This directory contains a portion of a .pileup file generated from 
    samtools pileup

After compilation, the command 

    BSNP -i 09.pileup -o 09.SNP -on 09.nSNP -os 09.SUM -v 1


Should rapidly (<1 second) produce the response

    All Done
    
and should produce the three names output files. In case there is any
problem, compressed versions of the expected output files are provided.

In the bash command interpreter for Linux, the compressed input file
can be used directly via the command:

    BSNP -i <( bzcat 09.pileup.bz2) -o 09.SNP -on 09.nSNP -os 09.SUM -v 1
    
Similarly, output might be redirected using:

    BSNP -i <( bzcat 09.pileup.bz2) -o >( bzip2 --best > 09.SNP.bz2) -on >( bzip2 --best > 09.nSNP.bz2) -os 09.SUM -v 1


-- Brad
2012-05-17
