Load sequence data stored in bam format into Jalview

Enable the user to load data from a bam file into Jalview. The user will need to provide the bam file and a corresponding index (.bai) file, as well as a reference query interval. (Jalview should check there are not an excessive number of reads before attempting to load them all!)

Imported reads should be aligned against each other and the reference sequence according to the CIGAR string associated with the read. So deletions (N/D in CIGAR) in a read have gaps inserted; insertions (I in CIGAR) in a read require a gap added to the reference sequence which in turn means a gap needs to be added to each read.

The user should be provided with an option to load or ignore soft-clipped regions on reads (S in CIGAR). If soft clip regions are also loaded they should be positioned so that the ends of the region closest to the read are aligned with each other, followed/preceded by a single gap, followed/preceded by the reads aligned to the reference. When displayed the singled gap region between the soft clips and the main reads should be displayed as a hidden column (allowing MSA to be performed independently on the soft clip regions).