Alignment bug fix

This fixes:

• A call to a crashing bug in seqan's bandedChainAlignment.
• Bugs in my trimming of low-quality ends of sdp chains.

IO Update: write full insertion sequence

This keeps track of the full insertion sequence so that additional downstream processing can be applied to vet candidate insertions.

Beta release for docker

Beta release for docker build.

Beta release for docker

Beta release for docker build.