Write meaningful filenames on disk
Write meaningful filenames on disk

This is being changed for two reasons:

1. It's easier to debug things (what does (input|output)N map to?)
2. Some tools (eg, htslib based things) look for auxilliary files by taking the
   basename and appending suffixes (eg, .bam -> .bam.bai).  This breaks if we
   have erased this information.

The downside is that duplicate names aren't supported, but this hasn't been an
issue in practice.

googlegenomics/pipelines-tools,googlegenomics/pipelines-tools