covi

The Compressed Overlap Index Data Structure (or covi) implementation.

This implementation creates an index for all the overlaps of a given set of words. The set of words must be given as a single input file containing all the words separated by a unique symbol choose by the user.

Compile

To be able to compile the covi codes:

• Install sdsl-lite. Follow the installation guide here: (https://github.com/simongog/sdsl-lite)
• Modify the location of the sdsl library in the CMakeLists.txt if necessary.
• Create the build folder and run:
  • cmake ..
  • make

Methods

-[CreateCOvI]:

Use: ./CreateCOvI <file_name> <opt>
  		<file_name>: Name of the file to be use to create the required data structure 
      	<opt>: 
		-o output_name:  String containing the name of the output file. Default file_name.covi
		-s separator:  (ASCII) Value used as separator between words. Default separator = 0
		-w Index_type. Default = 0
		  |  Index_type
		---+--------------------
		0 | COvI (Compressed Overlap Index)
    		1 | fullAC (Aho-Corasick)

      	output:  covi/fullAC file

	Example: ./CreateCOvI ./data/file -o file.covi -s 10 -w 0
	output:  file.covi  or file.fullac

-[TestOperations]:

Use: ./TestOperations <index_file_name> -w type

	output: Displays times per operation in the output

	Example: ./TestOperations file.covi  -w 0
	output:
		Max-ov(x,y) Time: 5.232 microsec
		Correlation(x,y) Time: 5.212 microsec
		all_right_overlaps(x) Time: 327.2 millis
		all_left_overlaps(x) Time: 615.8 millis
		global_max_ovelap() Time: 2841 millis

Note: These codes assume that the computer have enough RAM memory to create the Trie of the set of words