Merge Dev to Master

[chgibb]

Merge changes from the last 7 days.

A few bugs have been introduced:

1. Some bowtie output is being alerted in input after indexing 15 fastas at once.
2. Please confirm QC still works. OpenJDK 9 has broken FastQC. This will have to be investigated separately. Travis builds and runs tests fine under Oracle Java 7.
3. Pileup is throwing an exception when trying to view a pileup for an alignment with a 0% alignment rate. This error should be intercepted and turned into something nicer looking than a stack trace into Q.js.

@jsbrn please investigate 1.
@scs97liu please investigate 2.
@pynner please investigate 3.

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[chgibb]

Reviewed 6 of 46 files at r4, 6 of 46 files at r6, 6 of 54 files at r7, 48 of 48 files at r8.
Review status: all files reviewed at latest revision, all discussions resolved.

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[chgibb]

Reviewed 14 of 15 files at r9, 1 of 1 files at r10.
Review status: all files reviewed at latest revision, all discussions resolved.

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[chgibb]

Reviewed 3 of 3 files at r11.
Review status: all files reviewed at latest revision, all discussions resolved.

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