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ChangeLog
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101 lines (74 loc) · 3.71 KB
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2021-12-24 Benjamin Jean-Marie Tremblay <benjmtremblay@gmail.com>
* Transplanted markov shuffling code from bjmt/universalmotif, fixes #3
2021-10-15 Benjamin Jean-Marie Tremblay <benjmtremblay@gmail.com>
* Added '-n' option to shuffler to repeat shuffling
* shuffler version bumped to 1.4
2021-10-08 Benjamin Jean-Marie Tremblay <benjmtremblay@gmail.com>
* Fixed a couple compilation warnings and errors specific to g++
2019-05-04 Benjamin Jean-Marie Tremblay <benjmtremblay@gmail.com>
* use more pass by reference
* changed vector<char> letters --> string letters
* converted a lot of int variables to long
* faster char to int conversion in klets.cpp
* countlets is much faster when providing alphabet (using unordered_map)
* countlets version bumped to 1.3
* replaced all instances of endl with \n
* countfa version bumped to 1.2
* countwin version bumped to 1.1
* seqgen version bumped to 1.3
* shuffler version bumped to 1.3
2019-05-04 Benjamin Jean-Marie Tremblay <benjmtremblay@gmail.com>
* Don't bother and try to fill edges of unconnected vertices (shuffle_euler)
* Use unsigned int when not expecting negative values, size_t for sizes
* Added some internal benchmark code
2019-05-03 Benjamin Jean-Marie Tremblay <benjmtremblay@gmail.com>
* Removed default entries from getopt switch
* shuffler (euler) no longer calls make_klets(), making it faster and more
memory efficient at higher k
* shuffler version bumped to 1.2
* replaced all instances of count_klets() with count_klets2(), which does not
require a vector<string> of the actual klets to do counting
* K-lets with zero counts can be ommitted from countlets output
* faster countlets counting from a stream using map<string, int>
* countlets version bumped to 1.2
* seqgen no longer requires commas to separate alphabets made of single-char
letters
* seqgen version bumped to 1.2
2019-05-02 Benjamin Jean-Marie Tremblay <benjmtremblay@gmail.com>
* Made -h flag mandatory to see usage
2019-04-30 Benjamin Jean-Marie Tremblay <benjmtremblay@gmail.com>
* countwin v1.0 added
2019-04-27 Benjamin Jean-Marie Tremblay <benjmtremblay@gmail.com>
* Added .reserve() to a few variables
* seqgen streams new letters directly to output, not keeping entire new
sequence in memory
* seqgen version bumped to v1.1
* Dropped -p option for countlets
* countlets has a new -a option, allowing to specify alphabet to prevent
loading entire sequence into memory (at the cost of speed for higher k)
* countlets version bumped to v1.1
* countfa now reads one char at a time, version bumped to v1.1
2019-04-26 Benjamin Jean-Marie Tremblay <benjmtremblay@gmail.com>
* Added countfa v1.0
* shuffler -f now inserts newlines every 80 characters
* Streamlined shuffler internals: sequences in fasta files are loaded,
shuffled and output one at a time instead of keeping the entire file in
memory
* shuffler version bumped to v1.1
2019-04-25 Benjamin Jean-Marie Tremblay <benjmtremblay@gmail.com>
* Added seqgen v1.0
2019-04-24 Benjamin Jean-Marie Tremblay <benjmtremblay@gmail.com>
* countlets and shuffler are now v1.0
* New default shuffling method: euler
* The linear shuffling method can still be used with -l flag
* countlets can show progress with -p flag
* Rewrote count_klets() internals, much faster now
* shuffler can work on fasta-formatted input with -f flag
2019-04-20 Benjamin Jean-Marie Tremblay <benjmtremblay@gmail.com>
* For markov shuffling method verbose mode: instead of showing k-let counts,
shows before and after counts of individual letters
* make_klets() and count_klets() have been moved to klets.cpp
* Changed exit behaviour for requesting usage
* Count numbers are printed right aligned
2019-04-19 Benjamin Jean-Marie Tremblay <benjmtremblay@gmail.com>
* Initial release