Fix MNV and generateIndex

[zhuchcn]

Description

Two issues fixed in this PR:

1. Adjacent variants were not merged as MNVs successfully. The function always exited with nothing.
2. Because of the updating to on-disk GTF, the coding transcripts were not generated and saved successfully. filterFasta is the only command affected.

Closes #...

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.

[lydiayliu]

Adjacent variants were not merged as MNVs successfully. The function always exited with nothing.

None of them? XD Were the MNVs directly from VEP at least treated properly?

[zhuchcn]

None of them? XD Were the MNVs directly from VEP at least treated properly?

Those are fine. Just the adjacent grouping wasn't done. I moved around the code block a couple of times and it must go wrong then. It was a bad decision not to have any test cases.

[zhuchcn]

There might be still some inconsistency between mpg and bruteForce in turns of adjacent merged MNVs. I'll keep working on this but will merge it right now.