add Netbeans folder “nbproject” to .gitignore
fix comment typo
fix bamToFastq skipping reads after unpaired reads

It was correctly identifying reads whose “paired” flag was set, but then
it was incorrectly skipping over the read-pair that follows such an
incorrect read.

Also added a test for this behavior.
Merge pull request #132 from ryan-williams/fastq

Fix a bug in bamToFastq and add a test for it