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8aa455ad8a
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Python: made all commands handle output to buffer object (e.g. stdout)
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2020-07-24 16:09:48 +02:00 |
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46ca693ca9
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Cython: View: new method to print a view to a buffer (e.g. stdout)
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2020-07-24 16:03:23 +02:00 |
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9a9afde113
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Cython: progress bar: set default refresh rate to 5 seconds
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2020-07-24 15:29:12 +02:00 |
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8dd403a118
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grep: now prints the number of entries grepped
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2020-07-13 17:08:13 +02:00 |
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9672f01c6a
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alignpairedend: improved/fixed the output tags for the alignment score
and lengths. Removed minimum score option
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2020-07-13 15:59:50 +02:00 |
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ed9549acfb
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ngsfilter: unidentified sequences are now stored untrimmed
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2020-07-13 15:56:40 +02:00 |
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9ace9989c4
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Switch to version 3.0.0b27
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2020-07-07 16:47:21 +02:00 |
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a3ebe5f118
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C: AVL trees: fixed a bug where storing the difference between 2 crc64
values in an int64 would mess trees up resulting in failed data
dereplication
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2020-07-07 16:47:00 +02:00 |
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9100e14899
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obi uniq: quick fix for bug where some sequences are not correctly
dereplicated
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2020-07-03 17:36:57 +02:00 |
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ccda0661ce
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small help documentation improvement
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2020-07-01 18:20:38 +02:00 |
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aab59f2214
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obi clean: fixed a memory bug, fixed the behaviour when no sample info,
and added checks warnings and error handling when sample info not
dereplicated
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2020-07-01 18:17:47 +02:00 |
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ade1107b42
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switch to version 3.0.0b26
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2020-06-17 18:56:07 +02:00 |
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9c7d24406f
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export: dictionaries are now formatted like in the original OBITools
when exporting in tabular format and tuple formatting is cleaner
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2020-06-17 18:55:46 +02:00 |
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03bc9915f2
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Cython: utils: added handling of tuples to bytes2str_object function
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2020-06-17 18:54:14 +02:00 |
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24b1dab573
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Cython: Columns: added a keys() method that returns all element names
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2020-06-17 18:53:41 +02:00 |
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7593673f3f
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ngsfilter: now setting 'reversed' tag to False instead of None when
false
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2020-06-17 18:52:35 +02:00 |
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aa01236cae
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switch to version 3.0.0b25
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2020-06-13 21:48:49 +02:00 |
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7a39df54c0
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ls: fixed an issue where big DMS couldn't be read by ls
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2020-06-13 21:45:22 +02:00 |
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09e483b0d6
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switch to temporary version 3.0.0b24a
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2020-06-10 17:47:56 +02:00 |
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14a2579173
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uniq: now outputs an empty view if input view is empty instead of
displaying an error
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2020-06-10 17:47:26 +02:00 |
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36a8aaa92e
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grep: now creating empty views instead of displaying an error when
selecting on an unexisting column/tag
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2020-06-10 16:57:42 +02:00 |
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a17eb445c2
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ngsfilter: made one of the tag error messages more accurate
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2020-06-10 16:27:36 +02:00 |
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e4a32788c2
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Switch to version 3.0.0b24
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2020-06-09 14:36:58 +02:00 |
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2442cc80bf
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Cython: View: fixed bash history display
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2020-06-09 14:36:37 +02:00 |
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aa836b2ace
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uniq: improved progress bar of second browsing
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2020-06-09 14:36:02 +02:00 |
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b0b96ac37a
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version 3.0.0b23a
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2020-06-05 16:10:24 +02:00 |
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5fbbb6d304
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alignpairedend: fixed a bug when rebuilding joined (unaligned) sequences
where only the forward sequence was kept
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2020-06-05 16:06:43 +02:00 |
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359a9fe237
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Switch to version 3.0.0b23
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2020-06-04 15:35:03 +02:00 |
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f9b6851f75
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Python: correctly flagged some mandatory options as required
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2020-06-04 15:34:24 +02:00 |
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2a2c233936
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obi import: fixed a bug when skipping an entry
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2020-05-29 21:19:42 +02:00 |
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faf8ea9d86
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Switch to version 3.0.0b21
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2020-05-28 20:42:09 +02:00 |
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ffe2485e94
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Genbank parser: now reading ORIGIN lines with comments without
triggering error
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2020-05-28 20:41:34 +02:00 |
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6094ce2bbc
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obi import: skip on error more robust
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2020-05-28 20:40:36 +02:00 |
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a7dcf16c06
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Minor changes for pip release
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2020-05-20 15:59:04 +02:00 |
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f13f8f6165
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obi import: minor doc/display improvements
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2020-05-20 11:46:29 +02:00 |
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b5a29ac413
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Switch to version 3.0.0b19
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2020-05-20 10:29:36 +02:00 |
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ca6e3e7aad
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obi import: fixed to work with seq genbank extension
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2020-05-20 10:28:14 +02:00 |
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76ed8e18e5
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Switch to version 3.0.0b18 with version formatting that fits setuptools
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2020-05-18 17:08:55 +02:00 |
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fa834e4b8b
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obi import: small bug fix
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2020-05-18 17:06:58 +02:00 |
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a72fea3cc9
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Python: fasta parser: fixed a bug stopping the program when the last
line contained a single nucleotide
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2020-05-12 11:24:12 +02:00 |
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e9a37d8a6e
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Switch to version 3.0.0-beta16
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2020-05-07 17:09:26 +02:00 |
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ef074f8455
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typo
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2020-05-07 17:08:59 +02:00 |
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170ef3f1ba
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Views: added obi prefix to commands in bash history
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2020-05-07 17:07:01 +02:00 |
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f999946582
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obi uniq: fixed the remerging of already merged informations, and
efficiency improvements
|
2020-05-07 17:05:54 +02:00 |
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773b36ec37
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obi import: fixed the import of old obitools files with premerged
informations, and other minor improvements
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2020-05-07 17:03:04 +02:00 |
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69cb434a6c
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version 3.0.0-beta15c
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2020-04-29 14:25:33 +02:00 |
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55d4f98d60
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obi annotate: fixed annotation at ranks
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2020-04-29 14:24:40 +02:00 |
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0bec2631e8
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ecotag: fixed a bug where all the full DMS path weren't properly sent to
the C layer
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2020-04-29 10:35:55 +02:00 |
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e6b6c6fa84
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AVLs: Made an error message more informative
|
2020-04-29 10:14:04 +02:00 |
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974528b2e6
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build_ref_db: fixed bug erasing some of the higher LCAs (i.e. lowest
similarities)
|
2020-04-28 15:56:06 +02:00 |
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