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1bfb96023c
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obi import: rewriting a column now deletes the old one to save disk
space
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2020-02-01 15:31:14 +01:00 |
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c67d668989
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obi import: fixed a bug when the first entry would contain a dictionary
with one key. Switch to beta8
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2020-01-29 20:23:39 +01:00 |
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db0ac37d41
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switch to version 3.0.0-beta7
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2020-01-29 16:18:53 +01:00 |
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53212168a2
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History: added 'obi' in bash history for practical reasons
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2020-01-23 16:51:49 +01:00 |
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b4b2e62195
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Cleaner handling of reverse quality columns
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2020-01-18 19:28:12 +01:00 |
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ced82c4242
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Switching to version 3.0-beta6
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2020-01-18 17:29:23 +01:00 |
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a524f8829e
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New command: obi cat to concatenate views (not optimized yet)
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2020-01-18 17:28:31 +01:00 |
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822000cb70
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Fixes in documentation
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2020-01-18 17:26:18 +01:00 |
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b1f3e082f9
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ngsfilter: fixed a bug when there is only one tag introduced in latest
edit
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2020-01-06 13:53:38 +01:00 |
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6c018b403c
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ecopcr: fixed and improved the options to keep nuclotides around the
amplicon
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2019-12-26 20:45:54 +01:00 |
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694d1934a8
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Tagging version beta3
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2019-12-12 17:03:13 +01:00 |
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fc3ac03630
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clean_dms: now works with extension
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2019-12-12 17:02:50 +01:00 |
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d75e54a078
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uniq: added forced deletion of reverse sequence quality
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2019-12-12 17:02:36 +01:00 |
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6bfd7441f3
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ngsfilter: fixed sequence cutting when dealing with unaligned sequences.
Could use optimization
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2019-12-12 17:01:31 +01:00 |
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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
|
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.
|
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.
|
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
|
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
|
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
|
2019-09-17 12:31:03 +02:00 |
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f566618be6
|
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)
|
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
|
2019-09-15 19:27:47 +02:00 |
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f8d1fa678a
|
obi stats: improved display with str instead of bytes
|
2019-09-10 16:20:36 +02:00 |
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8f9f2a2d10
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obi ls: various improvements
|
2019-09-10 14:41:43 +02:00 |
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5e3c41b058
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C: Fixed opened DIR leak
|
2019-09-04 16:48:13 +02:00 |
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f296517716
|
Various display improvements
|
2019-09-03 21:46:39 +02:00 |
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53dcbc8ea3
|
Fixed log to be in str instead of bytes
|
2019-08-29 18:26:51 +02:00 |
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4e75514bad
|
obi import: fixed entry count
|
2019-08-29 18:26:09 +02:00 |
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