3d9f0352ff
obiclean parallelized
2019-06-20 19:44:04 +02:00
a04588da31
openmp on j loop (i loop probably better)
2019-05-24 16:51:04 +02:00
a3e6b7d913
obi import: fixed import of View_NUC_SEQS to another DMS
2019-03-31 15:42:07 +02:00
6841d879aa
obi history: fixed a bug when displaying ascii history
2019-03-31 10:51:52 +02:00
601a2cfd7d
obi uniq: various fixes...
2019-03-30 20:34:53 +01:00
f16bbca8e2
obi grep: fixed a bug where -p option didn't work
2019-03-30 19:10:42 +01:00
173483448a
Merge commit '3d842ff7'
2019-03-30 15:29:52 +01:00
ce686e9569
obi import: progress bar fixed when using --only option
2019-03-30 15:16:57 +01:00
3445579251
remove all the no more needed .cfiles
2019-03-29 16:56:58 +01:00
5007b02cbc
cleaning stage 2
2019-03-29 16:46:17 +01:00
cdd5975e8b
Cleaning first stage
2019-03-29 16:40:36 +01:00
ee9947217c
alignpairedend: fixed the worst memory leak and the handling of the case
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where 0 common kmers are found
2019-03-29 11:16:25 +01:00
ceaafca427
ngsfilter: fixed a bug (maybe 2) in the algo for the choice of the
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reverse primer when running on unaligned sequences
2019-03-29 10:56:17 +01:00
8e70bf1ee1
obi import: fixed bug when rewriting a column (keeping wrong type in
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import module)
2019-03-26 14:56:18 +01:00
802a3f5933
data import: entries now counted if there are multiple files
2019-03-18 18:16:39 +01:00
e8090a44c9
Fixed the ultimate bug with embl (and genbank) parsers: raising any
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exception in a python generator makes it unable to resume. So now,
exceptions are not raised but printed, then functions return None and
that's handled at higher level.
2019-03-15 16:06:06 +01:00
2a4f1b8feb
obi import: now properly uses macros for column names
2019-03-15 11:39:21 +01:00
478d19ab43
Cleaner stderr prints
2019-03-13 18:36:31 +01:00
d88390c6d8
Cython API: when importing a file in a DMS, its length is computed
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beforehand for the progress bar
2019-03-13 18:35:32 +01:00
b45c2ee653
Cython API: cleaner column rewriting API
2019-03-13 11:13:55 +01:00
4bc52c08c2
minor changes
2019-03-07 13:53:37 +01:00
9ccddd5280
better cfiles
2019-02-19 14:11:29 +01:00
e026e9ec83
Fixed the new alignpaired end to work after ngsfilter with the 9879847
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possible cases
2019-02-17 18:32:35 +01:00
08bcbcd357
ngsfilter: reworked to use apat library
2019-02-06 18:13:54 +01:00
c7f5b8d980
Alignpairedend: added alignment using shifting with best kmer similarity
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(low level layer in C and Cython API)
2019-01-21 17:30:46 +01:00
2a6a112d29
obi import: fixed writing quality in views when appropriate (but still
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not a satisfying solution)
2018-12-11 19:33:55 +01:00
c437931a35
Cython: fixed history dot graph for all views, and fixed history
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recording for build_ref_db and ecotag
2018-12-10 17:09:00 +01:00
eb586b2f53
New command and C functions: obi ecotag
2018-12-09 19:19:32 +01:00
579f56bb54
obi align (pouic): fixed bug with the saved config when aligning 2
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different views
2018-12-09 19:15:58 +01:00
ece942e771
new command: build_ref_db to build a reference database with metadata
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for the taxonomic assignment of sequences
2018-11-27 16:11:18 +01:00
4d51f4f015
obi import: better checking of whether to import quality
2018-11-19 11:23:39 +01:00
b0da36cb48
New command: obi align, except it's called obi pouic for now because of
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a Cython compilation bug
2018-11-07 16:05:48 +01:00
d1f1fd432e
Minor fixes
2018-11-07 16:04:17 +01:00
75a28929a7
Renamed Cython alignment library in an attempt to limit some compilation
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bugs potentially involving name conflicts
2018-11-07 16:03:32 +01:00
35f3e7c30b
All commands now handle outputing to another DMS + small fixes
2018-11-02 19:03:09 +01:00
d53323e7f4
Fixed comments bug with obi head and obi tail
2018-10-21 17:39:17 +02:00
e18b762d81
Weird buggy Eclipse commit with nothing changed
2018-10-21 17:35:18 +02:00
da0e3d4043
Cython: added full handling of NA strings when importing files
2018-10-17 16:41:15 +02:00
61ad2deeca
obi uniq: Added line breaks when printing informations to cut progress
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bar properly
2018-10-17 15:53:28 +02:00
df70086384
New command: obi export
2018-10-17 11:27:50 +02:00
ec73fa840a
Cython: obi stats fixed to work with reworked options (forgotten in a
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previous commit)
2018-10-17 11:25:53 +02:00
58589e04be
Cython: rearranged input and output format options to have both and
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updated commands accordingly
2018-10-17 11:19:48 +02:00
e31c8ea57a
New command: obi history to print DMS or view history in bash, dot or
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ascii formats
2018-10-07 19:11:36 +02:00
9e700ddc21
obi test: updated to test comments
2018-10-07 19:10:46 +02:00
e9a41c5b97
Commands: updated for JSON formatted comments with history
2018-10-07 19:10:34 +02:00
1b6b6d825a
obi grep: added all the missing filtering options
2018-08-14 17:11:41 +02:00
b57e938cc4
New command: obi stats
2018-08-13 15:08:10 +02:00
2dc7fcceac
Minor fixes
2018-08-10 10:39:46 +02:00
e096b929dc
New command: obi tail
2018-08-10 10:39:26 +02:00
2c634dae7c
New command: obi head
2018-08-10 10:29:37 +02:00
