Updating WHAM for the Yandell Group. #1
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VCF2R is a vcf parser I wrote after using WHAM on some genomic data I had generated. I like to use R and the ggplot2 package to visualize complex (large) data sets like those generated by WHAM. VCF2R parses WHAM (or any vcf) output and allows you to specify which fields to output, which chromosomes, and even specify unlimited regions within chromosomes (using bp coordinates) to restrict output. VCF2R is "smart"- it learns the valid fields of the vcf file by parsing for the header and information fields, it will optionally deparse fields that contain lists of comma separated values (like the AT field in WHAM- for instance) generating a separate column for each in the output data (think of it as a R data frame in waiting).
bug fix
added command line opts for --chr= range --chr=1-10,X,Y now works to grab chr 1,2,3,4,5,6,7,8,9,10,X,Y
Swap (unsigned long long) for (long long) to fix narrowing error
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