Interval: merge overlapping features

Operation

Collapse overlapping or book-ended intervals within a single set into single spans. This is the within-set companion to interval-overlap-filter (which compares two sets). Two tool families do it, and the corpus uses both as co-equals — pick by which family the surrounding workflow already uses.

• toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_mergebed (“bedtools Merge”) — the modern path; epigenetics and VGP.
• toolshed.g2.bx.psu.edu/repos/devteam/merge/gops_merge_1 (“Merge the overlapping intervals of a dataset”, part of “Operate on Genomic Intervals”) — the SARS-CoV-2 masking pipeline.

Parameter names are corpus-inferred from tool_state.

When to reach for it

• Deduplicate overlapping windows before quantifying (after interval-windowed-coverage‘s slop step, so a region isn’t counted twice).
• Union a concatenated set of regions into non-overlapping spans (the merge step of interval-mask-by-set-algebra).
• Reduce a noisy feature set to its covered footprint.

This merges a set with itself. To combine and compare two different sets, use interval-overlap-filter.

Parameters (bedtools mergebed)

• input: connected interval set.
• distance: -d gap tolerance. "0" (corpus) merges only truly overlapping/book-ended features; a positive value also merges features within that many bp.
• strand: "" (corpus) merges regardless of strand.
• c_and_o_argument_repeat: list of {column, operation} pairs to carry/aggregate attribute columns through the merge (bedtools -c/-o). Empty [] in the corpus — coordinates only.
• header: false in the corpus.

tool_id: toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_mergebed/2.31.1
tool_state:
  input: { __class__: ConnectedValue }
  distance: "0"
  strand: ""
  c_and_o_argument_repeat: []
  header: false

Parameters (gops_merge — Operate on Genomic Intervals)

• input1: connected interval set.
• returntype: true returns the merged intervals as 1-based interval records (the corpus value in consensus-from-variation).

tool_id: toolshed.g2.bx.psu.edu/repos/devteam/merge/gops_merge_1/1.0.0
tool_state:
  input1: { __class__: ConnectedValue }
  returntype: true

The gops_* “Operate on Genomic Intervals” family (gops_merge, gops_subtract, gops_concat) is co-equal with bedtools in the corpus, not deprecated — the SARS-CoV-2 masking recipe uses it throughout, and gops_subtract/gops_concat have no bedtools equivalent in the corpus at all. See iwc-interval-operations-survey for the open redundancy question.

Pitfalls

• Sort before merge. Both tools assume coordinate-sorted input to merge correctly; unsorted input merges only adjacent-in-file overlaps. IWC pipelines arrive pre-sorted from upstream peak/coverage steps, so the corpus rarely shows an explicit sort — but a hand-built set may need one. (Coordinate-aware sort is itself absent from the IWC corpus; see galaxy-interval-patterns §Gaps.)
• distance: 0 is not “no merge.” 0 still merges overlapping and book-ended (touching) features; it is the correct default for “collapse true overlaps.” Only a negative value would require an actual overlap of ≥1 bp.
• Attribute columns are dropped unless you ask. c_and_o_argument_repeat: [] keeps coordinates only; score/name columns vanish. Populate the repeat with {column, operation} pairs to carry them.
• gops_merge returntype. Leaving it unset changes the output coordinate convention; the corpus sets true.

See also

• galaxy-interval-patterns — the interval pattern map.
• interval-mask-by-set-algebra — uses gops_merge to union a concatenated set.
• interval-windowed-coverage — merges slop windows before coverage.
• iwc-interval-operations-survey — corpus evidence and the gops-vs-bedtools redundancy note.