Blacklist Overlap Filter

Exclude genomic intervals that overlap caller-supplied blacklist intervals.

Description

Blacklist filtering depends on the overlap inequalities and coordinate convention.

Blacklist filtering depends on the overlap inequalities and coordinate convention.^[1]

Exclude genomic intervals that overlap caller-supplied blacklist intervals.

When to use Blacklist Overlap Filter

Use this tool to exclude genomic intervals that overlap caller-supplied blacklist intervals.

Prepare the already measured signals, counts, coordinates, fitted coefficients or sequence strings requested. Keep assay definitions, units, aligned lists and caller-selected thresholds consistent.

How to use Blacklist Overlap Filter and understand its results

Prepare the already measured signals, counts, coordinates, fitted coefficients or sequence strings requested. Keep assay definitions, units, aligned lists and caller-selected thresholds consistent.
Enter intervalStarts, intervalEnds, blacklistStarts, blacklistEnds using the field table and calculation rules, then run the tool.
Read retainedIntervalIndexes, excludedIntervalIndexes, excludedCount. The explanation below defines the units, signs, ordering and any flags or placeholder values.
If the tool reports an input issue, correct the values and run it again. Apply the stated assumptions when interpreting a successfully returned result.

Input field	Meaning	Value type; see rules below	Requirement
intervalStarts	Interval starts	list of number	Required
intervalEnds	Interval ends	list of number	Required
blacklistStarts	Blacklist starts	list of number	Required
blacklistEnds	Blacklist ends	list of number	Required

Enter nonempty aligned intervals and aligned blacklist bounds with start≤end; return retained zero-based indices/excluded count. Empty blacklist is allowed.

overlap=start<blackEnd AND end>blackStart

Units, indexing, boundary conditions and exceptional cases are defined in the calculation rules above.

Output field	Meaning	Value type
retainedIntervalIndexes	Retained interval indexes	list of number
excludedIntervalIndexes	Excluded interval indexes	list of number
excludedCount	Excluded interval count	integer; minimum: 0

json

{
  "input": {
    "intervalStarts": [
      0,
      10,
      20
    ],
    "intervalEnds": [
      5,
      15,
      25
    ],
    "blacklistStarts": [
      12
    ],
    "blacklistEnds": [
      18
    ]
  },
  "output": {
    "retainedIntervalIndexes": [
      0,
      2
    ],
    "excludedIntervalIndexes": [
      1
    ],
    "excludedCount": 1
  }
}

Limitations and assumptions

Touching endpoints do not overlap; a zero-width interval inside an exclusion may still be removed. No chromosome/build or blacklist retrieval is supplied.

Numeric inputs, where present, must be finite. Follow the calculation-specific rules for overflow, underflow and exceptional cases. Lists are limited to 100,000 entries; the rules above may require smaller limits. Missing required fields, extra fields, wrong value types and violations of the calculation rules are input errors.

Alternative or Complementary methods

Use Probe Risk Filter: Filter probes against caller-supplied SNP-affected and cross-reactive ID lists. For a complementary task, use DMR Window Merger: Merge adjacent DMR windows within a selected distance.

References

Blacklist Overlap Filter — tool.io

Similar or alternative tools

Probe Risk Filter
Filter probes against caller-supplied SNP-affected and cross-reactive ID lists.
DMR Window Merger
Merge adjacent DMR windows within a selected distance.