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791ccfb92e
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Fixed include bug in previous version and switch to version 3.0.1b24
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2023-05-15 11:35:42 +12:00 |
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1c9a906f5b
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ngsfilter and ecopcr: now check for primers too long for apat library to
handle (31bp max) and switch to version 3.0.1b23
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2023-05-12 17:04:21 +12:00 |
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2130a949c7
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New command: obi taxonomy to add local taxa (closes #64)
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2023-02-13 10:59:20 +13:00 |
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02e9df3ad1
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alignpairedend and ngsfilter: ids of original sequences are now kept
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2022-09-21 11:32:19 +12:00 |
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53b3d81137
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small fixes and improvements
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2021-11-11 15:26:09 +13:00 |
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58b42cd977
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C: views: now correctly parses view names containing '.' when cleaning
unfinished views. Closes #115
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2021-09-08 10:52:42 +12:00 |
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f10e78ba3c
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C: fixed the printing of view informations from a DMS (fixes #114)
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2021-08-05 11:31:24 +12:00 |
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89168271ef
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ecopcr: now accepting taxonomy from a different DMS than the reference
sequences
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2021-08-05 11:28:57 +12:00 |
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747f3efbb2
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Improved taxonomy reading information display
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2021-07-21 15:20:44 +12:00 |
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6ff29c6a6a
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Increased maximum line count to 10E12
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2021-05-31 17:00:55 +12:00 |
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51a3c68fb5
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C: build_reference_db: fixed gcc warning/error
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2021-05-31 16:59:17 +12:00 |
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cb53381863
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ecotag: BEST_MATCH_TAXIDS now dereplicated (no repeated taxids in the
list) and switch to version 3.0.1b8
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2021-05-10 16:02:06 +12:00 |
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238e9f70f3
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alignpairedend: fixed bug that would cut out sequence ends when it
should not have
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2021-04-07 10:31:12 +12:00 |
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f5413381fd
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C: taxonomy: fixed a bug where some taxa would not be stored in the
merged index
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2021-03-29 09:02:18 +13:00 |
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3e93cfff7b
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import: Columns are now rewritten in OBI_FLOAT if a value is > INT32_MAX
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2021-03-29 09:00:52 +13:00 |
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425fe25bd2
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Made the OBITools3 more 'empty file friendly'
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2021-03-15 16:25:41 +13:00 |
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38f42cb0fb
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C: Made maximum file path length 2048 instead of 1024
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2021-03-11 15:23:22 +13:00 |
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7f0f63cf26
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C: now completely unmapping files before truncating them to a smaller
size (#68)
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2021-03-11 15:12:40 +13:00 |
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ad1fd3c341
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Now handling dictionaries with one key
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2021-03-10 16:50:30 +13:00 |
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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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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
|
2020-04-09 09:15:28 +02:00 |
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