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ccc877764e
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Patch a bug in the printing of the progress bar leading to a bus error
when compiled with some C compilers and Cython >= 0.24
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2016-08-03 10:12:23 +02:00 |
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000b9999ad
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Merge branch 'master' of git@git.metabarcoding.org:obitools/obitools3.git
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2016-07-03 09:22:22 +02:00 |
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aff9831c13
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Substitute fprintf call by fputs call to conform with the new ubuntu
compilation rules
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2016-07-03 09:21:56 +02:00 |
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0869b9ba3f
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Closes issue #47 by storing each view in a separate file named with the
view's name and created upon view creation.
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2016-06-30 11:41:30 +02:00 |
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38e603ed57
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Deleted some redundant cython code
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2016-06-10 10:34:47 +02:00 |
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f438c3d913
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OBIQUAL columns can now handle multiple elements per line
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2016-06-09 15:54:36 +02:00 |
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2a1ea3ba3f
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Setting NA values is now handled properly for OBI_SEQ, OBI_STR and
OBI_QUAL columns
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2016-06-09 14:22:36 +02:00 |
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69bf7ec2e7
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NA value for OBI_STR and OBI_SEQ columns is now NULL
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2016-06-03 18:53:22 +02:00 |
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f830389974
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Add some comment on the location of the align method.
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2016-05-29 12:58:31 +02:00 |
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2e35229357
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Add conversion checking on the value of a seq column
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2016-05-29 12:54:13 +02:00 |
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a8ed57dc6e
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few small changes
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2016-05-21 12:29:55 +02:00 |
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c3274d419c
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remove an extra debug log
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2016-05-21 12:29:08 +02:00 |
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cca0dbb46b
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Close issue #54 by adding a read1 method to the MagicKeyFile class
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2016-05-21 12:24:48 +02:00 |
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5a78157112
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increase parsing speed of the header
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2016-05-21 10:29:11 +02:00 |
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0b9a41d952
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Patch a bug about the reading of the last sequence
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2016-05-21 10:28:03 +02:00 |
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3b59043ea8
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Major update: New column type to store sequence qualities. Closes #41
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2016-05-20 16:45:22 +02:00 |
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b3c47809da
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First version of alignment functions (imported from suma* programs)
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2016-05-11 16:36:23 +02:00 |
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f961621f5d
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Minor improvements in _obidms Cython layer
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2016-05-04 13:43:26 +02:00 |
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bc12360490
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Reworked and commented a bit the cython layer for dms, columns and views
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2016-05-02 15:16:06 +02:00 |
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872071b104
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Removed a list of column pointers kept in the OBIView class that was not
really needed
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2016-05-02 14:23:42 +02:00 |
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baba2d742e
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commenting _obidms.pyx
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2016-04-29 16:07:03 +02:00 |
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0eca86107e
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Pseudo obihead for tests
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2016-04-27 14:27:28 +02:00 |
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0de953a3ef
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pseudo obigrep for tests
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2016-04-27 14:19:55 +02:00 |
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d159b921eb
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Fixed obi import trying to print all lines at the end (source of
segfault?)
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2016-04-27 13:14:19 +02:00 |
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4e4cf46b16
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Added all C files as source files for all cython files to stop having
that kind of problem with linux systems
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2016-04-27 10:44:24 +02:00 |
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6b61533650
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Added more C source files for _obiseq
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2016-04-27 10:41:00 +02:00 |
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419885485b
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Added files in _obitaxo C sources for cython
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2016-04-27 10:30:16 +02:00 |
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a6c8d35491
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import command a bit modified for tests
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2016-04-26 14:29:54 +02:00 |
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366264828e
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Renamed MurmurHash2.c file to murmurhash2.c as it could be a problem
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2016-04-26 14:29:17 +02:00 |
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87935c6678
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Fixed all compilation problems with new function names, locations etc
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2016-04-25 18:35:02 +02:00 |
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92980508c0
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Made the function to clone a column in the context of a view private
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2016-04-25 18:15:25 +02:00 |
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1fbbdd43f9
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Updated obiversion_t declaration
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2016-04-25 17:58:37 +02:00 |
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8cdfbb379e
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Documentation for views and reworked the code a little
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2016-04-25 17:58:12 +02:00 |
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7a88ca619a
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First obi import (doesn't import tags yet because NA values aren't
handled)
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2016-04-15 17:00:08 +02:00 |
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eddd19a245
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Changes in obi commands
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2016-04-15 16:59:21 +02:00 |
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2aafecc3b5
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Changed sequence 'description' to 'definition' everywhere
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2016-04-15 16:31:43 +02:00 |
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094b2371e9
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Deleted obsolete directory
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2016-04-15 14:44:31 +02:00 |
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c1034d300d
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merging and fixed git conflict with obiavl.h
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2016-04-15 13:23:29 +02:00 |
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02d67c257f
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The default name of an AVL is now the column name + '_indexer', and when
an AVL is opened (as opposed to created), it is read-only
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2016-04-15 12:55:26 +02:00 |
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e04ea85d1e
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Fixed problematic __str__ method and useless declarations in the
OBI_Nuc_Seq_Stored class
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2016-04-15 11:22:05 +02:00 |
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73d64e5aff
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Renamed 'unmap_header' function to 'close_header'
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2016-04-14 15:19:27 +02:00 |
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4cb52e1632
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Made the truncating of columns automatic when closing them (note:
already the case for AVLs)
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2016-04-14 15:13:30 +02:00 |
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9d042f7bd0
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Refactored and relocated the set and get functions of all column types,
both within and out of the context of a view
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2016-04-13 15:10:24 +02:00 |
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5ec2d8842e
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Character string indexer API
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2016-04-12 17:21:01 +02:00 |
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be05c889e2
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DNA_seq_indexer API
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2016-04-12 16:38:47 +02:00 |
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04e3a7b5a9
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Added more references in cython .cfiles files because it seems necessary
for linux distributions
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2016-04-12 15:10:54 +02:00 |
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d8107533d8
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Obiblob_indexer API
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2016-04-12 14:53:33 +02:00 |
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6fe4c6134a
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Allows for calling getConfiguration without parametter for geting the
default configuration
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2016-04-11 13:31:09 +02:00 |
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019dfc01b4
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Branch to refactor and debug (AVLs bugged)
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2016-04-08 15:38:57 +02:00 |
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45c9c5075c
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A first version of the fasta parser
|
2016-04-01 18:15:54 +02:00 |
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