Types of files in this directory:
=================================
*_reference files Reference set(s) containing the locations of the landmarks.

.c files          C-source code.

DEVIATION files  (or "run"-files) contain the raw deviation data (fp,
		 fn, fp+fn) with respect to the reference (functional)
		 sites obtained for runs of infocon when varying the
		 anchor. The parameter l stays the same for a given
		 file.

interval files   Are derived from DEVIATION files, and contain the 
                 intervals of invariance for the anchor value.

*bat* file       Command files for the tests.

make.best        Command file for producing the point data for the blocks 
		 in Figs 4A,B,C of the "Comparison of five methods..."
		 paper. Initiates infocon runs for the best sets of the
		 (a,l) parameters.

README           Summary of files/software/procedures.


Programs:
=========
button.c   * Initiates infocon test runs and for each computes the counts of
             false positives and false negatives with respect to a specified 
             set of landmarks (<ref_file>). The minimum length of the region 
             is fixed (specified as [S=]) while a is varied over [-10,2] during
             the procedure.

interval.c * Determines intervals of invariance for the anchor value, given 
             a DEVIATION file ('interval files').

min.c      * Determines the best fp+fn count for a DEVIATION file (l=ct). 
             Used in analysis for individual regions.
             *** source code in ../tools ***
  
min_interval.c Determines the best fp+fn count for an 'interval file' (ie, 
             for a file as the ones produced by the 'interval' command).
             Used in analysis for combined regions.
             *** source code in ../tools ***

NOTE: min and min_interval perform the same operation on files with different 
format. min operates on DEVIATION ("run") files, while min_interval operates
on interval files. 
             
merge.c    * Merges two interval files of anchor values, to produce an 
             interval file with a finer interleaving. Used in combined 
             region assessments.

crop.c     * 'Crops' a DEVIATION file to the runs which conform to the
	     specified true positives percentage cut. The last argument
	     in the command line is the total length of the functional
	     regions.
             *** source code in ../tools ***
crops_total.c
	   * Finds the a-intervals with the best "total count" among the
	     set of runs conforming to the specified true positives
	     percentage cut. Starts from a DEVIATION file, from which
	     it produces an intermediate interval-file.
crops_fp.c * Finds the a-intervals with the best "fp count" among the
             set of runs conforming to the specified true positives
             percentage cut. Starts from a DEVIATION file, from which
             it produces an intermediate interval-file.

Command files:
==============
/* A : per region assessment */
hs2bat     * Command file to produce data files (hs2_DEVIATION.l*) for the hs2 
             region.
hs3bat     * Same for hs3.
betabat    * Same for the HBB promoter.
araCe_bat  * Same for the araBAD-araC intergenic region.

bat_crops.hs2  * Command file to produce best a-intervals (for each l)
		 for the hs2 region, provided that only the runs
		 conforming to a given true positives percentage cut
		 are included.  
		 Output saved as hs2.best_total.cut60, hs2.best_total.cut80.  
                 (hs2.best_fp.cut60, hs2.best_fp.cut80 for "best fp count" 
                 evaluations).
bat_crops.hs3  * Same as before, for hs3.  
bat_crops.beta * Same as before, for the HBB promoter.
 

/* B : combined region assessment */
bat_merge  * Command file to produce the interval file for the overall hs2, 
             hs3 and HBB promoter regions. Output is saved in the 
             hs23b_DEVIATION.l* files. 
bat_merge.cut
           * Command file to produce the interval file for the overall hs2,
             hs3 and HBB promoter regions, for the 60% cut (that is, for each
             region only consider runs with < 40% fn count).  
             Can be modified for use with any value of the percentage cut 
             (eg, 80).

/* C : general */
min_bat    * Command file to output the list of minima for the region, based
             on the <region>_DEVIATION.l* files.