Start updating the readme for this specific branch
Merge branch 'master' into ZeldaAnalysis
Add thousands separators to CountAllReads
Merge branch 'ZeldaAnalysis' of github.com:petercombs/EisenLab-Code into ZeldaAnalysis
First version of the makefiles
Ignore autogenerated makefiles
Merge branch 'ZeldaAnalysis' of github.com:petercombs/EisenLab-Code into ZeldaAnalysis
Clean up changes in configure and Makefile
Cleanup config, make mapping and bam files atomic
Merge branch 'ZeldaAnalysis' of github.com:petercombs/EisenLab-Code into ZeldaAnalysis

Conflicts:
	Makefile
	configure
Prepend dmel on mel_good.gtf
Turns out $ is hard to input in makefiles
Awk fail. Bad Peter
Tweak MELGFF to remove CR#### genes
cufflinks now depends on fixed version of fasta file for bias correction
analyze.make now checks the sum of FPKMs
Simplify the confidence range parameter
Use optional configuration file to rename columns in MakeSummaryTable
MakeSummaryTable call in Makefile uses the config file to rename columns
Ignore Rp and mir- genes in the annotation as well