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PopLDdecay-3.45

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@hewm2008 hewm2008 released this 16 Jul 07:41
v3.45
5dcd070

PopLDdecay v3.45

Performance & Memory Optimization:

  • CPU: ~5% reduction vs v3.43 (TF=1 -MaxDist 10, BB.vcf.gz 495K SNPs × 57 samples)
  • Memory: ~34% RSS reduction (160 MB → 106 MB)

Key changes:

  • istringstream → strtoll() for position/genotype parsing
  • GetBestBase: pass-by-value → const & with find()
  • ostringstream → char lookup / int2str for single-digit conversion
  • Inlined TF=1 hot-loop kernel (eliminated statementVar + function call overhead)
  • Local variable storage for _MB function variants
  • Added missing pclose() in EHH routine

Correctness fixes (output verified bit-identical for TF=1..8 on VCF & Genotype):

  • typedef int llong → long long (fixes position overflow >2^31)
  • Memory leak fix: delete[] RRNum[InInt] last row in PairWiseComNewOUT_A
  • UB fix: memset(Var.DDE, 0, sizeof(Var.DDE)) in all _MA functions
  • Removing 5x unreachable break; after return
  • Removing if (D_A == 0.0) D_A = 0.0 no-op

Code cleanup:

  • Removed ~180 lines of dead/commented-out code
  • Unified version number to v3.45
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