1) Prep_bam.pl helper script updated
to deal with .sam lines corresponding to unmapped reads without
breaking. This also enables "one-step" mapping and .bam file preparation
using bowtie (see 'Quick Start' section below).
2) ShortStack.pl also
updated to prevent breaking upon encountering .sam lines corresponding
to unmapped reads.
3) Coloring of .bed files now dynamically adjusts to
make a nice 'rainbow' (from red through green to blue) regardless of the
size of the dicer range.
4) Finally, an additional filter was added to
prevent excessive splitting of initial de-novo clusters into
hairpin-associated clusters ... initial clusters are now prevented from
splitting if they would spawn more than --maxsplit child hairpins
(default, 3). This prevents inappropriate splitting of very large
clusters that might harbor a number of sub-optimal hairpins.