Region Masking

Feature documentation: Region Masking

Exclude specific regions from primer placement.

Overview

Region masking prevents primers from being placed in:

• Repeat regions (detected as lowercase from RepeatMasker)
• Unknown regions (N-masked segments)
• Custom exclusions (BED file)

Usage

Use the --mask flag with primerlab run:

# Auto-detect all masked regions
primerlab run pcr --config my.yaml --mask auto

# Only lowercase (RepeatMasker) regions
primerlab run pcr --config my.yaml --mask lowercase

# Only N-masked regions
primerlab run pcr --config my.yaml --mask n

Mask Modes

Mode	Description
auto	Detect both lowercase and N regions
lowercase	Only RepeatMasker-style lowercase
n	Only N-masked regions
none	No masking (default)

BED File Support

Define custom exclusion zones with a BED file:

# excluded_regions.bed
chr1    100    200    repeat_region
chr1    500    600    SNP_hotspot

Example Output

🎭 Region Masking Report
========================
Mode: auto
Detected Regions: 3

  [50-75]     lowercase   (26 bp)
  [120-145]   N-masked    (26 bp)
  [200-250]   lowercase   (51 bp)

Total Masked: 103 bp (8.7% of sequence)

How It Works

1. Detection — Identify masked regions in sequence
2. Exclusion — Mark regions as off-limits for primers
3. Design — Primer3 avoids placing primers in masked areas
4. Report — Show which regions were excluded