First major post-publication release

Changes since 0.9:

Bug fixes

• Improved ability to spot junction adaptor due to bug in previous logic.
• Removed some crashes that can occur if some of the stats counts are zero (ie. dividing zero by number of reads creates error).
• Corrected LSF submission to request correct amount of memory for NextClip (and provided option which will report memory requirements before running NextClip).
• The min_length parameter was 1 base out (i.e. specifying 25 gave reads of 24) - this is fixed, meaning that yields will appear to go down slightly. You can always decrease min_length to 24 if you want to recover this.
• Fixed PCR duplicate stats being wrong for counts > 99.
• Fixed help wording.

Improvements

• NextClip outputs number of bases written for each category and the pipeline PDF report shows this as well as approximate genome coverage.
• Ability to pass parameters through to the pipeline (e.g. minimum width, trim ends etc.).
• You can specify the pipeline stage to start at, so no need to redo all analysis in the event of a fail.
• The scripts directory is found automatically - no need to set it during installation.
• Moved PCR duplicate kmer offset to avoid lower quality bases at start of read. Should provide slightly more accurate estimates of PCR duplication.
• Queue name can be specified when running with LSF.
• Reduced size of hash table used to store PCR duplicates.