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Author SHA1 Message Date
Celine Mercier 32d8396ee2 Cython: Added fasta and fastq writers 2018-10-17 11:27:15 +02:00
Celine Mercier 6a8670d24a Cython: minor fixes 2018-10-17 11:26:13 +02:00
Celine Mercier ec73fa840a Cython: obi stats fixed to work with reworked options (forgotten in a 
previous commit)
 2018-10-17 11:25:53 +02:00
Celine Mercier 11032ec90b Cython: Sequence objects: Quality strings are now returned as bytes 
instead of str
 2018-10-17 11:24:44 +02:00
Celine Mercier 8a9ba8b0a8 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
 2018-10-17 11:23:07 +02:00
Celine Mercier 135d3b6e67 Cython: updated the URI decoding to handle outputs other than DMS 2018-10-17 11:21:29 +02:00
Celine Mercier 58589e04be Cython: rearranged input and output format options to have both and 
updated commands accordingly
 2018-10-17 11:19:48 +02:00
Celine Mercier e6bbe13d81 Cython: fasta and fastq parsers now return bytes and take NA string 
argument
 2018-10-17 11:16:20 +02:00
Celine Mercier 61b00d6013 Cython: fastq formatter 2018-10-09 16:41:14 +02:00
Celine Mercier 8029493c10 Cython: fasta and fastq header formatter 2018-10-09 16:41:00 +02:00
Celine Mercier aa5ee53478 Cython: fasta writer 2018-10-09 16:40:30 +02:00
Celine Mercier e31c8ea57a New command: obi history to print DMS or view history in bash, dot or 
ascii formats
 2018-10-07 19:11:36 +02:00
Celine Mercier 9e700ddc21 obi test: updated to test comments 2018-10-07 19:10:46 +02:00
Celine Mercier e9a41c5b97 Commands: updated for JSON formatted comments with history 2018-10-07 19:10:34 +02:00
Celine Mercier 35cf2962cc Cython: DMS: JSON formatted comments and history handling 2018-10-07 19:06:59 +02:00
Celine Mercier 74be3c39f0 Cython: Views: JSON formatted comments and history handling 2018-10-07 19:06:23 +02:00
Celine Mercier c6ee0bade9 Cython: Columns: goes with handling of JSON formatted comments 2018-10-07 19:04:50 +02:00
Celine Mercier ffd5bc76bf Cython utils: functions convert to bytes or str and to remove all empty 
objects from a complex object
 2018-10-07 19:03:38 +02:00
Celine Mercier 704d9b0474 Cython: Columns: added support for JSON formatted comments 2018-10-07 18:59:43 +02:00
Celine Mercier 86bb582a17 Views: implemented handling of JSON formatted comments 2018-10-07 18:56:46 +02:00
Celine Mercier bc8c394061 Columns: implemented handling of JSON formatted comments 2018-10-07 18:54:51 +02:00
Celine Mercier cef458f570 Obierrno: added errno for JSON related errors 2018-10-07 18:53:53 +02:00
Celine Mercier 2736a92699 DMS: implemented full information file with JSON formatted comments 2018-10-07 18:53:25 +02:00
Celine Mercier 79f4185757 C library to handle JSON formatted comments using the cJSON library 2018-10-07 18:51:27 +02:00
Celine Mercier 1b6b6d825a obi grep: added all the missing filtering options 2018-08-14 17:11:41 +02:00
Celine Mercier 3847850a9d Taxonomy Cython API: added is_ancestor() function 2018-08-14 17:09:40 +02:00
Celine Mercier b57e938cc4 New command: obi stats 2018-08-13 15:08:10 +02:00
Celine Mercier 2dc7fcceac Minor fixes 2018-08-10 10:39:46 +02:00
Celine Mercier e096b929dc New command: obi tail 2018-08-10 10:39:26 +02:00
Celine Mercier 2c634dae7c New command: obi head 2018-08-10 10:29:37 +02:00
Celine Mercier 7a4cdc0cfe New command: obi sort 2018-08-09 18:10:47 +02:00
