getAlignments: Get an alignment of a CCS read to the reference as well as...
In PacificBiosciences/ccsviewr: Examine subreads from a CCS alignment view.

1 - Gets the region of the reference genome that the CCS read aligns to 2 - Gets the CCS read and the subreads 3 - Aligns all reads to the section of the reference genome 4 - Returns a list of all these pairwise alignments with the CCS read alignment as the first element.

1	getAlignments(hole, ccs_name, subreads_name, fasta_name)

`hole`	Which ZMW to collect data for.
`ccs_name`	Full path of the aligned CCS BAM file.
`subreads_name`	Full path of the subreads BAM file
`fasta_name`	Full path of the fasta file used to generate the CCS alignment