d99702f56f
ngsfilter and alignpairedend: paired-end reads are now correctly
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reversed and labeled to be aligned correctly by alignpairedend
2019-07-23 18:56:51 +02:00
f765c6f41e
obi alignpairedend: fixed a bug where first seq was kept in result view
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instead of consensus seq
2019-07-06 16:29:32 +02:00
a83bf43ab9
obi stats: result display is now sorted
2019-07-06 16:27:51 +02:00
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
ac47bdce5d
history: fixed DMS history when multiple inputs
2019-03-31 15:44:20 +02:00
80068a3c19
ngsfilter: fixed parsing error
2019-03-31 15:42:30 +02:00
a3e6b7d913
obi import: fixed import of View_NUC_SEQS to another DMS
2019-03-31 15:42:07 +02:00
416c2d7ba0
Cython: made fasta formatter cleaner
2019-03-31 15:41:32 +02:00
2b8c066f8e
Cython: added possibility to output in tabular format
2019-03-31 15:39:38 +02:00
e39c1a7fbf
Cython: added tab formatter and parser (for obi export)
2019-03-31 15:38:34 +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
c293cfabbb
Python: embl parser: fixed a bug preventing taxids from being parsed
2019-03-30 15:15:49 +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
d8a7bd42bd
Cython API, taxonomy: fixed parental tree iterator (skipped second to
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last taxon, in OBI1 too)
2019-03-26 14:08:54 +01:00
06178d9d61
Genbank file parser functions that should have been included in a
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previous commit
2019-03-20 11:44:43 +01:00
3abe1b7ace
obi_errno_to_exception function now properly reads obi_errno global
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variable directly
2019-03-20 11:43:12 +01:00
802a3f5933
data import: entries now counted if there are multiple files
2019-03-18 18:16:39 +01:00
7e20870719
Added genbank parser
2019-03-15 16:06:27 +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
832f582802
Fixed no-skip-on-error option :p
2019-03-15 16:04:04 +01:00
58d0c850c2
Made skip on error option True by default......
2019-03-15 15:50:40 +01:00
7737211ac2
Small fix in embl and genbank features parser
2019-03-15 15:50:11 +01:00
c953f0cb00
Fixed embl import where sequences were not imported as Nuc_Seq objects
2019-03-15 11:41:07 +01:00
bb045c3ae9
added TAXID_COLUMN to C API declarations for Cython
2019-03-15 11:40:06 +01:00
2a4f1b8feb
obi import: now properly uses macros for column names
2019-03-15 11:39:21 +01:00
24a63f8732
URIs: URIs built with autocomplete now work too
2019-03-15 10:52:27 +01:00
478d19ab43
Cleaner stderr prints
2019-03-13 18:36:31 +01:00
e3c565d6be
Cleaner progress bar
2019-03-13 18:36:05 +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
49d5f6fb1e
removed deprecated comment
2019-03-13 11:17:04 +01:00
b45c2ee653
Cython API: cleaner column rewriting API
2019-03-13 11:13:55 +01:00
6afd1294a7
Cython API: Views: fixed a bug when rewriting a column with different
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attributes (last line is not written anymore)
2019-03-12 16:40:30 +01:00
2a1ab9db29
Cython API, Views: guessing an obitype from a python value is now done
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through the corresponding functions in utils
2019-03-07 13:57:37 +01:00
4bc52c08c2
minor changes
2019-03-07 13:53:37 +01:00
29c56572cf
Add cfiles everywhere ;-)
2019-02-19 15:04:30 +01:00
de3d12af17
Renamed CAPI file
2019-02-19 14:50:30 +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
4ddd1a1c37
embl iterator: only option on embl directories now works as intended
2019-02-12 16:46:08 +01:00
08bcbcd357
ngsfilter: reworked to use apat library
2019-02-06 18:13:54 +01:00
