Merge pull request #1 from denovogear/master

Merge Upstream
Merge pull request #3 from gatoravi/master

Update documentation.
Merge remote-tracking branch 'upstream/master'
cleaned up newmat directory
moved newmat to contrib directory
example pedigree graph
added checks to cmake file
Merge pull request #4 from gatoravi/master

use consistent column_name for SNP and INDEL outputs
Merge pull request #5 from gatoravi/master

increase memory allocation for number of trios in PED file.
Merge branch 'master' of github.com:denovogear/denovogear
Merged patch from Stephen Clayton <sc13@sanger.ac.uk>
Source: https://github.com/wtsi-hgi/DNG_dev/pull/1.patch
Merge pull request #7 from gatoravi/master

fix issues with bcf parsing.
Merge pull request #6 from reedacartwright/feature/fix_vcf_header_line_issues

Merged patch from Stephen Clayton <sc13@sanger.ac.uk>
Merge pull request #8 from denovogear/master

Merge changes commited to master to develop
Change meta headers to pass vcftools perl module parser
Merge pull request #9 from sc13-bioinf/develop

Change meta headers to pass vcftools perl module parser