add bwa version 0.7.2
Using DP4 to replace AD for samtools mpileup snv vcf output
Using DP4 to replace AD for samtools mpileup snv vcf output
Need to specify species for tier-bitmasks
Merge branch 'updated2' into gb_master
Support interpro db release 40.

*interpro version is now parameterized
*includes modified Bio::SeqIO::interpro with bugfix for issue that had been
 reported to bioperl previously.
Replaced hard-coded paths.

Calls to Genome::Sys dbpath are now used for files, and swpath for
executables in select cases in the somatic variation and rna-seq
pipelines.