obitools3

libecoPCR

Fixed gcc warnings

2019-09-25 11:38:00 +02:00

libjson

C: Json comments: added an obi_read_comment function to read one value

2019-08-31 18:28:51 +02:00

_sse.h

Weird buggy Eclipse commit with nothing changed

2018-10-21 17:35:18 +02:00

.gitignore

alignpairedend and ngsfilter: ids of original sequences are now kept

2022-09-21 11:32:19 +12:00

array_indexer.c

C: fixed remaining memory bug in array indexer

2019-09-01 17:24:57 +02:00

array_indexer.h

Weird buggy Eclipse commit with nothing changed

2018-10-21 17:35:18 +02:00

bloom.c

Commented #ifdef directive for detect_bucket_size function because it

2016-04-27 10:24:40 +02:00

bloom.h

Updated prototypes with no arguments with a void argument as suggested

2018-10-17 12:00:40 +02:00

build_reference_db.c

small fixes and improvements

2021-11-11 15:26:09 +13:00

build_reference_db.h

C: build_ref_db: now adds a comment with the threshold used to build the

2019-08-31 18:29:40 +02:00

char_str_indexer.c

Weird buggy Eclipse commit with nothing changed

2018-10-21 17:35:18 +02:00

char_str_indexer.h

Weird buggy Eclipse commit with nothing changed

2018-10-21 17:35:18 +02:00

CMakeLists.txt

CMake: unset gcc for nix

2019-09-26 21:04:42 +02:00

crc64.c

Weird buggy Eclipse commit with nothing changed

2018-10-21 17:35:18 +02:00

crc64.h

Weird buggy Eclipse commit with nothing changed

2018-10-21 17:35:18 +02:00

dna_seq_indexer.c

minor fixes and comments

2018-11-19 11:23:54 +01:00

dna_seq_indexer.h

Weird buggy Eclipse commit with nothing changed

2018-10-21 17:35:18 +02:00

encode.c

Now handling sequences with Uracil (U) nucleotides by converting to

2020-10-30 10:46:17 +01:00

encode.h

Now handling sequences with Uracil (U) nucleotides by converting to

2020-10-30 10:46:17 +01:00

hashtable.c

Weird buggy Eclipse commit with nothing changed

2018-10-21 17:35:18 +02:00

hashtable.h

Weird buggy Eclipse commit with nothing changed

2018-10-21 17:35:18 +02:00

kmer_similarity.c

alignpairedend: fixed bug that would cut out sequence ends when it

2021-04-07 10:31:12 +12:00

kmer_similarity.h

alignpairedend: improved/fixed the output tags for the alignment score

2020-07-13 15:59:50 +02:00

linked_list.c

Weird buggy Eclipse commit with nothing changed

2018-10-21 17:35:18 +02:00

linked_list.h

Weird buggy Eclipse commit with nothing changed

2018-10-21 17:35:18 +02:00

murmurhash2.c

Renamed MurmurHash2.c file to murmurhash2.c as it could be a problem

2016-04-26 14:29:17 +02:00

murmurhash2.h

Little annotations for the murmur hash function.

2016-04-21 13:53:29 +02:00

obi_clean.c

Made the OBITools3 more 'empty file friendly'

2021-03-15 16:25:41 +13:00

obi_clean.h

obi clean: fixed a memory bug, fixed the behaviour when no sample info,

2020-07-01 18:17:47 +02:00

obi_ecopcr.c

ecopcr: now accepting taxonomy from a different DMS than the reference

2021-08-05 11:28:57 +12:00

obi_ecopcr.h

ecopcr: now accepting taxonomy from a different DMS than the reference

2021-08-05 11:28:57 +12:00

obi_ecotag.c

ecotag: BEST_MATCH_TAXIDS now dereplicated (no repeated taxids in the

2021-05-10 16:02:06 +12:00

obi_ecotag.h

ecotag: added separate threshold for minimum circle identity (and switch

2020-09-25 16:22:09 +02:00

obi_lcs.c

Now handling dictionaries with one key

2021-03-10 16:50:30 +13:00

obi_lcs.h

C obi_lcs: updated deprecated column names and associated comments

2018-12-09 19:17:13 +01:00

obiavl.c

C: now completely unmapping files before truncating them to a smaller

2021-03-11 15:12:40 +13:00

obiavl.h

C: optimized dir opening

2019-08-29 16:35:10 +02:00

obiblob_indexer.c

Weird buggy Eclipse commit with nothing changed

2018-10-21 17:35:18 +02:00

obiblob_indexer.h

Weird buggy Eclipse commit with nothing changed

2018-10-21 17:35:18 +02:00

obiblob.c

Weird buggy Eclipse commit with nothing changed

2018-10-21 17:35:18 +02:00

obiblob.h

Weird buggy Eclipse commit with nothing changed

2018-10-21 17:35:18 +02:00

obidebug.h

Weird buggy Eclipse commit with nothing changed

2018-10-21 17:35:18 +02:00

obidms_taxonomy.c

Improved taxonomy reading information display

2021-07-21 15:20:44 +12:00

obidms_taxonomy.h

C: taxonomy: fixed a bug where some taxa would not be stored in the

2021-03-29 09:02:18 +13:00

obidms.c

C: fixed the printing of view informations from a DMS (fixes #114 )

