Flag for creating Index with gatherBamfiles and made temporary fix for pileup.js
Flag for creating Index with gatherBamfiles and made temporary fix for pileup.js

- Added flag for creating index file with GatherBAMFile. Default to TRUE
- Temporary fix allowing samtools to create index for GATKBaseRecalibration BAM instead of Picard to accomodate pileup.js

henrikstranneheim/MIP,henrikstranneheim/MIP