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SRmapper 0.1.2
copyright owned by the University of Missouri-Saint Louis
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SRmapper 0.1.0 is distributed with three programs:
  buildindex: making an index for a genome
  align: aligning short reads to a reference genome
  makereads: preparing simulated short reads from a genome

Compile these programs by:
g++ -o buildindex buildindex.cpp
g++ -o align align.cpp 
g++ -o makereads makereads.cpp

After compiling, set up your environment so that buildindex, 
align, and makereads can be located at run time.


Two bacterial genomes for different strains of tuberculosis 
( H37Rv.fa and F11.fa ) have been included to provide a means to run 
short tests on SRmapper.  One method of testing SRmapper would be to 
align reads from one genome (F11) to the other (H37Rv).  This can be 
done as follows:

buildindex { H37Rv.fa } H37Rv.sqn 
#builds the SRmapper index for H37Rv which will be used as the reference 
#genome for assembly.

makereads F11.fa F11 30
#creates a file containing simulated reads from F11.fa.They are 30bp long 
#and uniformly distributed with a sequence depth of 30x.  The third argument
#can be changed to change read length to produce a uniform sequence depth of
#argv[3]x.

align H37Rv.sqn { F11.fastq } alignment.sam -q 6 
#aligns the simulated reads from the genome F11.

The indexing step takes ~2sec of computer time on an Intel Xeon 2.8GHz processor.  
Real time varies depending on computer usage load. Making the reads from F11 takes 
~3.5sec of computer time on the same processor with real time varying per above note.
The alignment step requires ~81sec of computer time.  Slignly over 99.7% of the 
reference genome, H37Rv, is covered by reads from F11.
