fix for cases with semi-colon characters in reference name
fix for colour by strand option when XS tag is missing
change visibility of addIndexReferenceListener()
change visibility of getIndexFastaCombo()
change visibility of getOneLinePerEntryDisplay() and
getEntryGroupDisplay()
add index reference listener in openBamView()
use local EntryEdit in openBamView()
fix strand stack view with RNASeq strand specific option checked
update
fix for CDS IDs in multi-sequence GFF files
Merge pull request #134 from tcarver/master

misc