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81a179239c
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ngsfilter: fixed sequence cut bug on aligned sequences. Still exists for
unaligned sequences
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2019-12-10 18:13:27 +01:00 |
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35ce37c0f7
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ngsfilter: fixed a bug with unaligned chimeras (unpaired primers) and
made error annotations more explicit
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2019-12-10 13:43:32 +01:00 |
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53f18316b0
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ngsfilter: made more robust and practical to use with empty tags
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2019-11-29 15:21:08 +01:00 |
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8bc249b2f4
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Version 3.0.0-beta1
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2019-09-27 14:52:05 +02:00 |
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e308c2e822
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versioning 1.0.beta
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2019-09-26 21:05:05 +02:00 |
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be85c55c9e
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Python: URIs: fixed bug on linux systems
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2019-09-25 14:41:52 +02:00 |
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44517db51f
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Fixed gcc warnings
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2019-09-25 11:38:00 +02:00 |
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28b7fce59a
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Cython API: simpler column repr display
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2019-09-22 20:23:31 +02:00 |
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fa9555deb9
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obi stats: fixed bug with None values
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2019-09-22 20:21:53 +02:00 |
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d30f7e7317
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more cleaning
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2019-09-22 18:52:05 +02:00 |
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71276537a6
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obi import: fixed bug when importing a taxdump
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2019-09-22 16:45:30 +02:00 |
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ba9ba7aa60
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obi grep: now able to convert str to bytes in predicate expressions
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2019-09-22 16:44:45 +02:00 |
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336100f716
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obi less: now actually behaves like less
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2019-09-21 18:29:12 +02:00 |
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d83398c0e0
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Cython: View: lines from simple View instances are now displayed in tab
instead of dict format
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2019-09-21 18:28:56 +02:00 |
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974d25b815
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Cython: Fixed bug in tab formatter with header option always being set
to true
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2019-09-21 18:27:47 +02:00 |
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ec0737a600
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Added signal catching and handling in C and Cython
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2019-09-21 16:47:22 +02:00 |
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06f9d6da60
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obi import: importing a view to a DMS now uses the C API (more efficient
and imports all metadata)
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2019-09-21 12:49:29 +02:00 |
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f0f7edf152
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Python API: small option improvements
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2019-09-21 12:08:36 +02:00 |
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9e72c8d16a
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obi ls: improved taxonomy list
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2019-09-20 20:46:33 +02:00 |
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7c3fa14789
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obi import: fixed bug when reading output URI
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2019-09-20 20:43:48 +02:00 |
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ec874c095b
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new command: clean_dms to clean and unlock a DMS after a bad exit.
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2019-09-20 20:38:25 +02:00 |
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783a1343c4
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DMS are now locked when used by a command. Added checks and changed
cleaning mechanisms.
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2019-09-20 20:37:19 +02:00 |
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eb6c59dc1e
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obi import: proper check for taxonomy name already existing in DMS when
importing a taxdump
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2019-09-17 13:41:49 +02:00 |
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ad46056179
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obi export: if export format is not specified, it is guessed from the
view type
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2019-09-17 13:22:41 +02:00 |
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9063e9159d
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Export options: output option is now only non-positional for obi export
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2019-09-17 13:19:17 +02:00 |
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0159385943
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URI decoding: fixed bug with dms-only URI
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2019-09-17 12:50:37 +02:00 |
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a0c8deb806
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obi export: made output to stdout and pipe in less possible
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2019-09-17 12:31:03 +02:00 |
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f566618be6
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Added option for no progress bar and made output URI option non
positional (for stdout output)
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2019-09-17 12:29:33 +02:00 |
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88451116e8
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URIs: added stdout output (empty URI)
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2019-09-17 12:28:10 +02:00 |
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eb913b2742
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ecotag: trying to use a threshold lower than the ref db threshold now
returns an error instead of a warning
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2019-09-15 19:27:47 +02:00 |
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f8d1fa678a
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obi stats: improved display with str instead of bytes
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2019-09-10 16:20:36 +02:00 |
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8f9f2a2d10
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obi ls: various improvements
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2019-09-10 14:41:43 +02:00 |
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5e3c41b058
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C: Fixed opened DIR leak
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2019-09-04 16:48:13 +02:00 |
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f296517716
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Various display improvements
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2019-09-03 21:46:39 +02:00 |
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53dcbc8ea3
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Fixed log to be in str instead of bytes
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2019-08-29 18:26:51 +02:00 |
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4e75514bad
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obi import: fixed entry count
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2019-08-29 18:26:09 +02:00 |
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1ed2d45ac4
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obi grep: made an error message clearer (error could be eventually be
handled by program, looking for str in bytes returned by a column)
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2019-08-29 17:17:52 +02:00 |
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187053026f
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Better detection of missing taxonomy
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2019-08-29 16:10:09 +02:00 |
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dcf8cf1d64
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Improved obi stats
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2019-08-29 15:18:26 +02:00 |
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3cfe3a9b00
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Improved progress display when importing files in a DMS
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2019-08-29 10:12:06 +02:00 |
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728af51cb2
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Python: better display of tuple values in fasta format
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2019-08-28 15:55:36 +02:00 |
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99a397b842
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obi uniq: various improvements and fixes #66
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2019-08-27 20:27:36 +02:00 |
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580db2f710
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minor comment
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2019-08-27 20:25:54 +02:00 |
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dbe09f83a2
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Increased the threshold of elements per line in a column before they are
stored as a character string
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2019-08-27 20:25:14 +02:00 |
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3d1b2e8ed9
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Better handling of column lines with all values at NA
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2019-08-27 20:20:26 +02:00 |
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66441e0aef
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Fixed a bug when sending a DMS path to a C function from Cython
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2019-08-18 19:43:51 +02:00 |
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13952358b3
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Fixed a bug where some commands wouldn't work if the input DMS was not
in the current directory
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2019-07-25 11:59:19 +02:00 |
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9752ff8494
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embl parser: information display about progress when parsing multiple
files
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2019-07-23 18:59:07 +02:00 |
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d99702f56f
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ngsfilter and alignpairedend: paired-end reads are now correctly
reversed and labeled to be aligned correctly by alignpairedend
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2019-07-23 18:56:51 +02:00 |
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f765c6f41e
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obi alignpairedend: fixed a bug where first seq was kept in result view
instead of consensus seq
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2019-07-06 16:29:32 +02:00 |
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