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File format V4: shrink strings, add variant ids (backwards compat) #14

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merged 2 commits into from
Aug 15, 2024

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@dcdehaas dcdehaas commented Jul 1, 2024

This is a backwards compatible file-format change. I.e., the IGD parser will load both V3 and V4 files. V4 changes:

  • The lengths of strings is encoded as 32-bit integers instead of 64-bit. We don't expect any strings longer than 4 billion chars..
  • Similar to individual IDs, variant IDs can be copied over from VCF files. Generally I'd recommend putting all meta-data in a separate file (JSON or similar). You can do everything you need by selecting a set of variants/samples to operate on, then use the IGD data, and then post-process/display results using the separate metadata. There is no reason (other than convenience of having a single file) to keep meta-data with the actual genotype data.

This is a backwards compatible file-format change. I.e., the IGD
parser will load both V3 and V4 files. V4 changes:
* The lengths of strings is encoded as 32-bit integers instead of
  64-bit. We don't expect any strings longer than 4 billion chars..
* Similar to individual IDs, variant IDs can be copied over from
  VCF files. Generally I'd recommend putting _all_ meta-data in
  a separate file (JSON or similar). You can do everything you need
  by selecting a set of variants/samples to operate on, then use
  the IGD data, and then post-process/display results using the
  separate metadata. There is no reason (other than convenience of
  having a single file) to keep meta-data with the actual genotype
  data.
@dcdehaas dcdehaas merged commit e485e9f into main Aug 15, 2024
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@dcdehaas dcdehaas deleted the igd_fmt_v4 branch August 15, 2024 14:21
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