removed ira_out.py script
Update README.md
initialize QUAL to zero instead of LUMPY support
if refbase not found in fasta, replace with N
INV is two-sided inversion, otherwise it is a generic breakend BND
check type of BND events
fixed off by ones
vcfToBedpe plays nicely with updated bedpeToVcf
properly labels interchromal eventss
added ira's script for extracting split reads from a pos sorted BAM
added lumpy to ira out script
bedpeToVcf no longer requires a fasta or pysam
didn't need that backslash
bug when no fasta provided
fixed file close
removed extra column (total evidence, which was duplicated); fixed cols 12 and 13 (ispan and ospan)
added output schema and set qual to 0 for each SV
docs
updated docs, updated help on vcfToBedpe
docs