Get NIO writing working for both bams and vcfs in walkers

[droazen]

Writing output via NIO is currently broken, as reported by @jean-philippe-martin:

 /home/jpmartin/build/install/gatk/bin/gatk PrintReads -I inputs/CEUTrio.HiSeq.WEx.b37.NA12892.bam -L 10:1000000-2000000 -O gs://jpmartin/staging/out_tmp.bam
htsjdk.samtools.util.RuntimeIOException: Error opening file: /home/jpmartin/gs:/jpmartin/staging/out_tmp.bam
        at htsjdk.samtools.SAMFileWriterFactory.makeBAMWriter(SAMFileWriterFactory.java:246)

Now that the read support is in good shape, let's get the writing end working -- should hopefully be an easy fix.

[droazen]

For @jean-philippe-martin

[jean-philippe-martin]

GCS output works now for PrintReads. Next step is to switch all the other walkers to use the Path overload, too.

[jean-philippe-martin]

For what it's worth, this works but I should improve the error message. If you don't have the right permissions, currently you get an error that's something like this:

htsjdk.samtools.util.RuntimeIOException: Error opening file: file:///home/jpmartin//gatk/gs:/bobs-bucket-you-cant-write-to/test-output/printtogcs.bam

This is both

• confusing: it makes it look like the path is wrong even though the code actually tried the correct path
• improvable: it'd be nice if we gave the reason there was an error (403 Forbidden: user jpmartin doesn't have write access)