Vv ensembl dev susmi

[Peter-J-Freeman]

@John-F-Wagstaff. The main part of this commit is handling variants like NW_011332691.1(NM_012234.6):c.335+1G>C. See issue #657.

This transcript is on the reverse strand and is working. I have added in some tests too.

[gitguardian]

⚠️ GitGuardian has uncovered 5 secrets following the scan of your pull request.

Please consider investigating the findings and remediating the incidents. Failure to do so may lead to compromising the associated services or software components.

🔎 Detected hardcoded secrets in your pull request

GitGuardian id	GitGuardian status	Secret	Commit	Filename
1081033	Triggered	Generic Password	d08f447	db_dockerfiles/vvta/Dockerfile	View secret
1081033	Triggered	Generic Password	d08f447	configuration/docker.ini	View secret
1081033	Triggered	Generic Password	d08f447	Jenkinsfile	View secret
1081033	Triggered	Generic Password	d08f447	vvta_docker.df	View secret
1081033	Triggered	Generic Password	be1add8	configuration/docker.ini	View secret

🛠 Guidelines to remediate hardcoded secrets

1. Understand the implications of revoking this secret by investigating where it is used in your code.
2. Replace and store your secrets safely. Learn here the best practices.
3. Revoke and rotate these secrets.
4. If possible, rewrite git history. Rewriting git history is not a trivial act. You might completely break other contributing developers' workflow and you risk accidentally deleting legitimate data.

To avoid such incidents in the future consider

• following these best practices for managing and storing secrets including API keys and other credentials
• install secret detection on pre-commit to catch secret before it leaves your machine and ease remediation.

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^{🦉 GitGuardian detects secrets in your source code to help developers and security teams secure the modern development process. You are seeing this because you or someone else with access to this repository has authorized GitGuardian to scan your pull request.}