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Alpha 5.13: .map/.ped comment lines, no-0/0 VCF-import warning
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@chrchang chrchang released this 18 Aug 23:16
· 15 commits to alpha5_patch since this release
v2.00a5.13
0cbe314

Bugfixes:

  • .map/.ped import now allows comment lines, as originally specified in the PLINK 1.0 documentation.
  • "--export bgen-1.{2,3}" no longer generates an invalid .bgen when the sample-ID block must be omitted due to otherwise exceeding the size limit.
  • BgzfFlush() and BgzfFlushTry() in include/plink2_bgzf.h should work properly again.

This also adds a warning when it looks like GATK GenotypeGVCFs needs to be rerun with --include-non-variant-sites, along with the --vcf-allow-no-nonvar flag to suppress it.

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