v1.0.0

September 19, 2013. MAJOR UPDATE --- Version 1.0.x is a MAJOR update to ShortStack with several substantial changes.

ShortStack will now perform 3' adapter trimming on raw, untrimmed FASTA- or FASTQ-formatted small RNA-seq data.
ShortStack will also now perform alignment of trimmed small RNA-seq data to the reference genome (using bowtie, which is now a dependency). Along with the new adapter-trimming capability, this means users can now simply supply raw, untrimmed small RNA-seq data 'off-the-sequencer', along with a reference genome, and complete all pre-processing and analysis steps automatically.
The BAM formatting requirements have changed relative to previous versions. BAM files are now required to possess a proper header, and to contain a custom tag (XX:i:[int]) that ShortStack adds on. As before, they are also required to be sorted by coordinate. The new alignment capability of ShortStack handles all of this automatically. Unfortunately this means that old-style BAM files will not be accepted by version 1.0.0 and higher.
Alignment recommendations have changed: ShortStack now expects one alignment per read. For reads with multiple equally good possible alignment positions, ShortStack expects that just one was RANDOMLY selected, and the total number of possible positions was noted in the custom XX:i:[int] tag. Again, the new alignment capabilities of ShortStack handle all of this automatically for the user.
'Prep_bam.pl' has been obsoleted.
GFF3 browser files are now produced, instead of BED files as before.
Tutorial data and procedures updated at http://axtelldata.bio.psu.edu/data/ShortStack_TestData/
Several small bug fixes, performance optimizations, and improved help messages / documentation.