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  • a9ba7744cf obidistutils: added fPIC flag needed for linux compilation and set minimum python version to 3.7 cmercier 2019-03-12 14:20:59 +01:00
  • 185a95e667 cleaner Makefile Celine Mercier 2019-03-11 15:20:10 +01:00
  • 8835a1a983 removed -R compilaiton flag that gcc doesn't like Celine Mercier 2019-03-07 15:55:46 +01:00
  • 1ee50b7222 Fixed a bug when creating a column and checking the comments string if it was NULL Celine Mercier 2019-03-07 15:09:59 +01:00
  • 720bb65b24 Installation: basic Makefile that creates the shared obi3 library used by Cython Celine Mercier 2019-03-07 14:01:37 +01:00
  • 2a1ab9db29 Cython API, Views: guessing an obitype from a python value is now done through the corresponding functions in utils Celine Mercier 2019-03-07 13:57:37 +01:00
  • 4bc52c08c2 minor changes Celine Mercier 2019-03-07 13:53:37 +01:00
  • 306da846e3 obidistutils: link obi3 C shared library instead of compiling all C files with all modules (creating issues with global/static variables). EXCEPT RUNTIME LINKING DOESN'T WORK YET Celine Mercier 2019-03-07 13:50:29 +01:00
  • af57e532da obidistutils: create doc/sphinx dir if needed Celine Mercier 2019-03-07 13:47:23 +01:00
  • 52de6f2717 Update distutils for openmp and new version of pip Eric Coissac 2019-02-19 17:30:53 +01:00
  • 29c56572cf Add cfiles everywhere ;-) Eric Coissac 2019-02-19 15:04:30 +01:00
  • de3d12af17 Renamed CAPI file Celine Mercier 2019-02-19 14:50:30 +01:00
  • 9ccddd5280 better cfiles Celine Mercier 2019-02-19 14:11:29 +01:00
  • e026e9ec83 Fixed the new alignpaired end to work after ngsfilter with the 9879847 possible cases Celine Mercier 2019-02-17 18:32:35 +01:00
  • 4ddd1a1c37 embl iterator: only option on embl directories now works as intended Celine Mercier 2019-02-12 16:46:08 +01:00
  • 3015310535 Fixed a bug in kmer similarity computation where the fact that sequences could be switched was not accounted for Celine Mercier 2019-02-10 21:02:24 +01:00
  • 08bcbcd357 ngsfilter: reworked to use apat library Celine Mercier 2019-02-06 18:13:54 +01:00
  • 04a3682307 Cython API: added API to use apat (pattern search) C library Celine Mercier 2019-02-06 18:12:49 +01:00
  • 6ca6d27ecb ecoPCR: fixed amplicon length computation bug Celine Mercier 2019-02-06 18:11:20 +01:00
  • 8f18907566 Cython API: changed revcomp attribute of Nuc_Seq class to is_revcomp to be more explicit Celine Mercier 2019-02-06 18:09:11 +01:00
  • 0b62619e4e Various commentaries and insignificant fixes Celine Mercier 2019-01-21 17:32:44 +01:00
  • c7f5b8d980 Alignpairedend: added alignment using shifting with best kmer similarity (low level layer in C and Cython API) Celine Mercier 2019-01-21 17:30:46 +01:00
  • 59017c0d6b C: taxonomy: fixed a bug when checking for root node Celine Mercier 2019-01-21 17:23:25 +01:00
  • 9f6bba183f C: Added a function to get a nucleotide at a specific index in an encoded sequence Celine Mercier 2019-01-21 17:18:02 +01:00
  • 2a6a112d29 obi import: fixed writing quality in views when appropriate (but still not a satisfying solution) Celine Mercier 2018-12-11 19:33:55 +01:00
  • c437931a35 Cython: fixed history dot graph for all views, and fixed history recording for build_ref_db and ecotag Celine Mercier 2018-12-10 17:09:00 +01:00
  • eb586b2f53 New command and C functions: obi ecotag Celine Mercier 2018-12-09 19:19:32 +01:00
  • 9556130b11 C obi_lcs: updated deprecated column names and associated comments Celine Mercier 2018-12-09 19:17:13 +01:00
  • 005aaeec06 C obi_lcs: fixed checking for identical sequences when aligning 2 columns Celine Mercier 2018-12-09 19:16:44 +01:00
  • 579f56bb54 obi align (pouic): fixed bug with the saved config when aligning 2 different views Celine Mercier 2018-12-09 19:15:58 +01:00
  • da445066f3 C alignment filter: added a check for sequences not being equal when the threshold requires that they are Celine Mercier 2018-12-09 19:14:51 +01:00
  • 0a407436da C Views: made an error message more specific Celine Mercier 2018-12-09 19:14:05 +01:00
  • 54efff36c4 C build ref db: fixed 2 bugs when setting arrays: size of an element in in bits not bytes and using view API instead of column API Celine Mercier 2018-12-09 19:13:06 +01:00
  • 6acb21712a Missing commit for build_ref_db: C API file for cython Celine Mercier 2018-12-09 19:11:59 +01:00
