added doxyfile.in
Update: added writeFasta and updateStats

writeFasta generates a reads.fa file with all the inter-transcripts
reads. Used by gfrRibosomalFilter, gfrMitochondrialFilter and
gfrSmallScaleHomologyFilter
updateStats, used by the same programs, updates the numInter counts
after removing the reads
Update: changed int to float for some variables
Update: added support for reading from the configuration file