check file existence in formats.sam.count()
add option --single to assembly.automaton.tophat()
add expression.heterosis.mergeclean()
add option --type in formats.sam.count()
Add option to remove attribute(s) in formats.gff.format();
fix atg_name() regex in annotations.reformat
change apps.vecscreen to use Ecoli K12 DH10B instead
fix bug in graphics.histogram()
add apps.base.OptionParser.set_table()
Reinistate `id = accn` assignment in class GffLine();
slight logic changes to gff.format() remove_attrs action
ignore empty lines in formats.base.SetFile
Modified atg_name() regex to also work with new JGI locus names;
Modified PslLine logic when dealing with translated alignments
move dependency pybedtools into local scope in annotation.reformat
add assembly.geneticmap.path()
Some more minor changes to formats.psl parser; add `--jgi` param
to annotation.reformat.rename() to generate JGI style locus IDs
add breakpoint identification in assembly.geneticmap
improve breakpoint identification in assembly.geneticmap