Fix contig ordering for Tophat alignments.

This was causing GATK to fail due to a mismatch between the
BAM file header contig ordering and the reference file ordering.
Remove unused import.
Drop non-GATK coverage calculation for now.

chanjo as a dependency brings along some complexity, so shelve
this for now until that gets resolved upstream.
Remove chanjo dependency until distribute dependency issue resolved
Remove the -s call as it is too stringent (see issue #314)
Remove the pvar option, let hard filtering do the selection (like germline calling)
Merge pull request #349 from lbeltrame/freebayes-fixes

Miscellaneous fixes for FreeBayes
Add hard vcffilter to FreeBayes tumor calls to remove extremely low quality variants which cause issues with GATK post-processing #349