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f0f7edf152
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Python API: small option improvements
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2019-09-21 12:08:36 +02:00 |
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9e72c8d16a
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obi ls: improved taxonomy list
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2019-09-20 20:46:33 +02:00 |
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7c3fa14789
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obi import: fixed bug when reading output URI
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2019-09-20 20:43:48 +02:00 |
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ec874c095b
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new command: clean_dms to clean and unlock a DMS after a bad exit.
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2019-09-20 20:38:25 +02:00 |
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783a1343c4
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DMS are now locked when used by a command. Added checks and changed
cleaning mechanisms.
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2019-09-20 20:37:19 +02:00 |
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eb6c59dc1e
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obi import: proper check for taxonomy name already existing in DMS when
importing a taxdump
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2019-09-17 13:41:49 +02:00 |
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ad46056179
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obi export: if export format is not specified, it is guessed from the
view type
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2019-09-17 13:22:41 +02:00 |
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9063e9159d
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Export options: output option is now only non-positional for obi export
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2019-09-17 13:19:17 +02:00 |
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0159385943
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URI decoding: fixed bug with dms-only URI
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2019-09-17 12:50:37 +02:00 |
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a0c8deb806
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obi export: made output to stdout and pipe in less possible
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2019-09-17 12:31:03 +02:00 |
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f566618be6
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Added option for no progress bar and made output URI option non
positional (for stdout output)
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2019-09-17 12:29:33 +02:00 |
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88451116e8
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URIs: added stdout output (empty URI)
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2019-09-17 12:28:10 +02:00 |
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eb913b2742
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ecotag: trying to use a threshold lower than the ref db threshold now
returns an error instead of a warning
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2019-09-15 19:27:47 +02:00 |
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f8d1fa678a
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obi stats: improved display with str instead of bytes
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2019-09-10 16:20:36 +02:00 |
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bc55c5ef8c
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obi clean: fixed an openmp bug where the share size would be 0 blocking
the program
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2019-09-10 15:37:33 +02:00 |
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f3b0e10c7f
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fixed a comment
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2019-09-10 14:42:12 +02:00 |
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8f9f2a2d10
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obi ls: various improvements
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2019-09-10 14:41:43 +02:00 |
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045a751b0f
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Merge branch 'master' of git@git.metabarcoding.org:obitools/obitools3.git
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2019-09-05 17:20:13 +02:00 |
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ad3a72597f
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Little fixes for linux compilation
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2019-09-05 17:19:29 +02:00 |
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8899478237
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Update README.md
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2019-09-04 17:29:45 +02:00 |
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ec614e5d15
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Update README.md
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2019-09-04 17:23:30 +02:00 |
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f8cccebe19
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Update README.md
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2019-09-04 17:11:46 +02:00 |
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5e3c41b058
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C: Fixed opened DIR leak
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2019-09-04 16:48:13 +02:00 |
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b3a1011d36
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C: fixed a bug when opening or creating a new column directory where the
DMS was not saved in the struct
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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
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2019-09-04 12:55:21 +02:00 |
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f296517716
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Various display improvements
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2019-09-03 21:46:39 +02:00 |
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d491480af2
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C: fixed remaining memory bug in array indexer
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2019-09-01 17:24:57 +02:00 |
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073d98db08
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C: ecotag: now prints a warning if the demanded threshold is lower than
the db threshold
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2019-08-31 18:30:06 +02:00 |
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0ee728c4d0
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C: build_ref_db: now adds a comment with the threshold used to build the
DB
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2019-08-31 18:29:40 +02:00 |
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7423bacac0
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C: Json comments: added an obi_read_comment function to read one value
from comments
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2019-08-31 18:28:51 +02:00 |
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53dcbc8ea3
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Fixed log to be in str instead of bytes
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2019-08-29 18:26:51 +02:00 |
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4e75514bad
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obi import: fixed entry count
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2019-08-29 18:26:09 +02:00 |
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1ed2d45ac4
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obi grep: made an error message clearer (error could be eventually be
handled by program, looking for str in bytes returned by a column)
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2019-08-29 17:17:52 +02:00 |
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e43e49d6f1
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C: optimized dir opening
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2019-08-29 16:35:10 +02:00 |
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187053026f
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Better detection of missing taxonomy
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2019-08-29 16:10:09 +02:00 |
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dcf8cf1d64
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Improved obi stats
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2019-08-29 15:18:26 +02:00 |
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3cfe3a9b00
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Improved progress display when importing files in a DMS
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2019-08-29 10:12:06 +02:00 |
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728af51cb2
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Python: better display of tuple values in fasta format
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2019-08-28 15:55:36 +02:00 |
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99a397b842
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obi uniq: various improvements and fixes #66
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2019-08-27 20:27:36 +02:00 |
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f5c472ffd1
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C: fixed a memory bug in the array indexer
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2019-08-27 20:26:46 +02:00 |
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580db2f710
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minor comment
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2019-08-27 20:25:54 +02:00 |
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dbe09f83a2
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Increased the threshold of elements per line in a column before they are
stored as a character string
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2019-08-27 20:25:14 +02:00 |
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3d1b2e8ed9
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Better handling of column lines with all values at NA
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2019-08-27 20:20:26 +02:00 |
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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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66441e0aef
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Fixed a bug when sending a DMS path to a C function from Cython
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2019-08-18 19:43:51 +02:00 |
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13952358b3
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Fixed a bug where some commands wouldn't work if the input DMS was not
in the current directory
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2019-07-25 11:59:19 +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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