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

Add some .ignore files

2019-03-29 15:52:54 +01:00

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

Added signal catching and handling in C and Cython

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

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

C: Added a function to get a nucleotide at a specific index in an

2019-01-21 17:18:02 +01:00

encode.h

C: Added a function to get a nucleotide at a specific index in an

2019-01-21 17:18:02 +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

ngsfilter and alignpairedend: paired-end reads are now correctly

2019-07-23 18:56:51 +02:00

kmer_similarity.h

fixed a comment

2019-09-10 14:42:12 +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

Removed an OpenMP clause that was not obligatory and triggered a known

2020-01-24 16:00:53 +01:00

obi_clean.h

obiclean parallelized

2019-06-20 19:44:04 +02:00

obi_ecopcr.c

ecopcr: fixed and improved the options to keep nuclotides around the

2019-12-26 20:45:54 +01:00

obi_ecopcr.h

ecopcr: fixed and improved the options to keep nuclotides around the

2019-12-26 20:45:54 +01:00

obi_ecotag.c

Added signal catching and handling in C and Cython

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

obi_ecotag.h

New command and C functions: obi ecotag

2018-12-09 19:19:32 +01:00

obi_lcs.c

Fixed gcc warnings

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

obi_lcs.h

C obi_lcs: updated deprecated column names and associated comments

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

obiavl.c

C: optimized dir opening

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

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

Fixed gcc warnings

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

obidms_taxonomy.h

C, taxonomy: new function to get the lowest common ancestor of two taxa

2018-11-27 16:00:29 +01:00

obidms.c

C: closing DMS after cleaning it instead of counting on upper layer

2020-01-18 17:27:35 +01:00

obidms.h

DMS are now locked when used by a command. Added checks and changed

2019-09-20 20:37:19 +02:00

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

Fixed gcc warnings

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

obidmscolumn.h

DMS are now locked when used by a command. Added checks and changed

2019-09-20 20:37:19 +02:00

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

Added signal catching and handling in C and Cython

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

obitypes.c

Weird buggy Eclipse commit with nothing changed

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

obitypes.h

C: Changed obibool definitions because of conflict with R

2020-01-06 15:11:31 +01:00

obiview.c

C: Views: fixed a bug when trying to add a comment after changing the

2019-09-25 11:39:32 +02:00

obiview.h

Cleaner handling of reverse quality columns

2020-01-18 19:28:12 +01:00

sse_banded_LCS_alignment.c

C: Changed obibool definitions because of conflict with R

2020-01-06 15:11:31 +01:00

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