Improve support streaming inputs/outputs from/to stdin/stdout.

[cmnbroad]

Currently you can specify /dev/stdout on the command line as an alignment file output, and GATK (i.e. PrintReads) will stream compressed .bam output to stdout. But it will throw when trying to create an output index unless output index creation is manually suppressed. GATKTool.createSAMWriter should recognize that case and verify/suppress creation of output index and md5, as well as force text (.sam) output.

Same for createVCFWriter. And inputs too.