Partial implementation of handling of remote soft clips
RealignedRemoteSoftClipEvidence: adjusting SAMRecord to emulate aligner remote end alignment
This removes any special-case handling required for downstream processing (such as assembly) of remote soft-clip.
Fixed realigned remote soft clip read names
remote soft clip now has unique evidenceID
Incorporated remote soft clips into assembly. Now require 3 passes due to need to realign SCs before assemblies can be generated
Added remote evidenceID test case
Merge branch 'realigned_remote_sc'
Added soft clip length distribution to metrics
Tracking read counts, mapping and read pairing metrics