Initial commit
Fixed README
Eliminated dependency on GenomeTools...kind of
Added analysis of regulatory regions (1kb upstream and downstream of each gene)
Corrections for ambiguous nucleotides
Re-implemented stats.pl script in C
Fixed makefile
Updated documentation
Added kseq.h header
Updated stats calculations for spliced transcripts and combined introns
Added check for intron features in annotation file
Began implementing new data structure, directory organization
Integrated GsOutputFile class
Implemented GsSequence class
Integrated GsSequence class
Integrated final data structures and modules
Refactored code
Updated R script to handle new filenames
Implemented printing of data for ratio of introns to flanking exons
Intron/exon ratios, new graphics

With this commit, I got rid of the file dedicated to computing intron/exon GC-content ratios and simply added the necessary data regarding flanking exons to the existing single exon data file. I also updated the R script to calculate stats for this new distribution, as well as XY plots with trend lines for all of the length-vs-GC data.