Layout algebra

EFGDL 2 can describe a family of related input layouts without duplicating a whole protocol file. Four operators form a small, bounded algebra:

Syntax	Meaning
A B	concatenate adjacent terms: match A, then immediately match B
A | B	try A, then try B if A rejects the read
(A)?	prefer A, but allow it to be absent
(A)*N	repeat A exactly N times

Grouping uses parentheses. Layout operators are valid only inside input-read braces in a document with header { efgdl = 2 }; output construction remains deterministic and linear.

header { efgdl = 2 }

1{b<bc>[8](f[AAA] | f[CCC])(x[2])?r<read>:}
-> 1{<bc><read>}

This layout captures the same barcode and biological read around either of two linkers and permits an optional two-base spacer. Choice is ordered: if more than one alternative succeeds, the first source alternative wins.

Compilation and cost

seqproc normalizes the algebra at validation time. It never performs unbounded grammar search at runtime. Each normalized alternative becomes an isolated ANTISEQUENCE subgraph, and copy-on-write TryOp branching retries only rejected records. A linear layout still compiles directly and pays no branch overhead.

Normalization is deliberately bounded:

• at most 64 alternatives per read;
• at most 64 repetitions for one *N; and
• at most 4096 segments in one alternative.

seqproc validate rejects a Cartesian expansion beyond these limits instead of constructing an unexpectedly large graph. seqproc explain reports the alternative count and maximum normalized segment count for each input read.

Capture compatibility

Every alternative must expose the same named labels with the same interval and function definition. This makes later output templates and transformations well-typed regardless of the successful branch. Place shared captures outside a choice, or reference the same named definition in every arm:

header { efgdl = 2 }

bc = b[8]
1{(<bc>f[AAA] | f[CCC]<bc>)r<read>:}
-> 1{<bc><read>}

Repeated terms may contain named captures when their cardinality is statically fixed. Refer to an occurrence with a one-based index:

header { efgdl = 2 }

1{(b<round>[8]f[AAA])*3r<read>:}
-> #[header = append(" round3:", <round[3]>)]
   1{<round[1]><round[2]><round[3]><read>}

Every normalized alternative must expose the same number of occurrences for each public capture name. When a capture occurs more than once, an unindexed reference such as <round> is rejected; indices start at 1 and are checked at compile time. The compiler lowers each (capture, index) pair to an ordinary, short internal interval label, so indexing adds no per-read lookup or dynamic collection. Dynamically sized capture collections remain outside the bounded layout algebra.