Changed title
Allow dashes in user names
Merge pull request #2 from mp15/gatk_annot

Add ability to use GATK's VariantAnnotator to run-mpileup
Merge branch 'develop' of /software/vertres/git/origin/vr-codebase into develop
Final net base col and lanename filter
vcfcheck: New stats and graph, allelic r2 by AF; vcf_parse1: error recovery on missing FILTER/INFO/FORMAT tag definitions
plot-vcfcheck: fixed forgotten .pdf extension string
Merge branch 'develop' of /software/vertres/git/origin/vr-codebase into develop
plot-vcfcheck: removed forgotten debugging comments; merge of allelic r2 column in GCsAF
Retry bjobs several times before exiting.
Handle properly another odd case: the same POS in input and known_vcf but REF,ALT alleles swapped.
plot-vcfcheck: -T option to set PDF title; minor improvements in various plots
added -O to rsync command to avoid annoying directory time warnings
Make vcf-isec work in situations when the same file is given multiple times on the command line
Merge branch 'develop' of /software/vertres/git/origin/vr-codebase into develop
added -A to ssh command so that git commands work on precise-dev64 when user has a passphrase set on their key
Exclude sites with duplicate position
Merge branch 'develop' of /software/vertres/git/origin/vr-codebase into develop
vcf-fix-ploidy: reflect recent change in treatment of missing values in VCF::get_field
bamcheck: Fixed a bug introduced by previous change igcd to uint: not a good idea to init with -1.