Ensure tabix indexing of bgzipped VCF files during merging. Avoids errors from vcfcat which expected indexes
Use Heng Li's seqtk instead of a non-generalizable sed script for streaming conversion of illumina quality scores to standard quality
Provide better algorithm for distinguishing bwa-mem and bwa-aln usage. Now does random sampling of first 2 million reads instead of taking the first set of reads which may be non-generalizable. Fixes #218