Celine Mercier e8dc5eb123 Commands: ngsfilter and alignpairedend can now be used in whichever 
order
 2018-08-08 19:53:26 +02:00
Celine Mercier 3fcf29a76f More explicit predicate error when checking that sequences and qualities 
match
 2018-08-08 19:51:05 +02:00
Celine Mercier 080a97cccf Cython API: more explicit "Can't guess type" exception 2018-08-08 19:50:26 +02:00
Celine Mercier 9c9aec2556 Cython API: the associated sequence column for a quality column can now 
be specified at the Python level
 2018-08-08 19:49:56 +02:00
Celine Mercier 303648bd47 Cython: embl file parser 2018-07-28 17:14:10 +02:00
Celine Mercier 2ba6d16147 New command: obi ecopcr 2018-07-28 17:13:45 +02:00
Celine Mercier 275d85dc5d Cython: fixed a bug when reading an uncompressed file in binary mode 
where the first 4 characters would not be read
 2018-07-28 17:11:51 +02:00
Celine Mercier a39f9697be Views: added macro for taxid column name 2018-07-28 17:10:11 +02:00
Celine Mercier b98880b7fa Various non-important fixes and comments 2018-07-28 17:07:17 +02:00
Celine Mercier 895d09b133 obi import: 'taxid' columns are imported as 'TAXID' to fit view 
predicates, and fixed taxdump import and DMS closing
 2018-07-28 17:03:00 +02:00
Celine Mercier c02c15b93f Cython API: URI decoding now returns the character string with the 
object path if it could not be opened
 2018-07-28 17:00:42 +02:00
Celine Mercier 3e8c187f0b Cython API: added EMBL parser and files to import are now read in binary 
mode
 2018-07-28 16:57:01 +02:00
Celine Mercier 7f6d1597fc Taxonomy: added functions to check if a taxonomy already exists in a 
DMS, and added taxdump import from a compressed file
 2018-07-28 16:48:11 +02:00
Celine Mercier 1de308a856 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
 2018-05-31 15:11:41 +02:00
Celine Mercier 892ed83a33 Removed deprecated function declarations 2018-05-31 15:08:11 +02:00
Celine Mercier 6911bf4d70 obi clean: first version 2018-05-18 14:26:54 +02:00
Celine Mercier f0c147c252 C API: Added a function to set an entire column to a specified (atomic) 
value.
 2018-05-17 15:59:16 +02:00
Celine Mercier 4aef20add8 Fixed a bug where the line selection column of a view would not be 
flagged as finished
 2018-05-17 15:17:19 +02:00
Celine Mercier 62614a8538 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
Celine Mercier ffebc6acfb Cython API: better handling of default quality offset value 2018-05-17 15:01:25 +02:00
Celine Mercier b91b3176b0 obi uniq: fixed a bug where merged values were wrongly reinitialized 2018-05-17 14:58:15 +02:00
Celine Mercier 31d8ba5085 obi test: minor change 2018-05-17 14:54:45 +02:00
Celine Mercier a166a169cf obi ngsfilter: fixed a bug with -u option 2018-05-17 14:53:53 +02:00
Celine Mercier 8a10072d99 obi annotate: fixed a bug with --with-taxon-at-rank option and minor 
improvements
 2018-05-17 14:51:18 +02:00
Celine Mercier b380368264 Obi count command 2018-04-04 15:51:23 +02:00
Celine Mercier 1f4e82e6f6 Fixed three bugs in obi uniq 2018-04-04 15:50:10 +02:00
Celine Mercier 6825fc13ab Cython API: added ngsfilter file parser 2018-03-21 16:41:25 +01:00
Celine Mercier 49c17ab7b4 Cython API: added tabular file parser 2018-03-21 16:41:09 +01:00
Celine Mercier 2684535e26 New command: obi annotate 2018-03-21 16:39:31 +01:00
Celine Mercier 123fb9d7ba 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
Celine Mercier 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
