// Guidelines to run OnlineCall //

Compile OnlineCall.c using the following command:

gcc OnlineCall.c  -o OnlineCall -L/usr/lib -llapack -lblas -I/usr/include/atlas

Notes: You must have LAPACK and BLAS in /usr/lib and ATLAS in /usr/include. Change the paths to these if necessary.



Running OnlineCall

Use the command :

./OnlineCall source_file1 destination_file1 source_file2 destination_file2 ....

eg.

./OnlineCall /home/local/altair/phix174_76cycle/s_4_0080_int.txt /home/local/altair/OnlineCall/s_4_0080.fastq



source_file1 must be an Illumina intensity .txt file. Make sure the path is specified.
destination file1 is the output .fastq for source_file1.