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13adb479d3
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Adds an extern qualifier to the keep_running declaration.
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2021-02-05 15:59:43 +01:00 |
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8ba7acdfe1
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export: fixed a bug where exporting to tab format with a header would
not export the first line of data and switch to version 3.0.0b39
v3.0.0b39
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2021-01-13 16:09:04 +01:00 |
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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
v3.0.0b38
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2020-11-06 16:36:37 +01:00 |
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d27a5b9115
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Switch to version 3.0.0b37
v3.0.0b37
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2020-10-30 10:47:13 +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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2e191372d7
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Now handling sequences with Uracil (U) nucleotides by converting to
Thymine (T)
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2020-10-30 10:46:17 +01:00 |
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112e12cab0
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Taxonomy: new functions to find taxa by name
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2020-10-30 10:45:20 +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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199f3772e8
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Small fixes (potential compilation problems)
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2020-10-30 10:41:58 +01:00 |
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422a6450fa
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ecotag: clarified similarity circle documentation
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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
v3.0.0b36
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2020-09-29 17:51:39 +02:00 |
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b6648ae81e
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Revert "Fixed version numbering mistake (should be b34 not b35)"
This reverts commit f6dffbecfe
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2020-09-25 16:25:39 +02:00 |
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f6dffbecfe
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Fixed version numbering mistake (should be b34 not b35)
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2020-09-25 16:24:23 +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
v3.0.0b35
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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
v3.0.0b34
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2020-08-28 10:41:22 +02:00 |
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f23c40c905
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obi cat: fixed a bug introduced in 3.0.0b28 and switch to version
3.0.0b33
v3.0.0b33
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2020-08-27 18:38:16 +02:00 |
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f99fc13b75
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switch to version 3.0.0b32
v3.0.0b32
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2020-08-13 18:17:09 +02:00 |
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1da6aac1b8
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C: patch for failed creation of AVL with errno EEXIST
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2020-08-12 17:55:08 +02:00 |
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159803b40a
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export: now automatically sorts dictionary keys alphabetically for
tab/csv output
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2020-07-31 16:43:35 +02:00 |
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7dcbc34017
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import: fixed entry count estimation when importing fastq files
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2020-07-30 16:56:36 +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
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2020-07-30 16:14:37 +02:00 |
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d33ff97846
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switch to version 3.0.0b31
v3.0.0b31
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2020-07-28 09:31:19 +02:00 |
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1dcdf69f1f
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export: fixed a bug introduced in version 3.0.0b28
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2020-07-28 09:31:05 +02:00 |
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dec114eed6
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Python: added "date created" information in view representation
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2020-07-27 17:38:45 +02:00 |
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f36691053b
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Python: added the OBITools3 version that generated the view in view
comments
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2020-07-27 16:50:00 +02:00 |
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f2aa5fcf8b
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alignpairedend: fixed division by 0 bug and switch to version 3.0.0b30
v3.0.0b30
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2020-07-27 10:15:59 +02:00 |
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bccb3e6874
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switch to version 3.0.0b29
v3.0.0b29
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2020-07-26 17:40:26 +02:00 |
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f5a17bea68
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C: added a missing error check
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2020-07-26 17:39:55 +02:00 |
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e28507639a
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C and Cython: fixed and improved the associated columns system
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2020-07-26 17:39:29 +02:00 |
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e6feac93fe
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obi test: made less heavy to be faster
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2020-07-26 17:37:21 +02:00 |
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50b292b489
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obi import: added --space-priority option to import a view line by line
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2020-07-26 17:36:52 +02:00 |
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24a737aa55
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switch to version 3.0.0b28
v3.0.0b28
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2020-07-24 16:10:10 +02:00 |
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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
v3.0.0b27
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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
v3.0.0b26
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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
v3.0.0b25
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2020-06-13 21:48:49 +02:00 |
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