0.6.0

• Fixed a buffer overflow error in breakfast detect that could trigger when one of the read end anchors was aligned very close to the beginning or end of a chromosome
• Added support for local alignment BAM files by incorporating reads that have a lengthy leading or trailing softclip in the analysis as potential rearrangement-supporting reads (the softclip length must be greater or equal to the anchor length)
• Replaced the old breakfast blacklist command with an updated breakfast filter command that takes in a sample sheet and allows more fine-grained control over rearrangement filtering