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35f3e7c30b
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All commands now handle outputing to another DMS + small fixes
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2018-11-02 19:03:09 +01:00 |
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8a8e9e50b2
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Fixed declaration going with previous commit
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2018-10-31 18:01:04 +01:00 |
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c7ff53b948
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obi clean: temporary views are now deleted
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2018-10-31 17:52:51 +01:00 |
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1b7bccb236
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Small improvement when checking if a view exists
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2018-10-31 17:51:10 +01:00 |
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d09aa43133
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Cython API: added a function to get the full path to the DMS directory
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2018-10-31 14:46:25 +01:00 |
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123e5dc0ac
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Cython URI API: added an argument to only open the DMS and return the
rest as a character string
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2018-10-31 14:45:17 +01:00 |
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320561a582
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Views: Added argument to not automatically create default columns in
typed views, a function to delete a view and fixed view history bug
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2018-10-31 14:38:05 +01:00 |
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92c0fbc9bf
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Fixed a bug where an imported column was not flagged as finished,
resulting in its deletion when reopening the DMS.
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2018-10-29 17:39:30 +01:00 |
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b11d52d630
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Fixed a bug with the DMS counter being wrongly initialized to 0 instead
of 1 (generating memory bugs when using the counter)
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2018-10-29 16:12:37 +01:00 |
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6305282305
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obi clean: made more efficient with arrays (speed ~x15 compared with
OBI1)
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2018-10-21 17:59:02 +02:00 |
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d53323e7f4
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Fixed comments bug with obi head and obi tail
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2018-10-21 17:39:17 +02:00 |
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e18b762d81
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Weird buggy Eclipse commit with nothing changed
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2018-10-21 17:35:18 +02:00 |
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0a0f0682a9
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Better handling of errors and exceptions when new view name already
exists
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2018-10-17 19:47:40 +02:00 |
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4802e32f72
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Cython: Sequence objects: repr() method now returns a Fasta or Fastq
formatted string
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2018-10-17 16:53:42 +02:00 |
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b027762059
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Cython: export: fixed exception raising when no quality data when
exporting to fastq
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2018-10-17 16:52:51 +02:00 |
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da0e3d4043
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Cython: added full handling of NA strings when importing files
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2018-10-17 16:41:15 +02:00 |
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da76f911db
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Cython: Views: improved repr() method
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2018-10-17 15:54:03 +02:00 |
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61ad2deeca
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obi uniq: Added line breaks when printing informations to cut progress
bar properly
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2018-10-17 15:53:28 +02:00 |
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eb6d5581bd
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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
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2018-10-17 15:52:26 +02:00 |
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343dbc7e4d
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Cython: made the logger lighter (now prints just module name instead of
full module path)
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2018-10-17 15:49:55 +02:00 |
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6d018a2d28
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Cython: Added 'modulename' in the config informations
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2018-10-17 15:47:44 +02:00 |
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2c2df4e098
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C: Added a trick to suppress compilation warnings about an unused
function actually called in a macro
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2018-10-17 13:13:23 +02:00 |
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8ce6dd6d1a
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Updated prototypes with no arguments with a void argument as suggested
by compilation warnings
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2018-10-17 12:00:40 +02:00 |
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df70086384
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New command: obi export
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2018-10-17 11:27:50 +02:00 |
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32d8396ee2
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Cython: Added fasta and fastq writers
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2018-10-17 11:27:15 +02:00 |
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6a8670d24a
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Cython: minor fixes
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2018-10-17 11:26:13 +02:00 |
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ec73fa840a
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Cython: obi stats fixed to work with reworked options (forgotten in a
previous commit)
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2018-10-17 11:25:53 +02:00 |
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11032ec90b
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Cython: Sequence objects: Quality strings are now returned as bytes
instead of str
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2018-10-17 11:24:44 +02:00 |
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8a9ba8b0a8
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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
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2018-10-17 11:23:07 +02:00 |
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135d3b6e67
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Cython: updated the URI decoding to handle outputs other than DMS
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2018-10-17 11:21:29 +02:00 |
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58589e04be
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Cython: rearranged input and output format options to have both and
updated commands accordingly
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2018-10-17 11:19:48 +02:00 |
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e6bbe13d81
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Cython: fasta and fastq parsers now return bytes and take NA string
argument
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2018-10-17 11:16:20 +02:00 |
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61b00d6013
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Cython: fastq formatter
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2018-10-09 16:41:14 +02:00 |
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8029493c10
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Cython: fasta and fastq header formatter
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2018-10-09 16:41:00 +02:00 |
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aa5ee53478
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Cython: fasta writer
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2018-10-09 16:40:30 +02:00 |
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e31c8ea57a
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New command: obi history to print DMS or view history in bash, dot or
ascii formats
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2018-10-07 19:11:36 +02:00 |
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9e700ddc21
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obi test: updated to test comments
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2018-10-07 19:10:46 +02:00 |
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e9a41c5b97
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Commands: updated for JSON formatted comments with history
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2018-10-07 19:10:34 +02:00 |
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35cf2962cc
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Cython: DMS: JSON formatted comments and history handling
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2018-10-07 19:06:59 +02:00 |
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74be3c39f0
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Cython: Views: JSON formatted comments and history handling
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2018-10-07 19:06:23 +02:00 |
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c6ee0bade9
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Cython: Columns: goes with handling of JSON formatted comments
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2018-10-07 19:04:50 +02:00 |
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ffd5bc76bf
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Cython utils: functions convert to bytes or str and to remove all empty
objects from a complex object
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2018-10-07 19:03:38 +02:00 |
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704d9b0474
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Cython: Columns: added support for JSON formatted comments
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2018-10-07 18:59:43 +02:00 |
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86bb582a17
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Views: implemented handling of JSON formatted comments
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2018-10-07 18:56:46 +02:00 |
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bc8c394061
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Columns: implemented handling of JSON formatted comments
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2018-10-07 18:54:51 +02:00 |
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cef458f570
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Obierrno: added errno for JSON related errors
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2018-10-07 18:53:53 +02:00 |
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2736a92699
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DMS: implemented full information file with JSON formatted comments
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2018-10-07 18:53:25 +02:00 |
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79f4185757
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C library to handle JSON formatted comments using the cJSON library
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2018-10-07 18:51:27 +02:00 |
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1b6b6d825a
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obi grep: added all the missing filtering options
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2018-08-14 17:11:41 +02:00 |
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3847850a9d
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Taxonomy Cython API: added is_ancestor() function
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2018-08-14 17:09:40 +02:00 |
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