Peptides with variants that are incompetible with orf start

[zhuchcn]

Description

1. Peptides that carry variants overlap with the orf start nodes should not be called.
2. Previously we updated the PVGNode collapse rule for circRNA that only nodes with exact variants will be collapsed. This is also applied to pop-collapse now.
3. Fixed that in circRNA, cleavage gain from upstream node is added to the the wrong ORF. circRNA cleavage gain added to wrong ORF #783

Closes #780
Closes #782
Closes #783

Checklist

• This PR does NOT contain PHI or germline genetic data. A repo may need to be deleted if such data is uploaded. Disclosing PHI is a major problem.
• This PR does NOT contain molecular files, compressed files, output files such as images (e.g. .png, .jpeg), .pdf, .RData, .xlsx, .doc, .ppt, or other non-plain-text files. To automatically exclude such files using a .gitignore file, see here for example.
• I have read the code review guidelines and the code review best practice on GitHub check-list.
• The name of the branch is meaningful and well formatted following the standards, using [AD_username (or 5 letters of AD if AD is too long)]-[brief_description_of_branch].
• I have added the major changes included in this pull request to the CHANGELOG.md under the next release version or unreleased, and updated the date.
• All test cases passed locally.