Commits on Sep 26, 2015

1. Correctly split hg38 HLA contigs during configuration …

   When testing manta on hg38 full from the 1000 genomes distribution,
   there are problems handling the HLA contigs, which contain colons: `HLA-A*01:01:01:01`.
   
   Configuration fails with:
   ```
   CONFIGURATION ERROR:
   Reference fasta and 'Normal' BAM/CRAM file conflict on chromosome: 'HLA-A*01'
   ```
   when splitting the names from the BAM tags. This small fix resolves the
   problem. When running, there is also a downstream failure with a similar
   problem trying to parse ranges in names with colons:
   ```
   FATAL_ERROR: EstimateSVLoci EXCEPTION: ERROR: can't parse bam_region [err 1] HLA-A*01:01:01:02N:1-3291
   ```
   I worked around this by excluding HLA regions from manta, with
   `--region` but just as an additional related source of issues.

   

   chapmanb committed Sep 26, 2015
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