broke out bioperl-requiring subfunctions to a new file
if bioperl is required, call new bioperl_subfuncs.pl instead.
deleted intergenic_only.pl, as it is a subset of slice_fasta_file.pl
more cleanup
adding get_iupac_code
possible genericized version of vcf2fasta.pl
blast_to_ref takes a large alignment and a reference sequence and aligns the alignment to the reference sequence using BLASTN
can blast a series of reference sequences in a fasta file.
moved parse_nexus and parse_fasta to subfuncs.pl
added blastn-short for short ref seqs, added padding to ends of short sequences.
bug fix
added POD
cleaned up some unused flags
code cleanup, added POD and GetOptions.
code cleanup
moved melding functionality to subfuncs.pl, added melding to blast_to_ref.
vcf2fasta now uses phred genotype scores to choose alt allele.
code cleanup, added evalue flag.
delete extra line.
Merge branch 'reorganize-subfuncs'