Update scalpel.py

for ``min_cov`` consistently ``3``
Added option of providing sample names to write_empty_vcf and implemented recovery attempt of sample names in case of no variants detected in any region
Debugging marker removed
Added tabix indexing of empty vcf files when trying to rescue sample names in empty vcf files
Output proper headers in empty vcf files. Use pyvcf to fish out sample names from variant files with no variants.
vfilter.py fix for empty vcf files when performing freebayes hard filtering
Tabix indexing of empty filtered FreeBayes variant files
ensemble.py circumvented ensemble calling for empty callsets
Merge pull request #474 from mjafin/ensemble_fix

Ensemble fix
Merge pull request #473 from mjafin/patch-5

Update scalpel.py
Small documentation cleanups for scalpel changes: chapmanb/bcbio-nextgen#473