Performance improvements
Fixed bug in haplotype array used for storing map counts. Previously was not
allocating sufficient space, leading to occasional overflows.

Fix in variantutils, so now Platypus will read complex replacements from
input VCF source.
Removed some old code, and used some minor Cython optimisations.
Added Hang's change for the PG tag
Update samtoolsWrapper.pyx

Add DS field for @PG tag (error reported by Quang Le)
Added some old releases to the archive
VCF Validation

Includes some basic VCF validation
Increment version. Avoid problems caused by long reads, by capping maxReadLength
at maxSize.
Merge pull request #18 from dancooke/VcfValidation

VCF Validation
Merge pull request #16 from hangphan/patch-2

Update samtoolsWrapper.pyx
Added #!/usr/bin/python in Platypus.py so it can be run as an
executable.
Moved inline extract* functions to align.h and made them static inline. Hopefully this
will get rid of the build error on Mac OSX.
Add new incremental release. Platypus can now output VCF to stdout. Logging to
file always happens now, even if you specify --verbosity=0.

Added release 0.7.9.1 for these patches.
Minor bug-fix in GL calculation, where value of 'factor' was decided by variant index
instead of haplotype index.
Fixes for 0.7.9.1 release (=> 0.7.9.2)
- Avoid calling mergeVCFfiles when outputing variants to standard out
- Clean up recent isValidVcfLine addition to be a non-class function and use correct local name (`line`)
Merge pull request #22 from chapmanb/master

Fixes for 0.7.9.1 release (=> 0.7.9.2)
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