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.
vcfcreatemulti -- combine overlapping variants

Combines variants whose REF fields overlap, adjusting alternates.
vcfsom, add positive and negative training inputs

By using true and false VCFs we can "paint" the SOM generated in vcfsom,
and then apply the painting results (in terms of the fraction of true
variants at a given node) to estimate the probability that the variant
is true.
allow multiple reference sequences in vcfstreamsort, vcfuniq

And updates to documentation.
vcfuniqalleles
readme update
vcfgenosummarize, remove dependency from vcfsort
fixed problem with header in vcfgenosummarize
header line removal bug

Names that started the same as other fields could be removed
incorrectly.  Solution: check for comma after field name.
addition of vcfcat (just concatenates VCF files), other fixes
updates to vcfstats and vcffilter

vcfstats -- show biallelic SNP count and ts/tv
vcffilter -- allow tagging of failing sites as well as passing
initialize VariantCallFile::parsedHeader
update to vcflength, use +/- instead of abs(...)
update to vcfsamplediff, "strict" option

Require that there are no alternate observations when the germline call is
reference and the somatic one appears to differ.