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Accept PSAM files without FID column#687

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Eldergenix:eldergenix/fix-issue-666-psam-missing-fid
Open

Accept PSAM files without FID column#687
Eldergenix wants to merge 1 commit into
rgcgithub:masterfrom
Eldergenix:eldergenix/fix-issue-666-psam-missing-fid

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Fixes #666

Summary

  • allow .psam headers that start with #IID when #FID is absent
  • use an internal FID value of 0 for absent-FID PSAM samples
  • apply the same header and ID handling to the primary PGEN reader and external PGEN reader
  • keep malformed rows rejected, including rows missing a declared SEX column

Validation

  • g++ -std=c++11 -fsyntax-only src/Geno.cpp -I./src -I./external_libs/pgenlib -I./external_libs/pgenlib/simde -I./external_libs/pgenlib/include -I./external_libs/cxxopts/include -I./external_libs/LBFGSpp/include -I./external_libs/eigen-3.4.0 -I./external_libs/remeta -I./external_libs -I/tmp/regenie-bgen-v1.1.7 -I/tmp/regenie-bgen-v1.1.7/genfile/include -I/tmp/regenie-bgen-v1.1.7/3rd_party/boost_1_55_0 -I/tmp/regenie-bgen-v1.1.7/3rd_party/zstd-1.1.0/lib -I/tmp/regenie-bgen-v1.1.7/db/include -I/tmp/regenie-bgen-v1.1.7/3rd_party/sqlite3 - passed; warnings only from existing vendored/old dependency headers
  • git diff --check HEAD~1..HEAD - passed

Not run

  • Full local build/test suite was not run because cmake and gfortran are not installed in my local environment.
  • Docker-based build/test was not run because the Docker daemon is unavailable locally.

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Regenie requires FID to be present in .psam files although it is optional in the spec

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