Sort exons by start position depending on strand of the gene.  Also replace a 1 with a + strand.
Update the test reflecting the change from 1 to + for strand.
Pass on picard_version to fetch the software result for chimerascan.
Convert the BAM file to FASTQ using picard.
Add params for non-pf reads and non-primary alignments.
remove the FASTQ files after alignment.
Additional parameter parsing for FlexBar.
Add the text to include deduplication of RNA-seq BAM files if defined in processing profile
Add the parameters and comments about converting BAM to FASTQ and linking those files.
Do not require a reference_sequence and remove/comment out the default value.
The param for max_records_in_ram is a standard param for any picard command.