Novel ORF from coding transcripts

[zhuchcn]

Description

Novel ORF finding is now enabled from both callNoncoding and callVariant. The ORF ID is now added to the FASTA header if it's from novel ORFs for both coding and noncoding transcripts. Example:

Canonical ORF: ENST0001.1|SNV-101-A-T|1 Novel ORF: ENST0001.1|SNV-156-C-T|ORF2|1 Noncoding novel ORF: ENST0002.1|SNV-324-T-G|ORF3|2 Novel ORF with fusion: FUSION-ENST0001.1:92-ENST0077:968|ORF1|1

Closes #659

Checklist

• [X] 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.
• [X] 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.
• [X] I have read the code review guidelines and the code review best practice on GitHub check-list.
• [X] 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].
• [X] 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.
• [X] All test cases passed locally.

[zhuchcn]

Given that the callNoncoding now not only calls peptides from noncoding transcripts, I'm thinking of renaming it to callNovelORF, which better describes what it does, that calls peptides from novel ORFs.

[lydiayliu]

I like the look and sound of callNovelORF lol

Is this supported in callAltTranslation already as well?

[zhuchcn]

I like the look and sound of callNovelORF lol

OK I'll go ahead and rename it!

Is this supported in callAltTranslation already as well?

I didn't add this alt start finding in callAltTranslation, because I like to keep it only finding alt translation on canonical ORFs. But peptides with alt trans can be still called using callNoncoding (the new callNovelORF) with --w2f-reassignment