Overhaul of alignment and SAM formatting

[timbitz]

Overhaul of align.jl for accurate SAM output and performance increase:

• Replaced SGNode with SGAlignNode which contains SGAlignScore for each node.
• Fixed passed_edges handling to utilize passed SGAlignNodes.
• Improved alignment performance by 1-2 seconds per 1M reads
• Improved CIGAR calculated performance substantially