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ae5f42c260
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fixes #61 : now reading merged taxids information when building a
reference database
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2019-08-19 12:30:56 +02:00 |
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af7cecf59f
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Fixed a bug where a directory was not closed properly resulting in errno
24 sometimes
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2019-08-18 19:46:52 +02:00 |
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5f20be44b2
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Minor fixes
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2019-08-18 19:45:53 +02:00 |
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9f38cd8cf6
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updated a comment
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2019-07-23 19:03:24 +02:00 |
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946f9723b8
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ecotag: fixed a bug where the wrong taxid for the best match was
retrieved
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2019-07-23 19:02:17 +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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1759302829
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C: ecotag: fixed 2 memory bugs
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2019-07-06 16:31:19 +02:00 |
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86bfa96fbe
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C: kmer similarity: small improvements
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2019-07-06 16:30:32 +02:00 |
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3d9f0352ff
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obiclean parallelized
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2019-06-20 19:44:04 +02:00 |
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9b4c3537f9
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multithreaded obiclean working but not cleaned
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2019-06-19 17:29:58 +02:00 |
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fd0b7a9177
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j loop with critical (untested)
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2019-06-04 17:14:36 +02:00 |
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debf59b266
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i loop parallelized: bad
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2019-05-25 18:37:56 +02:00 |
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a04588da31
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openmp on j loop (i loop probably better)
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2019-05-24 16:51:04 +02:00 |
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ed5bb70c80
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CMake: setting compiler higher to avoid conflicts, and linking libopenmp
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2019-05-22 16:26:30 +02:00 |
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22a5ae72d1
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obi clean: not using tsearch library anymore, a simple byte array
instead. A lot more time and memory efficient. Closes #67
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2019-05-19 17:39:53 +02:00 |
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3afbbeb7e5
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CMake: made required version 3.10 for ubuntu
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2019-03-31 16:54:05 +02:00 |
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7f8d1e7196
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C: obi lcs: cleaner progress print
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2019-03-31 15:42:58 +02:00 |
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26fb149efb
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C: made build_ref_db cleaner
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2019-03-31 15:40:13 +02:00 |
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f0ff585455
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Removing trace
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2019-03-30 20:52:54 +01:00 |
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7c518300a0
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C: Views: fixed a bug when creating automatic columns with unformatted
comments
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2019-03-30 20:33:14 +01:00 |
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173483448a
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Merge commit '3d842ff7'
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2019-03-30 15:29:52 +01:00 |
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52b3a9fc39
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C: taxonomy: fixed a segfault on linux when trying to fclose an unopened
file
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2019-03-30 15:19:12 +01:00 |
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0847d618d6
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fixed typo
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2019-03-30 15:14:30 +01:00 |
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9fcebd7643
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C: build_reference_db: made some errors more explicit
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2019-03-30 15:11:49 +01:00 |
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0c466046f4
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Merge branch 'pip-standard-orig-python' into 'master'
The new install version based on classical setup.py
See merge request obitools/obitools3!1
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2019-03-29 16:25:01 +01:00 |
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bf62960ee8
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Add some .ignore files
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2019-03-29 15:52:54 +01:00 |
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52b8008bdc
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Add the location of install
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2019-03-29 15:21:30 +01:00 |
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ee9947217c
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alignpairedend: fixed the worst memory leak and the handling of the case
where 0 common kmers are found
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2019-03-29 11:16:25 +01:00 |
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10ab557259
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First version of the simplified setup.py script
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2019-03-26 15:40:31 +01:00 |
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50e7cd61a6
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added math.h import where needed
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2019-03-13 11:17:25 +01:00 |
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1ee50b7222
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Fixed a bug when creating a column and checking the comments string if
it was NULL
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2019-03-07 15:09:59 +01:00 |
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e026e9ec83
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Fixed the new alignpaired end to work after ngsfilter with the 9879847
possible cases
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2019-02-17 18:32:35 +01:00 |
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3015310535
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Fixed a bug in kmer similarity computation where the fact that sequences
could be switched was not accounted for
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2019-02-10 21:02:24 +01:00 |
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6ca6d27ecb
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ecoPCR: fixed amplicon length computation bug
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2019-02-06 18:11:20 +01:00 |
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0b62619e4e
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Various commentaries and insignificant fixes
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2019-01-21 17:32:44 +01:00 |
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c7f5b8d980
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Alignpairedend: added alignment using shifting with best kmer similarity
(low level layer in C and Cython API)
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2019-01-21 17:30:46 +01:00 |
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59017c0d6b
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C: taxonomy: fixed a bug when checking for root node
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2019-01-21 17:23:25 +01:00 |
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9f6bba183f
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C: Added a function to get a nucleotide at a specific index in an
encoded sequence
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2019-01-21 17:18:02 +01:00 |
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eb586b2f53
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New command and C functions: obi ecotag
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2018-12-09 19:19:32 +01:00 |
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9556130b11
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C obi_lcs: updated deprecated column names and associated comments
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2018-12-09 19:17:13 +01:00 |
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005aaeec06
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C obi_lcs: fixed checking for identical sequences when aligning 2
columns
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2018-12-09 19:16:44 +01:00 |
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da445066f3
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C alignment filter: added a check for sequences not being equal when the
threshold requires that they are
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2018-12-09 19:14:51 +01:00 |
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0a407436da
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C Views: made an error message more specific
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2018-12-09 19:14:05 +01:00 |
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54efff36c4
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C build ref db: fixed 2 bugs when setting arrays: size of an element in
in bits not bytes and using view API instead of column API
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2018-12-09 19:13:06 +01:00 |
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12087a6c3a
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C, views: made 'view_exists' function public (now 'obi_view_exists')
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2018-11-27 16:20:30 +01:00 |
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fbabbceb5a
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Fixed a bug in the array indexer where the value's length was no
properly set to 0 if the value was NA (ignore previous commit with the
same message)
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2018-11-27 16:18:34 +01:00 |
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b3bfa9ca65
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Fixed a bug in the array indexer where the value's length was not
properly set to 0 if the value was NA
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2018-11-27 16:12:41 +01:00 |
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ef8dc85f3c
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C, taxonomy: new function to get the lowest common ancestor of two taxa
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2018-11-27 16:00:29 +01:00 |
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f942dd856f
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C: new function to build a reference database with LCA and score
metadata for the taxonomic assignment of sequences
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2018-11-27 15:56:50 +01:00 |
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730ea99f85
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minor fixes and comments
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2018-11-19 11:23:54 +01:00 |
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