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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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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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3fcf29a76f
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More explicit predicate error when checking that sequences and qualities
match
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2018-08-08 19:51:05 +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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a39f9697be
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Views: added macro for taxid column name
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2018-07-28 17:10:11 +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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1de308a856
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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
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2018-05-31 15:11:41 +02:00 |
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892ed83a33
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Removed deprecated function declarations
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2018-05-31 15:08:11 +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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f0c147c252
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C API: Added a function to set an entire column to a specified (atomic)
value.
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2018-05-17 15:59:16 +02:00 |
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4aef20add8
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Fixed a bug where the line selection column of a view would not be
flagged as finished
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2018-05-17 15:17:19 +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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ffebc6acfb
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Cython API: better handling of default quality offset value
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2018-05-17 15:01:25 +02:00 |
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