This contains source code for a program, linearSat, that is part of a system to produce locally
ordered sequence for centromeres and other highly repetitious "satellite" DNA sequences.  To
make this simply type "make" in this directory.  The executable will be in the linearSat/linearSat
file.

The source code is in three directories.  The inc and lib directories contain a subset of the
public domain UCSC Genome Bioinformatics group libraries,  just enough to support the main program
in the linearSat directory.

The linearSat program takes two input files and produces a single output.  There are sample input file
included in the test portion of this directory. Here is a summary of the usage of the program,  a 
summary which also appears when you run the program from the command line
with no parameters:

linearSat - create a linear projection of satellite arrays using the probablistic model
of HuRef satellite graphs based on Sanger style reads.
usage:
   linearSat monomerFile.txt monomerOrder.txt output.txt
Where monomerFile is a list of reads with monomers parsed out, one read per
line, with the first word in the line being the read id and subsequent words the monomers
within the read. The monomerOrder.txt has one line per major monomer type with a word for
each variant. The lines are in the same order the monomers appear, with the last line
being followed in order by the first since they repeat.   The output.txt contains one line
for each monomer in the output, just containing the monomer symbol.
options:
   -size=N - Set max chain size, default 3
   -fullOnly - Only output chains of size above
   -chain=fileName - Write out word chain to file
   -afterChain=fileName - Write out word chain after faux generation to file for debugging
   -initialOutSize=N - Output this many words. Default 10000
   -maxOutSize=N - Expand output up to this many words if not all monomers output initially
   -maxToMiss=N - How many monomers may be missing from output. Default 0 
   -pseudoCount=N - Add this number to observed quantities - helps compensate for what's not
                observed.  Default 1
   -seed=N - Initialize random number with this seed for consistent results, otherwise
             it will generate different results each time it's run.
   -betweens - Add <m> lines in output that indicate level of markov model used join
   -unsubbed=fileName - Write output before substitution of missing monomers to file