6911bf4d70
obi clean: first version
2018-05-18 14:26:54 +02:00
f0c147c252
C API: Added a function to set an entire column to a specified (atomic)
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value.
2018-05-17 15:59:16 +02:00
4aef20add8
Fixed a bug where the line selection column of a view would not be
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flagged as finished
2018-05-17 15:17:19 +02:00
62614a8538
Cython API: fixed a bug in URI decoding and option handling where the
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quality offset would not be read properly
2018-05-17 15:10:52 +02:00
ffebc6acfb
Cython API: better handling of default quality offset value
2018-05-17 15:01:25 +02:00
b91b3176b0
obi uniq: fixed a bug where merged values were wrongly reinitialized
2018-05-17 14:58:15 +02:00
31d8ba5085
obi test: minor change
2018-05-17 14:54:45 +02:00
a166a169cf
obi ngsfilter: fixed a bug with -u option
2018-05-17 14:53:53 +02:00
8a10072d99
obi annotate: fixed a bug with --with-taxon-at-rank option and minor
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improvements
2018-05-17 14:51:18 +02:00
b380368264
Obi count command
2018-04-04 15:51:23 +02:00
1f4e82e6f6
Fixed three bugs in obi uniq
2018-04-04 15:50:10 +02:00
6825fc13ab
Cython API: added ngsfilter file parser
2018-03-21 16:41:25 +01:00
49c17ab7b4
Cython API: added tabular file parser
2018-03-21 16:41:09 +01:00
2684535e26
New command: obi annotate
2018-03-21 16:39:31 +01:00
123fb9d7ba
Cython API: in taxonomy, added get_taxon_at_rank() function for Taxonomy
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class and rank_idx property for Taxon class
2018-03-21 16:38:26 +01:00
4c3478d8f8
Removed the predicate to check for a quality column (because for example
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with obi annotate, clone view so clone predicate, then modify seq, so
quality is deleted, and predicate becomes a problem)
2018-03-21 16:37:19 +01:00
4a815785c4
obi import: added basic taxdump import
2018-03-21 16:35:44 +01:00
75b54c83ca
obi grep: fixed bug when reading URIs
2018-03-21 16:34:57 +01:00
53cb3354b8
obi ls command
2018-03-19 13:08:41 +01:00
ea58e254da
Cython API: repr function for DMS
2018-03-19 13:08:06 +01:00
9fb63d4894
Minor fixes
2018-03-16 19:05:09 +01:00
d4f7e02c85
New obi grep working with URI API
2018-03-16 19:04:54 +01:00
15e43bb9a1
Cython API: obi import can now import ngsfilter files and tabular files
2018-03-12 18:10:43 +01:00
8a0b95c1d6
New command: obi ngsfilter
2018-03-12 18:09:22 +01:00
dd225a255f
obi uniq: better error checking
2018-03-12 18:04:53 +01:00
dad21823ff
Cython API: trying to guess the type of a column when adding a None
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value does not generate an exception anymore, and RollbackException can
now rollback several views
2018-03-12 18:03:37 +01:00
96bf2daae8
Cython API: added slices in Seq classes and fixes
2018-03-12 17:51:41 +01:00
e6c49b7941
Cython API: moved an eval function to utils
2018-03-12 17:49:54 +01:00
4960662332
Cython API: tobytes() function now handles None values
2018-03-12 17:25:12 +01:00
b2cfa4b52f
Cython Sequence classes: reworked improved etc
2018-02-12 14:54:47 +01:00
94a899de12
Cython View API: added small tools
2018-02-12 14:48:27 +01:00
b48330a5c9
Fixed a little bug when cleaning unfinished views
2018-02-12 14:44:56 +01:00
74d880b817
Fixed default quality offset
2018-02-12 14:43:44 +01:00
00993d4215
Cython API: fixed a bug where the quality format would not be read
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properly from the configuration values
2018-02-12 14:42:30 +01:00
370fb9272c
obi uniq: better typing
2018-02-12 14:38:07 +01:00
c8097e14e1
obi import: removed old traces
2018-02-12 14:36:56 +01:00
01ef85658c
New command: obi alignpairedend
2018-02-12 13:30:06 +01:00
f5a00c9322
Cython alignment library
2018-02-12 13:28:20 +01:00
156fb04e88
Implemented functions to build reverse complement sequences
2018-01-05 16:08:36 +01:00
428c4eb5e6
obi import: fixed creation of quality columns (to discuss)
2017-12-19 11:07:00 +01:00
1a5b499b5c
Cython API to add an OBI_QUAL column after creating a view
2017-12-19 11:06:24 +01:00
b7b8ba7e5a
Better handling of elements names in Cython
2017-12-13 23:12:14 +01:00
e9e7fac999
New obi uniq: stores columns with too many elements per line as
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character strings, and keeps a minimum of things in the memory
2017-12-13 22:49:08 +01:00
1fd3323372
Columns: elements names informations are now kept in a memory arena of
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adapted size in the header, and added a boolean in the header indicating
whether the values should be evaluated (typically character strings to
be evaluated in Python)
2017-12-13 22:46:50 +01:00
2df5932b67
Cython column API: fixed a memory leak, optimized the reading of
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elements names, added a __len__ method to Column_line, and the API for
columns with character strings to evaluate
2017-12-13 22:27:36 +01:00
b93b982a18
Cython: added an option for input taxdump and and an option for the
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maximum number of elements in columns with multiple elements per line
2017-12-13 22:25:15 +01:00
ea73047fc7
Added rewinddir before each readdir so that the directories are always
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read properly
2017-11-24 18:04:58 +01:00
0998268955
Fixed two little potential bugs when cleaning unfinished columns and
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deleted old trace
2017-11-24 18:03:59 +01:00
31726407a3
Taxonomy: fixed a bug where a pointer was not properly reallocated, and
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a bug where the merged list of taxids was not built correctly
2017-11-24 18:01:30 +01:00
d21f4a6f90
Header parser: identifiers ending with ';' are now handled
2017-11-24 17:59:52 +01:00
