v2.02

• Addressed bug where some processing regions were being dropped
• Skip processing of intronic regions for RNA
• Various fixes to indel left alignment - this was causing several good realignments to be dropped since the switchover to semi-global contig alignment due to ambiguous cases.
• Set mapq of originally unmapped reads when realigned to max mapq (allow for inclusion in variant calling)
• Prioritize assembled contigs over secondary contigs when realignment is ambiguous
• Semi-global backtrack optimization