obitools3

_sse.h

First version of alignment functions (imported from suma* programs)

2016-05-11 16:36:23 +02:00

bloom.c

Commented #ifdef directive for detect_bucket_size function because it

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

bloom.h

Documented changes made in bloom functions

2016-04-21 11:22:31 +02:00

char_str_indexer.c

Major update: New column type to store sequence qualities. Closes #41

2016-05-20 16:45:22 +02:00

char_str_indexer.h

Major update: New column type to store sequence qualities. Closes #41

2016-05-20 16:45:22 +02:00

crc64.c

Fixed minor warning

2016-03-25 16:11:52 +01:00

crc64.h

Short doc for crc function

2016-04-21 13:23:52 +02:00

dna_seq_indexer.c

Major update: New column type to store sequence qualities. Closes #41

2016-05-20 16:45:22 +02:00

dna_seq_indexer.h

Documentation for DNA sequence indexing functions

2016-04-21 13:36:51 +02:00

encode.c

Replaced malloc+memset with calloc

2016-04-21 13:45:39 +02:00

encode.h

Updated encode functions documentation

2016-04-21 13:46:02 +02:00

hashtable.c

Major update: Column aliases. Columns are now identified in the context

2016-08-01 18:25:30 +02:00

hashtable.h

Major update: Column aliases. Columns are now identified in the context

2016-08-01 18:25:30 +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_align.c

Embryo of code for openMP parallelization of LCS alignment but

2016-12-20 11:46:58 +01:00

obi_align.h

Embryo of code for openMP parallelization of LCS alignment but

2016-12-20 11:46:58 +01:00

obiavl.c

Fixed major bug when cloning an AVL where the bloom filter was not

2016-09-15 11:47:02 +02:00

obiavl.h

Changed file name limits to adapt to system limits + minor changes

2016-09-22 18:05:07 +02:00

obiblob_indexer.c

Changed the inline functions syntax, which should make it compatible

2016-11-18 16:21:26 +01:00

obiblob_indexer.h

Changed the inline functions syntax, which should make it compatible

2016-11-18 16:21:26 +01:00

obiblob.c

Finished moving obiblob functions to obiblob files and documentation for

2016-04-21 15:18:14 +02:00

obiblob.h

Major update: New column type to store sequence qualities. Closes #41

2016-05-20 16:45:22 +02:00

obidebug.h

Doxygen documentation corrected and completed.

2015-09-30 12:03:46 +02:00

obidms_taxonomy.c

Taxonomy: functions to read the *.adx file (containing the deprecated

2017-01-06 15:52:21 +01:00

obidms_taxonomy.h

Taxonomy: functions to read the *.adx file (containing the deprecated

2017-01-06 15:52:21 +01:00

obidms.c

Added C functions to write .rdx, .tdx, .ndx binary taxonomy files from a

2016-10-14 17:03:10 +02:00

obidms.h

Added C functions to write .rdx, .tdx, .ndx binary taxonomy files from a

2016-10-14 17:03:10 +02:00

obidmscolumn_blob.c

Functions to get obiblobs through views

2016-11-18 15:59:50 +01:00

obidmscolumn_blob.h

Functions to get obiblobs through views

2016-11-18 15:59:50 +01:00

obidmscolumn_bool.c

Removed unused inclusions and definitions in all column types code

2016-04-22 15:50:19 +02:00

obidmscolumn_bool.h

Refactored and relocated the set and get functions of all column types,

2016-04-13 15:10:24 +02:00

obidmscolumn_char.c

Removed unused inclusions and definitions in all column types code

2016-04-22 15:50:19 +02:00

obidmscolumn_char.h

Refactored and relocated the set and get functions of all column types,

2016-04-13 15:10:24 +02:00

obidmscolumn_float.c

Removed unused inclusions and definitions in all column types code

2016-04-22 15:50:19 +02:00

obidmscolumn_float.h

Refactored and relocated the set and get functions of all column types,

2016-04-13 15:10:24 +02:00

obidmscolumn_idx.c

Finished adding all the functions to directly set and get indices in

2016-11-30 11:08:11 +01:00

obidmscolumn_idx.h

Finished adding all the functions to directly set and get indices in

2016-11-30 11:08:11 +01:00

obidmscolumn_int.c

Removed unused inclusions and definitions in all column types code

2016-04-22 15:50:19 +02:00

obidmscolumn_int.h

Fixed error in documentation

2016-11-28 10:55:23 +01:00

obidmscolumn_qual.c

Some comments updated

2016-06-16 11:26:54 +02:00

obidmscolumn_qual.h

Read-only AVLs are now hard-linked instead of copied when cloning an AVL

2016-06-03 19:02:46 +02:00

obidmscolumn_seq.c

Goes with 8f724f4f, forgotten file

2016-11-10 14:48:31 +01:00

obidmscolumn_seq.h

Updated the documentation for OBI_SEQ columns

2016-04-22 15:58:20 +02:00

obidmscolumn_str.c

Some code refactoring

2016-11-09 16:48:00 +01:00

obidmscolumn_str.h

Updated the documentation for OBI_STR columns

2016-04-22 15:59:32 +02:00

obidmscolumn.c

Goes with 5e0c9f87 (missing ';' and fixed compilation warnings)

2016-12-05 11:18:29 +01:00

obidmscolumn.h

Goes with 5e0c9f87 (missing ';' and fixed compilation warnings)

2016-12-05 11:18:29 +01:00

obidmscolumndir.c

Moved the functions getting full paths for files and directories to

2016-04-15 11:11:13 +02:00

obidmscolumndir.h

Comments in column headers are now working.

2015-11-10 10:56:45 +01:00

obierrno.c

closes #13 , obi_errno is initialized to 0

2015-10-02 13:46:34 +02:00

obierrno.h

Fixed typo

2016-09-05 12:31:06 +02:00

obilittlebigman.c

Doxygen documentation corrected and completed.

2015-09-30 12:03:46 +02:00

obilittlebigman.h

Doxygen documentation corrected and completed.

2015-09-30 12:03:46 +02:00

obitypes.c

First version of quality handling (not working yet) and now it is

2016-05-11 16:38:14 +02:00

obitypes.h

Goes with a0ebc2d8

2016-11-10 15:01:29 +01:00

obiview.c

Goes with 5e0c9f87 (missing ';' and fixed compilation warnings)

2016-12-05 11:18:29 +01:00

obiview.h

Goes with 5e0c9f87 (missing ';' and fixed compilation warnings)

2016-12-05 11:18:29 +01:00

sse_banded_LCS_alignment.c

LCS alignment: it is now checked that sequences are not longer than what

2016-12-22 17:06:23 +01:00

sse_banded_LCS_alignment.h

LCS alignment: documentation for all the lowest level functions

2016-12-22 17:03:51 +01:00

uint8_indexer.c

Major update: New column type to store sequence qualities. Closes #41

2016-05-20 16:45:22 +02:00

uint8_indexer.h

Major update: New column type to store sequence qualities. Closes #41

2016-05-20 16:45:22 +02:00

upperband.c

Added function to build kmer table for 2 columns, and fixed bug (with

2016-12-16 19:10:18 +01:00

upperband.h

Added function to build kmer table for 2 columns, and fixed bug (with

2016-12-16 19:10:18 +01:00

utils.c

Added a missing closedir

2016-09-15 11:58:34 +02:00

utils.h

First version of alignment functions (imported from suma* programs)

2016-05-11 16:36:23 +02:00