Key optimizations: 1. Early termination after first good solution (like original) 2. Vectorized distance calculations 3. Optimized constraint checking 4. Smart search ordering (best regions first) 5. Reduced memory allocations

Key optimizations: 1. Early termination after first good solution (like original) 2. Vectorized distance calculations 3. Optimized constraint checking 4. Smart search ordering (best regions first) 5. Reduced memory allocations

runASCAT_enhanced(
  lrr,
  baf,
  lrrsegmented,
  bafsegmented,
  chromosomes,
  dist_choice,
  distancepng = NA,
  copynumberprofilespng = NA,
  nonroundedprofilepng = NA,
  cnaStatusFile = "copynumber_solution_status.txt",
  gamma = 0.55,
  allow100percent,
  reliabilityFile = NA,
  min.ploidy = 1.6,
  max.ploidy = 4.8,
  min.rho = 0.1,
  max.rho = 1,
  min.goodness = 63,
  uninformative_BAF_threshold = 0.51,
  chr.names,
  analysis = "paired",
  smart_ordering = TRUE,
  early_termination = TRUE,
  verbose = TRUE
)