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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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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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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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b57e938cc4
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New command: obi stats
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2018-08-13 15:08:10 +02:00 |
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2dc7fcceac
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Minor fixes
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2018-08-10 10:39:46 +02:00 |
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e096b929dc
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New command: obi tail
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2018-08-10 10:39:26 +02:00 |
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2c634dae7c
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New command: obi head
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2018-08-10 10:29:37 +02:00 |
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7a4cdc0cfe
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New command: obi sort
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2018-08-09 18:10:47 +02:00 |
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e8dc5eb123
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Commands: ngsfilter and alignpairedend can now be used in whichever
order
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2018-08-08 19:53:26 +02:00 |
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080a97cccf
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Cython API: more explicit "Can't guess type" exception
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2018-08-08 19:50:26 +02:00 |
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9c9aec2556
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Cython API: the associated sequence column for a quality column can now
be specified at the Python level
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2018-08-08 19:49:56 +02:00 |
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303648bd47
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Cython: embl file parser
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2018-07-28 17:14:10 +02:00 |
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2ba6d16147
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New command: obi ecopcr
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2018-07-28 17:13:45 +02:00 |
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275d85dc5d
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Cython: fixed a bug when reading an uncompressed file in binary mode
where the first 4 characters would not be read
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2018-07-28 17:11:51 +02:00 |
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b98880b7fa
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Various non-important fixes and comments
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2018-07-28 17:07:17 +02:00 |
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895d09b133
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obi import: 'taxid' columns are imported as 'TAXID' to fit view
predicates, and fixed taxdump import and DMS closing
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2018-07-28 17:03:00 +02:00 |
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c02c15b93f
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Cython API: URI decoding now returns the character string with the
object path if it could not be opened
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2018-07-28 17:00:42 +02:00 |
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3e8c187f0b
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Cython API: added EMBL parser and files to import are now read in binary
mode
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2018-07-28 16:57:01 +02:00 |
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7f6d1597fc
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Taxonomy: added functions to check if a taxonomy already exists in a
DMS, and added taxdump import from a compressed file
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2018-07-28 16:48:11 +02:00 |
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6911bf4d70
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obi clean: first version
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2018-05-18 14:26:54 +02:00 |
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62614a8538
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Cython API: fixed a bug in URI decoding and option handling where the
quality offset would not be read properly
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2018-05-17 15:10:52 +02:00 |
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