2021-08-05 11:31:24 +12:00

obidms.h

C: Made maximum file path length 2048 instead of 1024

2021-03-11 15:23:22 +13:00

obidmscolumn_array.c

Fixed a bug in the array indexer where the value's length was no

2018-11-27 16:18:34 +01:00

obidmscolumn_array.h

Weird buggy Eclipse commit with nothing changed

2018-10-21 17:35:18 +02:00

obidmscolumn_blob.c

Weird buggy Eclipse commit with nothing changed

2018-10-21 17:35:18 +02:00

obidmscolumn_blob.h

Weird buggy Eclipse commit with nothing changed

2018-10-21 17:35:18 +02:00

obidmscolumn_bool.c

Weird buggy Eclipse commit with nothing changed

2018-10-21 17:35:18 +02:00

obidmscolumn_bool.h

Weird buggy Eclipse commit with nothing changed

2018-10-21 17:35:18 +02:00

obidmscolumn_char.c

Weird buggy Eclipse commit with nothing changed

2018-10-21 17:35:18 +02:00

obidmscolumn_char.h

Weird buggy Eclipse commit with nothing changed

2018-10-21 17:35:18 +02:00

obidmscolumn_float.c

Weird buggy Eclipse commit with nothing changed

2018-10-21 17:35:18 +02:00

obidmscolumn_float.h

Weird buggy Eclipse commit with nothing changed

2018-10-21 17:35:18 +02:00

obidmscolumn_idx.c

Weird buggy Eclipse commit with nothing changed

2018-10-21 17:35:18 +02:00

obidmscolumn_idx.h

Weird buggy Eclipse commit with nothing changed

2018-10-21 17:35:18 +02:00

obidmscolumn_int.c

Weird buggy Eclipse commit with nothing changed

2018-10-21 17:35:18 +02:00

obidmscolumn_int.h

Weird buggy Eclipse commit with nothing changed

2018-10-21 17:35:18 +02:00

obidmscolumn_qual.c

Weird buggy Eclipse commit with nothing changed

2018-10-21 17:35:18 +02:00

obidmscolumn_qual.h

Weird buggy Eclipse commit with nothing changed

2018-10-21 17:35:18 +02:00

obidmscolumn_seq.c

Weird buggy Eclipse commit with nothing changed

2018-10-21 17:35:18 +02:00

obidmscolumn_seq.h

Weird buggy Eclipse commit with nothing changed

2018-10-21 17:35:18 +02:00

obidmscolumn_str.c

Weird buggy Eclipse commit with nothing changed

2018-10-21 17:35:18 +02:00

obidmscolumn_str.h

Weird buggy Eclipse commit with nothing changed

2018-10-21 17:35:18 +02:00

obidmscolumn.c

C: now completely unmapping files before truncating them to a smaller

2021-03-11 15:12:40 +13:00

obidmscolumn.h

Increased maximum line count to 10E12

2021-05-31 17:00:55 +12:00

obidmscolumndir.c

C: fixed a bug when opening or creating a new column directory where the

2019-09-04 13:16:28 +02:00

obidmscolumndir.h

C: made it so column DIR* are not kept open to handle very large DMS

2019-09-04 12:55:21 +02:00

obierrno.c

Weird buggy Eclipse commit with nothing changed

2018-10-21 17:35:18 +02:00

obierrno.h

Added signal catching and handling in C and Cython

2019-09-21 16:47:22 +02:00

obilittlebigman.c

Weird buggy Eclipse commit with nothing changed

2018-10-21 17:35:18 +02:00

obilittlebigman.h

Weird buggy Eclipse commit with nothing changed

2018-10-21 17:35:18 +02:00

obisig.c

Added signal catching and handling in C and Cython

2019-09-21 16:47:22 +02:00

obisig.h

Adds an extern qualifier to the keep_running declaration.

2021-02-05 15:59:43 +01:00

obitypes.c

Weird buggy Eclipse commit with nothing changed

2018-10-21 17:35:18 +02:00

obitypes.h

import: Columns are now rewritten in OBI_FLOAT if a value is > INT32_MAX

2021-03-29 09:00:52 +13:00

obiview.c

C: views: now correctly parses view names containing '.' when cleaning

2021-09-08 10:52:42 +12:00

obiview.h

Now handling dictionaries with one key

2021-03-10 16:50:30 +13:00

sse_banded_LCS_alignment.c

C: SSE lcs alignment: band-aid for memory bug I don't understand

2020-04-17 15:07:52 +02:00

sse_banded_LCS_alignment.h

Weird buggy Eclipse commit with nothing changed

2018-10-21 17:35:18 +02:00

uint8_indexer.c

Weird buggy Eclipse commit with nothing changed

2018-10-21 17:35:18 +02:00

uint8_indexer.h

Weird buggy Eclipse commit with nothing changed

2018-10-21 17:35:18 +02:00

upperband.c

updated a comment

2019-07-23 19:03:24 +02:00

upperband.h

Weird buggy Eclipse commit with nothing changed

2018-10-21 17:35:18 +02:00

utils.c

C: optimized dir opening

2019-08-29 16:35:10 +02:00

utils.h

Weird buggy Eclipse commit with nothing changed

2018-10-21 17:35:18 +02:00