2009-08-28  H. Gene Shin  <shin@jimmy.harvard.edu>>
	Version 0.9.8.2 (upgrade sitepro so that it can receive either multiple WIG files 
        and a single BED or a single WIG file and multiple BED files as inputs))
	
	* sitepro (version 0.6.2)

	Now, sitepro shows the arguments on the screen so that the user easily get what 
        arguments they punched in.
        This version of sitepro also allows either multiple WIG files and a single BED 
        file or a single WIG file and multiple BED files as inputs. The resulted average
        signals are drawn in a single plot with appropriate legends. 

2009-10-08 H. Gene Shin <shin@jimmy.harvard.edu> 
	version 0.9.8.3 (fixed a bug in metagene average profile)

	* ceas (version 0.9.8)

	With a certain choice of --pf-res, the last point of the metagene (i.e. 3000bp) 
	was missing. The bug has been fixed in this version

2009-10-18 H. Gene Shin <shin@jimmy.harvard.edu>
	version 0.9.8.4 (fixed a bug in gca)

	* gca (version 0.1.6)

	Some genes have negative distances to their nearest binding sites. The bug has
	been fixed in this version

2009-10-26 H. Gene Shin <shin@jimmy.harvard.edu>
	version 0.9.8.5 (fixed a bug in ceas)

	* ceas (version 0.9.8.1)

	When the last chromosome's name does not follow a regular chromosome name 
	(e.g. chr1), average signal profile part produces an error. The bug has been
	fixed in this version

2009-10-30 H. Gene Shin <shin@jimmy.harvard.edu>
	version 0.9.8.6 (fixed a bug in sitepro)

	* sitepro (0.6.3)

	Found a syntax error found while running --dump. The bug has been fixed.

2009-11-20 H. Gene Shin <shin@jimmy.harvard.edu>
	package version 0.9.9 (fixed a bug in ceas and improved gca)

	* ceas (0.9.8.7)

	In the previous versions, in order to speed up the annotation on the extra
        regions (-e), the extra regions are assumed not to overlap with each other.
        Thus, if a bed file with overlapped regions is given, the annotation was not
        run correctly. In the new version, 0.9.9, the union of the regions is taken and
        used for the annotation.

        * gca (0.1.7)

        The precision of the numbers in the xls file generated by GCA was reduced for better
        visualization.

2010-02-16 H. Gene Shin <shin@jimmy.harvard.edu>
	package version 0.9.9.1 (fixed a bug in ceas)

	* ceas (0.9.8.8)

	Previously, the chromosome overview produced an error if no chromosome information 
	was given. The bug was fixed; when no chromosome information is given, only empty
	string is returned.        

2010-02-25 H. Gene Shin <shin@jimmy.harvard.edu>
	Package version 0.9.9.2 (improved the color scheme in gene profiling)

	* ceas (0.9.8.9) and sitepro (0.6.4)

	A better color mapping was added to ceas and sitepro. When calculating multiple profiles
	the current package provides more smooth and beautiful colors than before. 

2010-03-31 H. Gene Shin <shin@jimmy.harvard.edu>
	Package version 0.9.9.3 (improved the 'dump' function of sitepro)

	* sitepro (0.6.5)

	With --dump option activated, the names of the bed regions, if there are, will be printed 
	out to the dump file.

2010-05-11 H. Gene Shin <shin@jimmy.harvard.edu>
	Package version 0.9.9.4 (fixed a bug in ChIP annotation)

	* ceas (0.9.9.0)

	It was found that the enrichment level of exon regions, including UTR regions was 
	slightly under-represented. (or equivalently, intron regions are slightly over-represented.) That has 
	been fixed and updated gene annotation tables are provided.

2010-05-19 H. Gene Shin <shin@jimmy.harvard.edu>
	Package version 0.9.9.5 (increased peak file size)

	* ceas (0.9.9.1)

	The file size limit for the peak file has been increased to 5M from 1M.

2010-08-26 H. Gene Shin <shin@jimmy.harvard.edu>
	Package version 0.9.9.7 (increased peak file size)

	* ceas (0.9.9.3)

	A routine to check the validity of ChIP bed file has been added. If the second or third columns of the bed file are not integers or 
	numbers in the third column is smaller than 2nd column, the program stops. 

2010-09-18 H. Gene Shin <shin@jimmy.harvard.edu>
	Package version 0.9.9.8 (substitute the error calling with a warning message in case the ChIP bed file size is larger than 5M)

	* ceas (0.9.9.4)

	5M limit on the ChIP bed file size may be too strict. Thus, the error was substituted with a warning message.

2010-10-27 H. Gene Shin <shin@jimmy.harvard.edu>
	Package version 0.9.9.9 (fix the error that occurs when one or more gene group files are given, but no genes remain on the last chromosome in CEAS)

	* ceas (0.9.9.5)

	Previously, an error (IndexError) popped when no genes remain in the gene groups when the last chromosome was traversed by wig profiling. This error
	has been fixed.

2010-11-16 H. Gene Shin <shin@jimmy.harvard.edu>
	Package version 1.0 (update inout.py so that it could automatically adjust the ylim for ChIP signal average plots even when no enough data is given)

	* ceas (0.9.9.6)

	Previously, if ChIP signal is incomplete (e.g. only several chromosomes are given), an error occurred in estimating the slim for the average plots. This
	was updated so that the slim can be determined automatically.

2010-11-24 H. Gene Shin <shin@jimmy.harvard.edu>
	Package version 1.0.1 (fixed a bug in sitepro dir function)

	* sitepro (0.6.6)

	Previously, dir (direction consideration) could be turned on even in case that it was not selected. This error has been fixed in the new version.

2010-11-30 H. Gene Shin <shin@jimmy.harvard.edu>
	Package version 1.0.2 (fixed bugs in Annotator and AnnotatorGBG classes in annotator.py and corrected cease and build_genomeBG accordingly)

	* cease (0.9.9.7) and build_genomeBG(0.1.6)

	Previously, AnnotatorGBG class in annotator.py underestimated the proportion of promoter and downstream regions but slightly overestimated genic regions
	in the genome background (ChIP annotator is no problem). This error has been fixed. Another, when --bg option was used, some syntax errors happened, 
	but they have been fixed. 

	

	