  • 12087a6c3a C, views: made 'view_exists' function public (now 'obi_view_exists') Celine Mercier 2018-11-27 16:20:30 +01:00
  • fbabbceb5a Fixed a bug in the array indexer where the value's length was no properly set to 0 if the value was NA (ignore previous commit with the same message) Celine Mercier 2018-11-27 16:18:34 +01:00
  • 6f27734d71 Cython: fxed a bug in INT tuple columns where values were converted to double instead of int Celine Mercier 2018-11-27 16:14:56 +01:00
  • b3bfa9ca65 Fixed a bug in the array indexer where the value's length was not properly set to 0 if the value was NA Celine Mercier 2018-11-27 16:12:41 +01:00
  • ece942e771 new command: build_ref_db to build a reference database with metadata for the taxonomic assignment of sequences Celine Mercier 2018-11-27 16:11:18 +01:00
  • ef8dc85f3c C, taxonomy: new function to get the lowest common ancestor of two taxa Celine Mercier 2018-11-27 16:00:29 +01:00
  • f942dd856f C: new function to build a reference database with LCA and score metadata for the taxonomic assignment of sequences Celine Mercier 2018-11-27 15:56:50 +01:00
  • 730ea99f85 minor fixes and comments Celine Mercier 2018-11-19 11:23:54 +01:00
  • 4d51f4f015 obi import: better checking of whether to import quality Celine Mercier 2018-11-19 11:23:39 +01:00
  • e9c1d5e48d AVLs: made maximum number of nodes per AVL 5 millions, as this combined with keeping all AVLs mapped seems the most efficient. Now 1 million sequences more or less constantly takes 1 minute. Celine Mercier 2018-11-19 11:22:26 +01:00
  • 7fc1b578cf AVLs: AVLs in a group are not unmapped and remapped constantly anymore when adding new values, fixed a bug when calculating if an AVL data file has reached the maximum size, fixed a casting bug, and added a boolean so read-only AVLs files are not truncated Celine Mercier 2018-11-19 11:19:07 +01:00
  • 31053591b5 Fixed 2 bugs when checking qualities matching sequences predicate: now closing and reopening indexers so that they are mapped properly, and fixed memory leak when reading sequences Celine Mercier 2018-11-19 11:05:53 +01:00
  • b0da36cb48 New command: obi align, except it's called obi pouic for now because of a Cython compilation bug Celine Mercier 2018-11-07 16:05:48 +01:00
  • d1f1fd432e Minor fixes Celine Mercier 2018-11-07 16:04:17 +01:00
  • 75a28929a7 Renamed Cython alignment library in an attempt to limit some compilation bugs potentially involving name conflicts Celine Mercier 2018-11-07 16:03:32 +01:00
  • d076ea9900 Alignment: updated functions to align columns (LCS) Celine Mercier 2018-11-07 16:00:58 +01:00
  • 6b1c41f3fb Changed an error message to be more specific Celine Mercier 2018-11-07 13:37:25 +01:00
  • 362df50fe9 Removed a deprecated element from the DMS structure Celine Mercier 2018-11-07 13:36:08 +01:00
  • b1090574da View import: associated column informations are now correctly updated with the new versions Celine Mercier 2018-11-07 13:35:11 +01:00
  • 8faabd3ebf Cython, URI: Fixed a bug when using an output URI with just a view name to use the default DMS Celine Mercier 2018-11-02 19:04:27 +01:00
  • 35f3e7c30b All commands now handle outputing to another DMS + small fixes Celine Mercier 2018-11-02 19:03:09 +01:00
  • 8a8e9e50b2 Fixed declaration going with previous commit Celine Mercier 2018-10-31 18:01:04 +01:00
  • c7ff53b948 obi clean: temporary views are now deleted Celine Mercier 2018-10-31 17:52:51 +01:00
  • 1b7bccb236 Small improvement when checking if a view exists Celine Mercier 2018-10-31 17:51:10 +01:00
  • d09aa43133 Cython API: added a function to get the full path to the DMS directory Celine Mercier 2018-10-31 14:46:25 +01:00
  • 123e5dc0ac Cython URI API: added an argument to only open the DMS and return the rest as a character string Celine Mercier 2018-10-31 14:45:17 +01:00
  • 320561a582 Views: Added argument to not automatically create default columns in typed views, a function to delete a view and fixed view history bug Celine Mercier 2018-10-31 14:38:05 +01:00
  • 92c0fbc9bf Fixed a bug where an imported column was not flagged as finished, resulting in its deletion when reopening the DMS. Celine Mercier 2018-10-29 17:39:30 +01:00
  • b11d52d630 Fixed a bug with the DMS counter being wrongly initialized to 0 instead of 1 (generating memory bugs when using the counter) Celine Mercier 2018-10-29 16:12:37 +01:00
  • 6305282305 obi clean: made more efficient with arrays (speed ~x15 compared with OBI1) Celine Mercier 2018-10-21 17:59:02 +02:00
