#Filtering with Gapped q-Grams

##Synopsis Approximate string matching which compares q-grams (substrings of length q) and text is well-studied and very popular. However, as shown in paper written by Burkhardt S. and Kärkkäinen J. gapped q-grams can provide more efficient filtering. Main objective of this project is, based on mentioned paper, calculating filter parameter called optimal threshold.

##Motivation Project is created as assignment within the course Bioinformatics on Faculty of Electrical Engineering and Computing, University of Zagreb.

##Installation Compile the source files by running make or compile.sh from main directory in root directory of project.

##Usage Depending on parameters sent in program different data is shown. If inputs are size of shape Q (q) and distance (k) then optimal threshold is calculated for span (s) varying from q up to 50-k with string length (m) of 50. For this option available distance (k) values are 4 and 5. Alternatively, except for q and k, it is possible to define both s and m. With these 4 parameters their optimal threshold is calculated.

###Run program with: run script run.sh with 2 or 4 arguments as mentioned before.

###Example

Run with 4 arguments: run.sh m k q s

command: run.sh 50 5 3 5
output: 
31	#--##

Run with 2 arguments: run.sh k q

command: run.sh 4 5
output: 
s: 5 threshold: 26 satisfied: 1 for shape: #####
s: 6 threshold: 25 satisfied: 1 for shape: #-####
s: 7 threshold: 24 satisfied: 1 for shape: #--####
s: 8 threshold: 23 satisfied: 1 for shape: #---####
s: 9 threshold: 22 satisfied: 1 for shape: #----####
s: 10 threshold: 21 satisfied: 1 for shape: #-----####
s: 11 threshold: 20 satisfied: 1 for shape: #------####
s: 12 threshold: 20 satisfied: 1 for shape: #--##----#-#
s: 13 threshold: 19 satisfied: 1 for shape: #----##-#---#
s: 14 threshold: 18 satisfied: 1 for shape: #------#-#--##
s: 15 threshold: 17 satisfied: 1 for shape: #--------#--###
s: 16 threshold: 16 satisfied: 1 for shape: #--------#--##-#
s: 17 threshold: 16 satisfied: 1 for shape: #-----#-----#-#-#
s: 18 threshold: 15 satisfied: 1 for shape: #-------#-##-----#
s: 19 threshold: 14 satisfied: 1 for shape: #-----------#-#--##
s: 20 threshold: 13 satisfied: 1 for shape: #-------------#--###
s: 21 threshold: 12 satisfied: 1 for shape: #---------------#-###
... 

Contributing

1. Fork it!
2. Create your feature branch: git checkout -b my-new-feature
3. Commit your changes: git commit -am 'Add some feature'
4. Push to the branch: git push origin my-new-feature
5. Submit a pull request

##License

The MIT License (MIT)

Copyright (c) 2016 Antun Flaš, Manuela Kajkara, Marija Kaselj

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.