Edited the script to accept VCF files as input and adds more information to the output csv file. The VCF input can either be in a directory or given individually to work with galaxy.
Fixed a bug where files were being opened in the current directory. Now full path is being used
Added an additional column with strand information
fixed chomp on an array and removed an uncessary if-else
Removed unecessary if-else statement and incremented directly; Changed the complement sub to the really cool way Phil showed me; Now printing the output file names to user; Fixed the flag issue; Now added a flag to suppress all the warnings.
fixed typo
Merge pull request #9 from mariamiskander/master

Edited the script to accept VCF files as input and adds more information...