 2020-04-29 14:25:33 +02:00
Celine Mercier 55d4f98d60 obi annotate: fixed annotation at ranks 2020-04-29 14:24:40 +02:00
Celine Mercier 0bec2631e8 ecotag: fixed a bug where all the full DMS path weren't properly sent to 
the C layer
 2020-04-29 10:35:55 +02:00
Celine Mercier e6b6c6fa84 AVLs: Made an error message more informative 2020-04-29 10:14:04 +02:00
Celine Mercier 974528b2e6 build_ref_db: fixed bug erasing some of the higher LCAs (i.e. lowest 
similarities)
 2020-04-28 15:56:06 +02:00
Celine Mercier 1b346b54f9 ecotag: better specificity by now correctly looking for similarities 
within refs above best score instead of ecotag threshold
 2020-04-28 15:10:07 +02:00
Celine Mercier 058f2ad8b3 ecopcr: fixed a bug where sequences were considered circular (generating 
false positives)
 2020-04-27 14:44:35 +02:00
Celine Mercier 60bfd3ae8d obi annotate: now defaults to setting str if expression is not valid 2020-04-24 11:35:20 +02:00
Celine Mercier 67bdee105a C: build_ref_db: added progress display for each step 2020-04-18 14:24:08 +02:00
Celine Mercier 0f745e0113 C: Columns: optimizing column file growth 2020-04-18 13:55:47 +02:00
Celine Mercier 8d0b17d87d Switch to version 3.0.0-beta14 2020-04-15 17:47:26 +02:00
Celine Mercier 343999a627 Taxonomy: fixed a critical memory bug when building the list of merged 
taxids
 2020-04-15 17:46:13 +02:00
Celine Mercier e9a40630e9 C: Columns: rounding column growth to ceil to avoid looping on small 
values
 2020-04-13 19:02:10 +02:00
Celine Mercier 8dbcd3025a C: Columns: reduced column growth factor from 2 to 1.3 to avoid errno28 2020-04-13 14:47:56 +02:00
Celine Mercier 4cf635d001 Switch to version 3.0.0-beta13 2020-04-12 17:42:58 +02:00
Celine Mercier b7e7cc232a Made completion script cleaner 2020-04-12 17:41:59 +02:00
Celine Mercier b6ab792ceb C: made error message more detailed when checking that sequences and 
qualities match
 2020-04-12 17:40:24 +02:00
Celine Mercier ddea5a2964 obi import: fixed inconsequential error when precomputing number of 
entries in some formats
 2020-04-12 17:38:42 +02:00
Celine Mercier 30852ab7d5 View bash history: removed useless shebang 2020-04-12 17:36:04 +02:00
Celine Mercier 4d0299904e all commands (almost): cleaner DMS closing at the end 2020-04-12 17:31:58 +02:00
Celine Mercier eef5156d95 obi stats: fixed error when printing bool keys 2020-04-12 17:12:04 +02:00
Celine Mercier e62c991bbc goes with previous commit 2020-04-10 11:22:26 +02:00
Celine Mercier 1218eed7fd ecopcr: now printing a warning instead of interrupting with an error 
when a taxid is not found
 2020-04-10 11:22:04 +02:00
Celine Mercier cd9cea8c97 obi import: fixed critical bug where the last entry of embl and genbank 
files was not imported
 2020-04-09 19:26:27 +02:00
Celine Mercier 98cfb70d73 ecopcr: made some errors more informative 2020-04-09 09:15:28 +02:00
Celine Mercier b9f68c76c8 ecopcr: added warnings and check of primer length (related to #75) 2020-04-05 18:40:56 +02:00
Celine Mercier 0b98371688 ngsfilter: added warning about primer length in -h (#75) 2020-04-05 18:39:20 +02:00
Celine Mercier f0d152fcbd ngsfilter: now checking primer length (fixes #75) 2020-04-05 18:29:10 +02:00
Celine Mercier 8019dee68e ecotag: now closing all DMS properly 2020-04-05 13:20:49 +02:00
Celine Mercier 0b4a234671 Swich to version 3.0.0-beta11 2020-02-12 14:23:42 +01:00
Celine Mercier d32cfdcce5 ecotag: fixed the generated column comments formatting that would 
generate errors
 2020-02-12 14:23:17 +01:00
Celine Mercier 219c0d6fdc obi cat: Fixed the handling when concatenating views with dictionaries 
having different key sets
 2020-02-12 14:21:39 +01:00
Celine Mercier dc9f897917 switch to version 3.0.0-beta10 2020-02-02 21:15:27 +01:00
Celine Mercier bb72682f7d obi import: new option --preread to do a first readthrough of the 
dataset if it contains huge dictionaries for a much faster import.
