Merge pull request #10 from henrikstranneheim/master

Updating
Added QCCollect and ranking file(s) to sampleInfo, fixed bug in creating directory GATKHC
Fixed BUg in GATKReducedReads
Fixed Bug in GATHHaplotypeCombined, cleaned upp intersectCollect
Removed sequentiell SNV and INDEL mode in GATKVRecal to mode BOTH for exome and rapid
Added pedigreeFile path in sampleInfo
Added original pedigreeFile to sampleInfo
Minor changes
- Added autodetect of .gz human reference
- Automatic decompression of .gz human reference before analysis
- fixed merged target list interval directory
- clean-up of intersectCollect.pl, add_depth.pl and qcCollect.pl
- Fixed GATKReduceReads filending typo
- Added sub routine for checking if a file is compressed or not
- Rewrote InfilesReformat using new sub routine
Fixed polyphen columnNames
Merge branch 'release/v1.5.0'