Update cpopulation.pyx

Added code to write alignment scores of reads to haplotypes within a window
Update variantcaller.pyx

Added code to open alignScoreFile if option is chosen
Update variantutils.py

Added options for long haplotypes (facilitate reading haplotypes provided to Platypus in HLA calling)
Update runner.py

Added option to write alignScoreFile
Platypus can now read input regions from .bed files
Merge pull request #23 from hangphan/patch-3

Update cpopulation.pyx
Merge pull request #24 from hangphan/patch-4

Update variantcaller.pyx
Merge pull request #25 from hangphan/patch-5

Update variantutils.py
Merge pull request #26 from hangphan/patch-6

Update runner.py
Merged Hang's changes. Can now output a text file of alignment scores. Also,
optionally don't trim long replacement variants in input VCFs.