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3e45c34491
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import: now imports and adds taxids for SILVA and RDP files, added
import of lists, fixed skipping of errors (was not overwriting), and
fixed --no-progress-bar option
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2021-06-01 09:21:07 +12:00 |
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c2f3d90dc1
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build_ref_db: set default threshold to 0.99
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2021-06-01 09:11:17 +12:00 |
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6b732d11d3
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align: fixed column URI parsing
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2021-06-01 09:10:21 +12:00 |
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9eb833a0af
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typo fix
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2021-06-01 09:09:16 +12:00 |
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6b7b0e3bd1
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cat: fixed the handling of dictionary columns
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2021-06-01 09:06:13 +12:00 |
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47691a8f58
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count: added option to specify the count column
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2021-06-01 09:05:14 +12:00 |
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b908b581c8
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clean: hid not implemented option
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2021-06-01 09:04:22 +12:00 |
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03c174fd7a
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grep: added taxonomy check
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2021-05-31 17:03:39 +12:00 |
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c884615522
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obi stats: various fixes and improvements
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2021-05-31 16:51:06 +12:00 |
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e099a16624
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small fixes
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2021-04-07 10:28:02 +12:00 |
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169b6514b4
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small doc fixes
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2021-03-29 13:07:48 +13:00 |
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ecc4c2c78b
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stats: improved the tabular display
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2021-03-29 09:03:32 +13:00 |
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3e93cfff7b
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import: Columns are now rewritten in OBI_FLOAT if a value is > INT32_MAX
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2021-03-29 09:00:52 +13:00 |
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824deb7e21
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new command: obi rm: deletes any view (for now the user deleting a view
accepts that there will be missing information when running obi history
if other views came from the deleted view)
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2021-03-18 09:17:06 +13:00 |
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10e5ebdbc0
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ngsfilter: fixed critical bug where barcodes shorter than the forward
primer would be missed
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2021-03-16 15:09:28 +13:00 |
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904823c827
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uniq: now OK to use -m option even if only one unique key in information
to merge (e.g. one sample)
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2021-03-15 16:48:22 +13:00 |
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425fe25bd2
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Made the OBITools3 more 'empty file friendly'
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2021-03-15 16:25:41 +13:00 |
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8f1d94fd24
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obi test: fixed bug introduced in ad1fd3c3
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2021-03-11 16:31:31 +13:00 |
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ad1fd3c341
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Now handling dictionaries with one key
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2021-03-10 16:50:30 +13:00 |
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5cc3e29f75
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obi test: made less heavy by default
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2021-02-10 17:28:15 +13:00 |
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38051b1e4f
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Removed spurious commentaries
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2021-01-13 16:07:42 +01:00 |
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52a2e21b38
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grep: fixed --id-list option
and switch to version 3.0.0b38
|
2020-11-06 16:36:37 +01:00 |
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20bd3350b4
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New command: obi addtaxids to add NCBI taxids to sequences from their
taxon name.
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2020-10-30 10:46:55 +01:00 |
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b9b4cec5b5
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import: now can import SILVA fasta files
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2020-10-30 10:43:04 +01:00 |
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422a6450fa
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ecotag: clarified similarity circle documentation
|
2020-09-29 17:57:29 +02:00 |
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137c109f86
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obi ls: now done in C (preparing things for R packages to read DMS) and
switch to version 3.0.0b36
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2020-09-29 17:51:39 +02:00 |
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c4696ac865
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ecotag: added separate threshold for minimum circle identity (and switch
to version 3.0.0b35
|
2020-09-25 16:22:09 +02:00 |
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11a0945a9b
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obi cat: fixed open file descriptor leak and switch to version 3.0.0b34
|
2020-08-28 10:41:22 +02:00 |
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f23c40c905
|
obi cat: fixed a bug introduced in 3.0.0b28 and switch to version
3.0.0b33
|
2020-08-27 18:38:16 +02:00 |
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159803b40a
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export: now automatically sorts dictionary keys alphabetically for
tab/csv output
|
2020-07-31 16:43:35 +02:00 |
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db2202c8b4
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uniq: added a check to make sure that there is more than one element for
one tag when merging its information
|
2020-07-30 16:14:37 +02:00 |
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dec114eed6
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Python: added "date created" information in view representation
|
2020-07-27 17:38:45 +02:00 |
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e6feac93fe
|
obi test: made less heavy to be faster
|
2020-07-26 17:37:21 +02:00 |
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50b292b489
|
obi import: added --space-priority option to import a view line by line
|
2020-07-26 17:36:52 +02:00 |
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8aa455ad8a
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Python: made all commands handle output to buffer object (e.g. stdout)
|
2020-07-24 16:09:48 +02:00 |
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8dd403a118
|
grep: now prints the number of entries grepped
|
2020-07-13 17:08:13 +02:00 |
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9672f01c6a
|
alignpairedend: improved/fixed the output tags for the alignment score
and lengths. Removed minimum score option
|
2020-07-13 15:59:50 +02:00 |
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ed9549acfb
|
ngsfilter: unidentified sequences are now stored untrimmed
|
2020-07-13 15:56:40 +02:00 |
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a3ebe5f118
|
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
|
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
|
2020-07-03 17:36:57 +02:00 |
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ccda0661ce
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small help documentation improvement
|
2020-07-01 18:20:38 +02:00 |
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aab59f2214
|
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
|
2020-07-01 18:17:47 +02:00 |
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7593673f3f
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ngsfilter: now setting 'reversed' tag to False instead of None when
false
|
2020-06-17 18:52:35 +02:00 |
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7a39df54c0
|
ls: fixed an issue where big DMS couldn't be read by ls
|
2020-06-13 21:45:22 +02:00 |
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14a2579173
|
uniq: now outputs an empty view if input view is empty instead of
displaying an error
|
2020-06-10 17:47:26 +02:00 |
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36a8aaa92e
|
grep: now creating empty views instead of displaying an error when
selecting on an unexisting column/tag
|
2020-06-10 16:57:42 +02:00 |
|
|
|
a17eb445c2
|
ngsfilter: made one of the tag error messages more accurate
|
2020-06-10 16:27:36 +02:00 |
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aa836b2ace
|
uniq: improved progress bar of second browsing
|
2020-06-09 14:36:02 +02:00 |
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f9b6851f75
|
Python: correctly flagged some mandatory options as required
|
2020-06-04 15:34:24 +02:00 |
|
|
|
2a2c233936
|
obi import: fixed a bug when skipping an entry
|
2020-05-29 21:19:42 +02:00 |
|
