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99a397b842
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obi uniq: various improvements and fixes #66
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2019-08-27 20:27:36 +02:00 |
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580db2f710
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minor comment
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2019-08-27 20:25:54 +02:00 |
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3d1b2e8ed9
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Better handling of column lines with all values at NA
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2019-08-27 20:20:26 +02:00 |
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66441e0aef
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Fixed a bug when sending a DMS path to a C function from Cython
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2019-08-18 19:43:51 +02:00 |
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d99702f56f
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ngsfilter and alignpairedend: paired-end reads are now correctly
reversed and labeled to be aligned correctly by alignpairedend
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2019-07-23 18:56:51 +02:00 |
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ac47bdce5d
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history: fixed DMS history when multiple inputs
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2019-03-31 15:44:20 +02:00 |
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3445579251
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remove all the no more needed .cfiles
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2019-03-29 16:56:58 +01:00 |
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5007b02cbc
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cleaning stage 2
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2019-03-29 16:46:17 +01:00 |
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cdd5975e8b
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Cleaning first stage
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2019-03-29 16:40:36 +01:00 |
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ee9947217c
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alignpairedend: fixed the worst memory leak and the handling of the case
where 0 common kmers are found
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2019-03-29 11:16:25 +01:00 |
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d8a7bd42bd
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Cython API, taxonomy: fixed parental tree iterator (skipped second to
last taxon, in OBI1 too)
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2019-03-26 14:08:54 +01:00 |
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3abe1b7ace
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obi_errno_to_exception function now properly reads obi_errno global
variable directly
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2019-03-20 11:43:12 +01:00 |
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bb045c3ae9
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added TAXID_COLUMN to C API declarations for Cython
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2019-03-15 11:40:06 +01:00 |
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49d5f6fb1e
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removed deprecated comment
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2019-03-13 11:17:04 +01:00 |
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b45c2ee653
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Cython API: cleaner column rewriting API
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2019-03-13 11:13:55 +01:00 |
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6afd1294a7
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Cython API: Views: fixed a bug when rewriting a column with different
attributes (last line is not written anymore)
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2019-03-12 16:40:30 +01:00 |
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2a1ab9db29
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Cython API, Views: guessing an obitype from a python value is now done
through the corresponding functions in utils
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2019-03-07 13:57:37 +01:00 |
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29c56572cf
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Add cfiles everywhere ;-)
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2019-02-19 15:04:30 +01:00 |
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de3d12af17
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Renamed CAPI file
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2019-02-19 14:50:30 +01:00 |
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e026e9ec83
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Fixed the new alignpaired end to work after ngsfilter with the 9879847
possible cases
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2019-02-17 18:32:35 +01:00 |
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04a3682307
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Cython API: added API to use apat (pattern search) C library
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2019-02-06 18:12:49 +01:00 |
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8f18907566
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Cython API: changed revcomp attribute of Nuc_Seq class to is_revcomp to
be more explicit
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2019-02-06 18:09:11 +01:00 |
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c7f5b8d980
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Alignpairedend: added alignment using shifting with best kmer similarity
(low level layer in C and Cython API)
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2019-01-21 17:30:46 +01:00 |
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c437931a35
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Cython: fixed history dot graph for all views, and fixed history
recording for build_ref_db and ecotag
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2018-12-10 17:09:00 +01:00 |
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eb586b2f53
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New command and C functions: obi ecotag
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2018-12-09 19:19:32 +01:00 |
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6acb21712a
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Missing commit for build_ref_db: C API file for cython
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2018-12-09 19:11:59 +01:00 |
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6f27734d71
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Cython: fxed a bug in INT tuple columns where values were converted to
double instead of int
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2018-11-27 16:14:56 +01:00 |
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ece942e771
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new command: build_ref_db to build a reference database with metadata
for the taxonomic assignment of sequences
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2018-11-27 16:11:18 +01:00 |
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b0da36cb48
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New command: obi align, except it's called obi pouic for now because of
a Cython compilation bug
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2018-11-07 16:05:48 +01:00 |
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d09aa43133
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Cython API: added a function to get the full path to the DMS directory
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2018-10-31 14:46:25 +01:00 |
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320561a582
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Views: Added argument to not automatically create default columns in
typed views, a function to delete a view and fixed view history bug
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2018-10-31 14:38:05 +01:00 |
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d53323e7f4
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Fixed comments bug with obi head and obi tail
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2018-10-21 17:39:17 +02:00 |
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e18b762d81
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Weird buggy Eclipse commit with nothing changed
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2018-10-21 17:35:18 +02:00 |
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0a0f0682a9
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Better handling of errors and exceptions when new view name already
exists
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2018-10-17 19:47:40 +02:00 |
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4802e32f72
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Cython: Sequence objects: repr() method now returns a Fasta or Fastq
formatted string
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2018-10-17 16:53:42 +02:00 |
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da76f911db
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Cython: Views: improved repr() method
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2018-10-17 15:54:03 +02:00 |
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6a8670d24a
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Cython: minor fixes
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2018-10-17 11:26:13 +02:00 |
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11032ec90b
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Cython: Sequence objects: Quality strings are now returned as bytes
instead of str
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2018-10-17 11:24:44 +02:00 |
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8a9ba8b0a8
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Cython: Added Column line methods to get a Column line as a str or
bytes, and elements (keys, values) with None values are not returned
anymore
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2018-10-17 11:23:07 +02:00 |
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35cf2962cc
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Cython: DMS: JSON formatted comments and history handling
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2018-10-07 19:06:59 +02:00 |
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74be3c39f0
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Cython: Views: JSON formatted comments and history handling
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2018-10-07 19:06:23 +02:00 |
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c6ee0bade9
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Cython: Columns: goes with handling of JSON formatted comments
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2018-10-07 19:04:50 +02:00 |
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704d9b0474
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Cython: Columns: added support for JSON formatted comments
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2018-10-07 18:59:43 +02:00 |
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3847850a9d
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Taxonomy Cython API: added is_ancestor() function
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2018-08-14 17:09:40 +02:00 |
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080a97cccf
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Cython API: more explicit "Can't guess type" exception
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2018-08-08 19:50:26 +02:00 |
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9c9aec2556
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Cython API: the associated sequence column for a quality column can now
be specified at the Python level
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2018-08-08 19:49:56 +02:00 |
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2ba6d16147
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New command: obi ecopcr
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2018-07-28 17:13:45 +02:00 |
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b98880b7fa
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Various non-important fixes and comments
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2018-07-28 17:07:17 +02:00 |
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7f6d1597fc
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Taxonomy: added functions to check if a taxonomy already exists in a
DMS, and added taxdump import from a compressed file
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2018-07-28 16:48:11 +02:00 |
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6911bf4d70
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obi clean: first version
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2018-05-18 14:26:54 +02:00 |
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