update
improved parsing performance, vcffilter memory leak fix
fix small bug from last commit
vcfentropy --- entropy of flanking and centered sequence
update vcfcleancomplex
added MIT license
vcf set GT via GL
cleanup a few bugs in the gl -> gt application
vcf multiway comparison scripts
improve handling of overlapping variants in union

When one record contains more allelic information than the input, remove
the input and use the record with more combined information.
fix problem with tagged intersections

Records were not being printed when they didn't contain any matches.
updated smithwaterman
fix primitives resolution problem for indels
error in check for SNP case in alternate allele parsing
remove potentially problematic adjustment stanza from primitive parsing
shorter padding length improves stability
vcfregionreduce

When given a series of gzipped VCF files for a list of genomic regions,
such as might be produced in the parallel processing of a large dataset,
these scripts can efficiently concatenate the files.
allele-specific tag addition on intersection

Allows the user to add tags from the same allele in another file.  This
is useful for comparing indel callsets, where the indel position may not
be identical even if the allele is and standard line-based merging
strategies for annotations will fail.
updated fastahack
clarify git clone command