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a39f9697be
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Views: added macro for taxid column name
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2018-07-28 17:10:11 +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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895d09b133
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obi import: 'taxid' columns are imported as 'TAXID' to fit view
predicates, and fixed taxdump import and DMS closing
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2018-07-28 17:03:00 +02:00 |
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c02c15b93f
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Cython API: URI decoding now returns the character string with the
object path if it could not be opened
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2018-07-28 17:00:42 +02:00 |
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3e8c187f0b
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Cython API: added EMBL parser and files to import are now read in binary
mode
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2018-07-28 16:57:01 +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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1de308a856
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obi clean: option to only keep heads now works, fixed a bug where last
sequence was not properly labelled, and code is cleaned, fixed and error
checked
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2018-05-31 15:11:41 +02:00 |
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892ed83a33
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Removed deprecated function declarations
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2018-05-31 15:08:11 +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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f0c147c252
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C API: Added a function to set an entire column to a specified (atomic)
value.
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2018-05-17 15:59:16 +02:00 |
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4aef20add8
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Fixed a bug where the line selection column of a view would not be
flagged as finished
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2018-05-17 15:17:19 +02:00 |
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62614a8538
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Cython API: fixed a bug in URI decoding and option handling where the
quality offset would not be read properly
|
2018-05-17 15:10:52 +02:00 |
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ffebc6acfb
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Cython API: better handling of default quality offset value
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2018-05-17 15:01:25 +02:00 |
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b91b3176b0
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obi uniq: fixed a bug where merged values were wrongly reinitialized
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2018-05-17 14:58:15 +02:00 |
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31d8ba5085
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obi test: minor change
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2018-05-17 14:54:45 +02:00 |
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a166a169cf
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obi ngsfilter: fixed a bug with -u option
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2018-05-17 14:53:53 +02:00 |
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8a10072d99
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obi annotate: fixed a bug with --with-taxon-at-rank option and minor
improvements
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2018-05-17 14:51:18 +02:00 |
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b380368264
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Obi count command
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2018-04-04 15:51:23 +02:00 |
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1f4e82e6f6
|
Fixed three bugs in obi uniq
|
2018-04-04 15:50:10 +02:00 |
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6825fc13ab
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Cython API: added ngsfilter file parser
|
2018-03-21 16:41:25 +01:00 |
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49c17ab7b4
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Cython API: added tabular file parser
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2018-03-21 16:41:09 +01:00 |
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2684535e26
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New command: obi annotate
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2018-03-21 16:39:31 +01:00 |
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123fb9d7ba
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Cython API: in taxonomy, added get_taxon_at_rank() function for Taxonomy
class and rank_idx property for Taxon class
|
2018-03-21 16:38:26 +01:00 |
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4c3478d8f8
|
Removed the predicate to check for a quality column (because for example
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 |
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4a815785c4
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obi import: added basic taxdump import
|
2018-03-21 16:35:44 +01:00 |
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75b54c83ca
|
obi grep: fixed bug when reading URIs
|
2018-03-21 16:34:57 +01:00 |
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53cb3354b8
|
obi ls command
|
2018-03-19 13:08:41 +01:00 |
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ea58e254da
|
Cython API: repr function for DMS
|
2018-03-19 13:08:06 +01:00 |
|
|
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9fb63d4894
|
Minor fixes
|
2018-03-16 19:05:09 +01:00 |
|
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d4f7e02c85
|
New obi grep working with URI API
|
2018-03-16 19:04:54 +01:00 |
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15e43bb9a1
|
Cython API: obi import can now import ngsfilter files and tabular files
|
2018-03-12 18:10:43 +01:00 |
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|
|
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 |
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dad21823ff
|
Cython API: trying to guess the type of a column when adding a None
value does not generate an exception anymore, and RollbackException can
now rollback several views
|
2018-03-12 18:03:37 +01:00 |
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96bf2daae8
|
Cython API: added slices in Seq classes and fixes
|
2018-03-12 17:51:41 +01:00 |
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|
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 |
|
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|
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
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 |
|
