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An Example RFC

This is an example of an ADAM RFC. It is meant to demonstrate syntax of an RFC as well as example headings and structure. You can view the source for this RFC online.

Schema

The following schema defines how to store FASTA formatted data in ADAM. The following schema captures all FASTA content.

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record ADAMFastaFragment {
    union {null, string } description = null;
    union {null, long } start = null;
    union {null, long } end = null;
    union {null, string } sequence = null;
}

All fields are optional and default to null.

Performance Considerations

The end field can be elided as it can be inferred from the start and sequence length. However, for performance, a pushdown predicate on the start and end position would be faster than materializing the sequence.

Predicates

A commonly used predicate would be to find all sequences with a specific description that start and end within a specified range.

Common Operations

  1. Reading the entire sequence
  2. Reading a portion of the sequence that falls in a specified range.

Open Questions

  1. Should we require that the end field is always specified for performance?
  2. Should we break up the description into the superset of all sequence identifiers?

Filename extension

Once coverted to ADAM, the file extension will be .fasta.adam.

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