Celine Mercier 4a815785c4 obi import: added basic taxdump import 2018-03-21 16:35:44 +01:00
Celine Mercier 75b54c83ca obi grep: fixed bug when reading URIs 2018-03-21 16:34:57 +01:00
Celine Mercier 53cb3354b8 obi ls command 2018-03-19 13:08:41 +01:00
Celine Mercier ea58e254da Cython API: repr function for DMS 2018-03-19 13:08:06 +01:00
Celine Mercier 9fb63d4894 Minor fixes 2018-03-16 19:05:09 +01:00
Celine Mercier d4f7e02c85 New obi grep working with URI API 2018-03-16 19:04:54 +01:00
Celine Mercier 15e43bb9a1 Cython API: obi import can now import ngsfilter files and tabular files 2018-03-12 18:10:43 +01:00
Celine Mercier 8a0b95c1d6 New command: obi ngsfilter 2018-03-12 18:09:22 +01:00
Celine Mercier dd225a255f obi uniq: better error checking 2018-03-12 18:04:53 +01:00
Celine Mercier 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
Celine Mercier 96bf2daae8 Cython API: added slices in Seq classes and fixes 2018-03-12 17:51:41 +01:00
Celine Mercier e6c49b7941 Cython API: moved an eval function to utils 2018-03-12 17:49:54 +01:00
Celine Mercier 4960662332 Cython API: tobytes() function now handles None values 2018-03-12 17:25:12 +01:00
Celine Mercier b2cfa4b52f Cython Sequence classes: reworked improved etc 2018-02-12 14:54:47 +01:00
Celine Mercier 94a899de12 Cython View API: added small tools 2018-02-12 14:48:27 +01:00
Celine Mercier b48330a5c9 Fixed a little bug when cleaning unfinished views 2018-02-12 14:44:56 +01:00
Celine Mercier 74d880b817 Fixed default quality offset 2018-02-12 14:43:44 +01:00
Celine Mercier 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
Celine Mercier 370fb9272c obi uniq: better typing 2018-02-12 14:38:07 +01:00
Celine Mercier c8097e14e1 obi import: removed old traces 2018-02-12 14:36:56 +01:00
Celine Mercier 01ef85658c New command: obi alignpairedend 2018-02-12 13:30:06 +01:00
Celine Mercier f5a00c9322 Cython alignment library 2018-02-12 13:28:20 +01:00
Celine Mercier 156fb04e88 Implemented functions to build reverse complement sequences 2018-01-05 16:08:36 +01:00
Celine Mercier 428c4eb5e6 obi import: fixed creation of quality columns (to discuss) 2017-12-19 11:07:00 +01:00
Celine Mercier 1a5b499b5c Cython API to add an OBI_QUAL column after creating a view 2017-12-19 11:06:24 +01:00
Celine Mercier b7b8ba7e5a Better handling of elements names in Cython 2017-12-13 23:12:14 +01:00
Celine Mercier 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
Celine Mercier 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
Celine Mercier 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
Celine Mercier 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
Celine Mercier ea73047fc7 Added rewinddir before each readdir so that the directories are always 
read properly
 2017-11-24 18:04:58 +01:00
Celine Mercier 0998268955 Fixed two little potential bugs when cleaning unfinished columns and 
deleted old trace
 2017-11-24 18:03:59 +01:00
Celine Mercier 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
Celine Mercier d21f4a6f90 Header parser: identifiers ending with ';' are now handled 2017-11-24 17:59:52 +01:00
Celine Mercier 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
Celine Mercier ee5d647d0d Taxonomy: fixed a bug un parental tree iterator 2017-11-24 17:55:17 +01:00
Celine Mercier 38fef5b9d4 obi test: better taxonomy testing 2017-11-24 17:54:10 +01:00
Celine Mercier 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