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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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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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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
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2020-09-25 16:22:09 +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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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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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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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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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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49b8810a76
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C: made indexer opening/closing cleaner
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2020-06-13 21:47:03 +02:00 |
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8776ce22e6
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C: fixed a bug where indexers referring to tuples of certain types were
not properly closed and imported
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2020-06-09 14:34:43 +02:00 |
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4aa772c405
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ecotag: Added list of taxids for all best matches (closes #80)
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2020-06-09 14:33:14 +02:00 |
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687e42ad22
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C: kmer alignment: fixed a bug where scores of 0 were at
(0+kmer_length-1) (and now setting alignment direction to None if score
is 0
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2020-06-05 16:09:33 +02:00 |
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aec5e69f2c
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C, views: no more automatic COUNT column if MERGED_sample column exists
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2020-05-07 17:08:07 +02:00 |
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e6b6c6fa84
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AVLs: Made an error message more informative
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2020-04-29 10:14:04 +02:00 |
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974528b2e6
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build_ref_db: fixed bug erasing some of the higher LCAs (i.e. lowest
similarities)
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2020-04-28 15:56:06 +02:00 |
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1b346b54f9
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ecotag: better specificity by now correctly looking for similarities
within refs above best score instead of ecotag threshold
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2020-04-28 15:10:07 +02:00 |
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058f2ad8b3
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ecopcr: fixed a bug where sequences were considered circular (generating
false positives)
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2020-04-27 14:44:35 +02:00 |
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67bdee105a
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C: build_ref_db: added progress display for each step
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2020-04-18 14:24:08 +02:00 |
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0f745e0113
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C: Columns: optimizing column file growth
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2020-04-18 13:55:47 +02:00 |
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4d36538c6e
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C: SSE lcs alignment: band-aid for memory bug I don't understand
(triggered on specific db on ubuntu)
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2020-04-17 15:07:52 +02:00 |
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343999a627
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Taxonomy: fixed a critical memory bug when building the list of merged
taxids
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2020-04-15 17:46:13 +02:00 |
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e9a40630e9
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C: Columns: rounding column growth to ceil to avoid looping on small
values
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2020-04-13 19:02:10 +02:00 |
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8dbcd3025a
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C: Columns: reduced column growth factor from 2 to 1.3 to avoid errno28
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2020-04-13 14:47:56 +02:00 |
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b6ab792ceb
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C: made error message more detailed when checking that sequences and
qualities match
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2020-04-12 17:40:24 +02:00 |
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e62c991bbc
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goes with previous commit
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2020-04-10 11:22:26 +02:00 |
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1218eed7fd
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ecopcr: now printing a warning instead of interrupting with an error
when a taxid is not found
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2020-04-10 11:22:04 +02:00 |
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98cfb70d73
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ecopcr: made some errors more informative
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2020-04-09 09:15:28 +02:00 |
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b9f68c76c8
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ecopcr: added warnings and check of primer length (related to #75)
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2020-04-05 18:40:56 +02:00 |
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d32cfdcce5
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ecotag: fixed the generated column comments formatting that would
generate errors
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2020-02-12 14:23:17 +01:00 |
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1bfb96023c
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obi import: rewriting a column now deletes the old one to save disk
space
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2020-02-01 15:31:14 +01:00 |
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d0c21ecd39
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Removed an OpenMP clause that was not obligatory and triggered a known
gcc bug involving macros
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2020-01-24 16:00:53 +01:00 |
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b4b2e62195
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Cleaner handling of reverse quality columns
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2020-01-18 19:28:12 +01:00 |
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5c9091e9eb
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C: closing DMS after cleaning it instead of counting on upper layer
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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
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2020-01-06 15:11:31 +01:00 |
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6c018b403c
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ecopcr: fixed and improved the options to keep nuclotides around the
amplicon
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2019-12-26 20:45:54 +01:00 |
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3b3cf9359d
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CMake: unset gcc for nix
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2019-09-26 21:04:42 +02:00 |
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6282242a04
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C: Views: fixed a bug when trying to add a comment after changing the
file name of a finished view
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2019-09-25 11:39:32 +02:00 |
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44517db51f
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Fixed gcc warnings
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2019-09-25 11:38:00 +02:00 |
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ec0737a600
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Added signal catching and handling in C and Cython
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2019-09-21 16:47:22 +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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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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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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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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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 |
|
