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v2.1 - Better tools, better unphased data handling, bug fixes

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@dcdehaas dcdehaas released this 23 Dec 15:16
· 4 commits to main since this release
  • Add igdtools, which handles conversion, filtering, and stats of an IGD file.
  • Proper support for unphased data. Instead of just treating it identically to phased data (storage-wise), we now have numCopies defined on each variant in the index. For unphased diploid data, numCopies=1 is a heterozygote and numCopies=2 is a homozygote. numCopies=0 is unused (correspond to homozygous w.r.t. reference). igdtools supports unphased data in this way, as does VCF conversion. There is an example in examples/ that demonstrates how to compute runs-of-homozygosity (ROH) using this format.
  • Increment file format to V4 (backwards-compatible). Shrinks string representations a bit.
  • Speed up and simplify IGD writing by constructing each variant row in RAM prior to writing.
  • Properly clang-format the code in picovcf.hpp