  • d53323e7f4 Fixed comments bug with obi head and obi tail Celine Mercier 2018-10-21 17:39:17 +02:00
  • e18b762d81 Weird buggy Eclipse commit with nothing changed Celine Mercier 2018-10-21 17:35:18 +02:00
  • 0a0f0682a9 Better handling of errors and exceptions when new view name already exists Celine Mercier 2018-10-17 19:47:40 +02:00
  • 4802e32f72 Cython: Sequence objects: repr() method now returns a Fasta or Fastq formatted string Celine Mercier 2018-10-17 16:53:42 +02:00
  • b027762059 Cython: export: fixed exception raising when no quality data when exporting to fastq Celine Mercier 2018-10-17 16:52:51 +02:00
  • da0e3d4043 Cython: added full handling of NA strings when importing files Celine Mercier 2018-10-17 16:41:15 +02:00
  • da76f911db Cython: Views: improved repr() method Celine Mercier 2018-10-17 15:54:03 +02:00
  • 61ad2deeca obi uniq: Added line breaks when printing informations to cut progress bar properly Celine Mercier 2018-10-17 15:53:28 +02:00
  • eb6d5581bd Cython: Progress bar: added a cut option to choose whether to do line breaks every tenth of the full bar, set to False by default for lighter printing Celine Mercier 2018-10-17 15:52:26 +02:00
  • 343dbc7e4d Cython: made the logger lighter (now prints just module name instead of full module path) Celine Mercier 2018-10-17 15:49:55 +02:00
  • 6d018a2d28 Cython: Added 'modulename' in the config informations Celine Mercier 2018-10-17 15:47:44 +02:00
  • 2c2df4e098 C: Added a trick to suppress compilation warnings about an unused function actually called in a macro Celine Mercier 2018-10-17 13:13:23 +02:00
  • 8ce6dd6d1a Updated prototypes with no arguments with a void argument as suggested by compilation warnings Celine Mercier 2018-10-17 12:00:40 +02:00
  • df70086384 New command: obi export Celine Mercier 2018-10-17 11:27:50 +02:00
  • 32d8396ee2 Cython: Added fasta and fastq writers Celine Mercier 2018-10-17 11:27:15 +02:00
  • 6a8670d24a Cython: minor fixes Celine Mercier 2018-10-17 11:26:13 +02:00
  • ec73fa840a Cython: obi stats fixed to work with reworked options (forgotten in a previous commit) Celine Mercier 2018-10-17 11:25:53 +02:00
  • 11032ec90b Cython: Sequence objects: Quality strings are now returned as bytes instead of str Celine Mercier 2018-10-17 11:24:44 +02:00
  • 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 Celine Mercier 2018-10-17 11:23:07 +02:00
  • 135d3b6e67 Cython: updated the URI decoding to handle outputs other than DMS Celine Mercier 2018-10-17 11:21:29 +02:00
  • 58589e04be Cython: rearranged input and output format options to have both and updated commands accordingly Celine Mercier 2018-10-17 11:19:48 +02:00
  • e6bbe13d81 Cython: fasta and fastq parsers now return bytes and take NA string argument Celine Mercier 2018-10-17 11:16:20 +02:00
  • 61b00d6013 Cython: fastq formatter Celine Mercier 2018-10-09 16:41:14 +02:00
  • 8029493c10 Cython: fasta and fastq header formatter Celine Mercier 2018-10-09 16:41:00 +02:00
  • aa5ee53478 Cython: fasta writer Celine Mercier 2018-10-09 16:40:30 +02:00
  • e31c8ea57a New command: obi history to print DMS or view history in bash, dot or ascii formats Celine Mercier 2018-10-07 19:11:36 +02:00
  • 9e700ddc21 obi test: updated to test comments Celine Mercier 2018-10-07 19:10:46 +02:00
  • e9a41c5b97 Commands: updated for JSON formatted comments with history Celine Mercier 2018-10-07 19:10:34 +02:00
  • 35cf2962cc Cython: DMS: JSON formatted comments and history handling Celine Mercier 2018-10-07 19:06:59 +02:00
  • 74be3c39f0 Cython: Views: JSON formatted comments and history handling Celine Mercier 2018-10-07 19:06:23 +02:00
  • c6ee0bade9 Cython: Columns: goes with handling of JSON formatted comments Celine Mercier 2018-10-07 19:04:50 +02:00
  • ffd5bc76bf Cython utils: functions convert to bytes or str and to remove all empty objects from a complex object Celine Mercier 2018-10-07 19:03:38 +02:00
  • 704d9b0474 Cython: Columns: added support for JSON formatted comments Celine Mercier 2018-10-07 18:59:43 +02:00
  • 86bb582a17 Views: implemented handling of JSON formatted comments Celine Mercier 2018-10-07 18:56:46 +02:00
  • bc8c394061 Columns: implemented handling of JSON formatted comments Celine Mercier 2018-10-07 18:54:51 +02:00
  • cef458f570 Obierrno: added errno for JSON related errors Celine Mercier 2018-10-07 18:53:53 +02:00