2. Alignments run through SamTranscriptomeParser after alignment
2. Added flag to reverse strand in STP if paired-end && sequencingApplicationCode = APP2/APP3
3. Added functionality to run all input fastq files through fastqc prior to aligning
4. Added code to create relative read coverage tracks using the Sam2USeq app
5. Added code to run genomic alignments through CalculatePerCycleErrorRate
6. Fixed bug where new Analysis Report dir was not created
