fix: c4gh deploy

[mmalenic]

Features

• Add component which fetches secrets from AWS Secrets Manager.
  • Currently this can fetch private/public C4GH keys, and is used by the CDK deployment code to enable C4GH.

Fixes

• Allow passing additional compiler flags to CDK code.
• Fix an issue with C4GHStorage which failed to read the correct amount data from the underlying stream.
  • The fix involves first determining the size of the C4GH header, and then sending another request to read the rest of the data.
  • This has to be done in two steps because it is not possible to know the amount of data that needs to be fetched without first knowing the size of the C4GH header.
• Fixed a failing test due to reused ports.

Misc

• Noting that the Crypt4GH edit list parsing (when reading the edit lists) has a bug which does not allow skipping bytes to the end of the file. See bug: reading edit list packets fails when skipping bytes to the end of the file EGA-archive/crypt4gh-rust#4.

[brainstorm]

Kudos! 🚀