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
...
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
...
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
...
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
...
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
...
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
...
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
...
read properly
2017-11-24 18:04:58 +01:00
0998268955
Fixed two little potential bugs when cleaning unfinished columns and
...
deleted old trace
2017-11-24 18:03:59 +01:00
31726407a3
Taxonomy: fixed a bug where a pointer was not properly reallocated, and
...
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
9e3ac477eb
OBIDMS: Opened DMS now have a counter associated so that DMS are not
...
actually opened several times by the same program, which triggers the
cleaning of unfinished views and columns (to discuss)
2017-11-24 17:58:47 +01:00
ee5d647d0d
Taxonomy: fixed a bug un parental tree iterator
2017-11-24 17:55:17 +01:00
38fef5b9d4
obi test: better taxonomy testing
2017-11-24 17:54:10 +01:00
3ba7ce1c91
View rollback: version files and column directories aren't deleted
...
anymore to prevent indexer bug, and fixed a freeing bug
2017-11-15 17:27:26 +01:00
9a50803c00
Added tuple columns containing immutable indexed data arrays of any type
2017-11-15 13:48:59 +01:00
1684f96b79
Fixed a bug when flagging a read-only column as finished
2017-10-26 19:11:29 +02:00
43f65e7fd0
obi uniq: fixed bug where dictionary indexes were not read properly, and
...
added view rollback in case of an exception.
2017-10-26 19:00:05 +02:00
dfd51939a0
Views are now rollbacked if an error occurs, and unfinished views and
...
columns are deleted when an OBIDMS is opened.
2017-10-26 18:58:48 +02:00
1ae634d56b
Added atexit command to obi import, obi uniq and obi less
2017-10-16 11:09:55 +02:00
04e065094a
All DMS opened by a program are now listed and closed with atexit system
2017-10-16 10:35:07 +02:00
5ddd1d9ae6
obi uniq: added taxonomy handling
2017-10-04 16:13:07 +02:00
9fc6868341
Increased maximum length for elements names
2017-10-04 16:10:53 +02:00
f2ece573ff
Removed deprecated command
2017-10-04 16:09:41 +02:00
fb9b219abe
Fixed a bug with taxonomy URIs not being read correctly
2017-10-04 16:00:30 +02:00
09a5f89849
Column API: improvements to be more flexible when referring to elements
...
in columns with several elements per line.
2017-10-04 15:59:23 +02:00
535692b020
Taxonomy: new functions and improvements
2017-10-04 15:55:13 +02:00
