nh13/DWGSIM — pull request #2 by colinhercus (2013-01-03 07:11:31+00:00)
Title: Fix for long Indels

1) Fix: Position of long indels was affected by read orientation
2) Fix: Make VCF file better match to VCFs generated by samtools & bcfutils.
3) Don't mutate base 0 of reference to avoid VCF format problem for indels.