Bundle Update: callVariant & parseVEP

[zhuchcn]

Description

Fixed

• Fixed callVariant that variant bubble not identified correctly.

• Fixed parseVEP that failed records will now be skipped with --skip-failed. a variant crashes the parseVEP #902

• Fixed callVariant with variant bubble finding error starting from a out-bridge node.

• Fixed callVariant that peptide annotation not created correctly with SEC

Changed

• A check added when converting a genomic location to gene coordinate to ensure they overlap.

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.

[zhuchcn]

Fuzz test good after 10,870 cases.

---------------------------------------------------------
|                  FUZZ TEST SUMMARY                    |
---------------------------------------------------------
|                       pass    fail    none    total   |
| ----------------------------------------------------- |
| snv                   2710    0       0       2710    |
| indel                 2850    0       0       2850    |
| comprehensive         5310    0       0       5310    |
| ----------------------------------------------------- |
| sum                   10870   0       0       10870   |
---------------------------------------------------------