Bugfix Merge, Whippet v0.5.1

[timbitz]

This is an initial pull request for a bugfix merge to trigger release of Whippet v0.5.1

• [x] Fix one-gene index (and last gene) alignment for paired-end fastq files.
• [x] Fix SAM formatting of initial offset for '-' strand reads
• [x] Fix SAM CIGAR string formatting
• [x] Fix SGAlignment recurse to passed edges

[timbitz]

Current coverage is 46.63% (diff: 75.70%)

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[timbitz]

This pull request is meant to fix #37.