allow overwriting filter field, vcffilter
minor fixes
putative fix for #8
add missing vcfstreamsort.cpp
convert from '.' format to './.' for null genotypes
generate phased genotypes from complex alleles (vcfallelicprimitives)

Now it is possible to commute complex alleles with many component
allelic primitives (snps and indels) into phased genotypes across
samples using vcfallelicprimitives.  They can be converted back using
vcfgeno2haplo and a window size equivalent to that used during
detection.
tag variants which are parsed from complex variants
updated vcfgenotypecompare and vcfgeno2haplo

Fix problems with genotype concordance counting.

Ensure last variant is not output twice in vcfgeno2haplo.
add vcfroc, vcfcheck, default value for vcf2tsv

vcfroc: Recevier-Operator-Characteristic for VCF files given a truth set
including all true sites and a test file.

vcfcheck: verify that REF fields match reference

Default value for vcf2tsv, allows users to specify a default (e.g. 0 or
NA) for when a field does not have a value in the INFO field of a VCF
record.
updates, addition of fsom library
vcfsom initial commit

Classify VCF records on the basis of INFO fields using an self-ordering
map.  Both training and classification methods using previous SOMs are
possible.
updates to clean up vcfsom
improve help text for vcfsom
large cleanup of indentation, addition of Variant::varCigar
make cigar in varCigar default to BAM-compliant
cleanup problems in Variant.h (duplicate definition of varCigar)
minor change
fix Makefile
correct vcfsom --help documentation
documentation!

In markdown format.  Currently only for C++ executables in vcflib.