Modified mismatch handling in RNAseq.sh and RNAseq_process_data.sh.
Above scripts generate more run log files.
Modified output of qc.sh to include more stats.
Added G: to getopt string
Added a nonewtranscripts option.
Added no_new_txpts
Updated how a GTF file is used.
Added max/min_length flags.
Added script to calculate map efficiency.
Added script to count mapped reads in a bam file.