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5c9091e9eb
|
C: closing DMS after cleaning it instead of counting on upper layer
|
2020-01-18 17:27:35 +01:00 |
|
|
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b9cd9bee9a
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C: Changed obibool definitions because of conflict with R
|
2020-01-06 15:11:31 +01:00 |
|
|
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6c018b403c
|
ecopcr: fixed and improved the options to keep nuclotides around the
amplicon
|
2019-12-26 20:45:54 +01:00 |
|
|
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3b3cf9359d
|
CMake: unset gcc for nix
|
2019-09-26 21:04:42 +02:00 |
|
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6282242a04
|
C: Views: fixed a bug when trying to add a comment after changing the
file name of a finished view
|
2019-09-25 11:39:32 +02:00 |
|
|
|
44517db51f
|
Fixed gcc warnings
|
2019-09-25 11:38:00 +02:00 |
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ec0737a600
|
Added signal catching and handling in C and Cython
|
2019-09-21 16:47:22 +02:00 |
|
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783a1343c4
|
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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eb913b2742
|
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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bc55c5ef8c
|
obi clean: fixed an openmp bug where the share size would be 0 blocking
the program
|
2019-09-10 15:37:33 +02:00 |
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f3b0e10c7f
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fixed a comment
|
2019-09-10 14:42:12 +02:00 |
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8f9f2a2d10
|
obi ls: various improvements
|
2019-09-10 14:41:43 +02:00 |
|
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ad3a72597f
|
Little fixes for linux compilation
|
2019-09-05 17:19:29 +02:00 |
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5e3c41b058
|
C: Fixed opened DIR leak
|
2019-09-04 16:48:13 +02:00 |
|
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b3a1011d36
|
C: fixed a bug when opening or creating a new column directory where the
DMS was not saved in the struct
|
2019-09-04 13:16:28 +02:00 |
|
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a7fabff1c7
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C: made it so column DIR* are not kept open to handle very large DMS
|
2019-09-04 12:55:21 +02:00 |
|
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|
f296517716
|
Various display improvements
|
2019-09-03 21:46:39 +02:00 |
|
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d491480af2
|
C: fixed remaining memory bug in array indexer
|
2019-09-01 17:24:57 +02:00 |
|
|
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073d98db08
|
C: ecotag: now prints a warning if the demanded threshold is lower than
the db threshold
|
2019-08-31 18:30:06 +02:00 |
|
|
|
0ee728c4d0
|
C: build_ref_db: now adds a comment with the threshold used to build the
DB
|
2019-08-31 18:29:40 +02:00 |
|
|
|
7423bacac0
|
C: Json comments: added an obi_read_comment function to read one value
from comments
|
2019-08-31 18:28:51 +02:00 |
|
|
|
e43e49d6f1
|
C: optimized dir opening
|
2019-08-29 16:35:10 +02:00 |
|
|
|
99a397b842
|
obi uniq: various improvements and fixes #66
|
2019-08-27 20:27:36 +02:00 |
|
|
|
f5c472ffd1
|
C: fixed a memory bug in the array indexer
|
2019-08-27 20:26:46 +02:00 |
|
|
|
ae5f42c260
|
fixes #61 : now reading merged taxids information when building a
reference database
|
2019-08-19 12:30:56 +02:00 |
|
|
|
af7cecf59f
|
Fixed a bug where a directory was not closed properly resulting in errno
24 sometimes
|
2019-08-18 19:46:52 +02:00 |
|
|
|
5f20be44b2
|
Minor fixes
|
2019-08-18 19:45:53 +02:00 |
|
|
|
9f38cd8cf6
|
updated a comment
|
2019-07-23 19:03:24 +02:00 |
|
|
|
946f9723b8
|
ecotag: fixed a bug where the wrong taxid for the best match was
retrieved
|
2019-07-23 19:02:17 +02:00 |
|
|
|
d99702f56f
|
ngsfilter and alignpairedend: paired-end reads are now correctly
reversed and labeled to be aligned correctly by alignpairedend
|
2019-07-23 18:56:51 +02:00 |
|
|
|
1759302829
|
C: ecotag: fixed 2 memory bugs
|
2019-07-06 16:31:19 +02:00 |
|
|
|
86bfa96fbe
|
C: kmer similarity: small improvements
|
2019-07-06 16:30:32 +02:00 |
|
|
|
3d9f0352ff
|
obiclean parallelized
|
2019-06-20 19:44:04 +02:00 |
|
|
|
9b4c3537f9
|
multithreaded obiclean working but not cleaned
|
2019-06-19 17:29:58 +02:00 |
|
|
|
fd0b7a9177
|
j loop with critical (untested)
|
2019-06-04 17:14:36 +02:00 |
|
|
|
debf59b266
|
i loop parallelized: bad
|
2019-05-25 18:37:56 +02:00 |
|
|
|
a04588da31
|
openmp on j loop (i loop probably better)
|
2019-05-24 16:51:04 +02:00 |
|
|
|
ed5bb70c80
|
CMake: setting compiler higher to avoid conflicts, and linking libopenmp
|
2019-05-22 16:26:30 +02:00 |
|
|
|
22a5ae72d1
|
obi clean: not using tsearch library anymore, a simple byte array
instead. A lot more time and memory efficient. Closes #67
|
2019-05-19 17:39:53 +02:00 |
|
|
|
3afbbeb7e5
|
CMake: made required version 3.10 for ubuntu
|
2019-03-31 16:54:05 +02:00 |
|
|
|
7f8d1e7196
|
C: obi lcs: cleaner progress print
|
2019-03-31 15:42:58 +02:00 |
|
|
|
26fb149efb
|
C: made build_ref_db cleaner
|
2019-03-31 15:40:13 +02:00 |
|
|
|
f0ff585455
|
Removing trace
|
2019-03-30 20:52:54 +01:00 |
|
|
|
7c518300a0
|
C: Views: fixed a bug when creating automatic columns with unformatted
comments
|
2019-03-30 20:33:14 +01:00 |
|
|
|
173483448a
|
Merge commit '3d842ff7'
|
2019-03-30 15:29:52 +01:00 |
|
|
|
52b3a9fc39
|
C: taxonomy: fixed a segfault on linux when trying to fclose an unopened
file
|
2019-03-30 15:19:12 +01:00 |
|
|
|
0847d618d6
|
fixed typo
|
2019-03-30 15:14:30 +01:00 |
|
|
|
9fcebd7643
|
C: build_reference_db: made some errors more explicit
|
2019-03-30 15:11:49 +01:00 |
|
|
|
0c466046f4
|
Merge branch 'pip-standard-orig-python' into 'master'
The new install version based on classical setup.py
See merge request obitools/obitools3!1
|
2019-03-29 16:25:01 +01:00 |
|
|
|
bf62960ee8
|
Add some .ignore files
|
2019-03-29 15:52:54 +01:00 |
|
