Started editing Intro section
Replaced LIBDIR with LDFLAGS
File added
Made executable.  Added use Getopt::Long;
Removed the second output file (tab-delimted read table file), as we don't use it in practice
R script to get upper quantil of mapping distance for CNV clustering
Lots of hacking--main alignment commands are there now
Added more doc on compilation and introduced the master script
initial draft completed
Added how to copy exectuables into ~/bin
Fixed OUTFILE when I meant OUTDIR error
Changed check on argv < 7 to argv < 6 to account for diff no. of arguments
Added missing argument (orig. fastq file name) to command line for fastq_to_table
added missing ; to find command
Added use of ForkManager to parallelize serial steps
Documenting use of pecnv.pl
This script gets the reference genome ready.
Documented processRef.pl
Documented output
Fixed formatting issue