vrtracking_tool resets snps for pathogens
vrtracking_tool resets mapping for pathogens
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
Exclude sites with duplicate position
Merge branch 'develop' of /software/vertres/git/origin/vr-codebase into develop
fix qw depricated warnings in sam
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.
Allow joining of multiallelic sites
New stats and graphs: singletons and depth by sample; new -s switch; more values in summary table
adding new databases to web tools
rnaseq tests pass
bamcheck: max quality value increased to 255 to handle missing qual field; pairs with IS=0 can still count as paired; output IS=0 stats as well
Merge branch 'develop' of /software/vertres/git/origin/vr-codebase into develop
updated npg database connection
correctly handle discontinous genes
Merge pull request #160 from andrewjpage/rna_seq_exon

Rna seq exon
plot-vcfcheck: Added missing legend into SNP/indel-counts-by-AF graphs
plot-vcfcheck: Fix in merging per-sample average depth - average, not sum