Cleaned README.txt
Disabled .gitattributes for now.
Changed GTF version in HTSeq.
Updated HTSeq manual.
Deleted .hgignore.
Changed dispersion parameter default value in DEXSeq.
Typos fixed in HTSeq description.
Updated the description of two group test.
Zebrafish chip removed from Agilent normalization tool.
Reorganized IntersectBED.
Updated IntersectBED manual.
Clarified the Illumina import manual.
Changed parameter optionality in IntersectBED.
IntersectBED parameter optionality.
BAM parameter in IntersectBED.
Added CNA-seq to manual front page.
Impoved update_bundle() and transform_bundle().
Little test.
Little test again.
Saren test.