 2020-02-02 21:12:34 +01:00
Celine Mercier 52920c3c71 URI decoding: dirty temp fix for bug where default dms makes a mess when 
should guess file
 2020-02-02 21:11:05 +01:00
Celine Mercier 18c22cecf9 switch to version 3.0.0-beta9 2020-02-01 15:48:55 +01:00
Celine Mercier 1bfb96023c obi import: rewriting a column now deletes the old one to save disk 
space
 2020-02-01 15:31:14 +01:00
Celine Mercier c67d668989 obi import: fixed a bug when the first entry would contain a dictionary 
with one key. Switch to beta8
 2020-01-29 20:23:39 +01:00
Celine Mercier db0ac37d41 switch to version 3.0.0-beta7 2020-01-29 16:18:53 +01:00
Celine Mercier d0c21ecd39 Removed an OpenMP clause that was not obligatory and triggered a known 
gcc bug involving macros
 2020-01-24 16:00:53 +01:00
Celine Mercier 53212168a2 History: added 'obi' in bash history for practical reasons 2020-01-23 16:51:49 +01:00
Celine Mercier b4b2e62195 Cleaner handling of reverse quality columns 2020-01-18 19:28:12 +01:00
Celine Mercier ced82c4242 Switching to version 3.0-beta6 2020-01-18 17:29:23 +01:00
Celine Mercier a524f8829e New command: obi cat to concatenate views (not optimized yet) 2020-01-18 17:28:31 +01:00
Celine Mercier 5c9091e9eb C: closing DMS after cleaning it instead of counting on upper layer 2020-01-18 17:27:35 +01:00
Celine Mercier 822000cb70 Fixes in documentation 2020-01-18 17:26:18 +01:00
Celine Mercier b9cd9bee9a C: Changed obibool definitions because of conflict with R 2020-01-06 15:11:31 +01:00
Celine Mercier b1f3e082f9 ngsfilter: fixed a bug when there is only one tag introduced in latest 
edit
 2020-01-06 13:53:38 +01:00
Celine Mercier 6c018b403c ecopcr: fixed and improved the options to keep nuclotides around the 
amplicon
 2019-12-26 20:45:54 +01:00
Celine Mercier 694d1934a8 Tagging version beta3 2019-12-12 17:03:13 +01:00
Celine Mercier fc3ac03630 clean_dms: now works with extension 2019-12-12 17:02:50 +01:00
Celine Mercier d75e54a078 uniq: added forced deletion of reverse sequence quality 2019-12-12 17:02:36 +01:00
Celine Mercier 6bfd7441f3 ngsfilter: fixed sequence cutting when dealing with unaligned sequences. 
Could use optimization
 2019-12-12 17:01:31 +01:00
Celine Mercier 81a179239c ngsfilter: fixed sequence cut bug on aligned sequences. Still exists for 
unaligned sequences
 2019-12-10 18:13:27 +01:00
Celine Mercier 35ce37c0f7 ngsfilter: fixed a bug with unaligned chimeras (unpaired primers) and 
made error annotations more explicit
 2019-12-10 13:43:32 +01:00
Celine Mercier 53f18316b0 ngsfilter: made more robust and practical to use with empty tags 2019-11-29 15:21:08 +01:00
Celine Mercier 8bc249b2f4 Version 3.0.0-beta1 2019-09-27 14:52:05 +02:00
Celine Mercier e308c2e822 versioning 1.0.beta 2019-09-26 21:05:05 +02:00
Celine Mercier 3b3cf9359d CMake: unset gcc for nix 2019-09-26 21:04:42 +02:00
Celine Mercier be85c55c9e Python: URIs: fixed bug on linux systems 2019-09-25 14:41:52 +02:00
Celine Mercier 6d5b904888 Cleaning 2019-09-25 11:58:00 +02:00
Celine Mercier 50e8374f6f Added website URL in readme file 2019-09-25 11:40:00 +02:00
Celine Mercier 6282242a04 C: Views: fixed a bug when trying to add a comment after changing the 
file name of a finished view
 2019-09-25 11:39:32 +02:00
Celine Mercier 44517db51f Fixed gcc warnings 2019-09-25 11:38:00 +02:00
Celine Mercier c3b9e46291 more cleaning 2019-09-24 13:58:53 +02:00
Celine Mercier 28b7fce59a Cython API: simpler column repr display 2019-09-22 20:23:31 +02:00
Celine Mercier fa9555deb9 obi stats: fixed bug with None values 2019-09-22 20:21:53 +02:00
Celine Mercier d30f7e7317 more cleaning 2019-09-22 18:52:05 +02:00
Celine Mercier 4fa38d9886 cleaning 2019-09-22 17:38:28 +02:00
Celine Mercier 71276537a6 obi import: fixed bug when importing a taxdump 2019-09-22 16:45:30 +02:00
Celine Mercier ba9ba7aa60 obi grep: now able to convert str to bytes in predicate expressions 2019-09-22 16:44:45 +02:00
Celine Mercier 7b4046c288 Bash completion script for commands, dms and views 2019-09-21 23:46:08 +02:00
Celine Mercier e2ba76002a Cleaned setup script and put to my name ;) 2019-09-21 23:44:24 +02:00
Celine Mercier 336100f716 obi less: now actually behaves like less 2019-09-21 18:29:12 +02:00
Celine Mercier d83398c0e0 Cython: View: lines from simple View instances are now displayed in tab 
instead of dict format
 2019-09-21 18:28:56 +02:00
Celine Mercier 974d25b815 Cython: Fixed bug in tab formatter with header option always being set 
to true
 2019-09-21 18:27:47 +02:00