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remove exhaustive deconstruct from README -- thanks, tests!
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glennhickey committed May 20, 2024
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Expand Up @@ -396,14 +396,6 @@ vg index hla.vg -x hla.xg
vg deconstruct hla.xg -e -p "gi|568815592:29791752-29792749" > hla_variants.vcf
```

Variants can also be inferred strictly from topology by not using `-e`, though unlike the above example, cycles are not supported. "Deconstruct" the VCF variants that were used to construct the graph. The output will be similar but identical to `small/x.vcf.gz` as `vg construct` can add edges between adjacent alts and/or do some normalization:

<!-- !test check Deconstruct from construct -->
```sh
# using the same graph from the `map` example
vg deconstruct x.xg -p x > x.vcf
```

Haplotype paths from `.gbz` or `.gbwt` indexes input can be considered using `-z` and `-g', respectively.

As with `vg call`, it is best to compute snarls separately and pass them in with `-r` when working with large graphs.
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@adamnovak
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vg CI tests complete for branch deconstruct. View the full report here.

0 tests passed, 16 tests failed and 0 tests skipped in 521 seconds

Failed tests:

  • test_sim_chr21_snp1kg (34 seconds)
  • test_full_brca2_cactus (35 seconds)
  • test_full_brca2_primary (32 seconds)
  • test_full_brca2_snp1kg (32 seconds)
  • test_map_brca1_cactus (30 seconds)
  • test_map_brca1_primary (31 seconds)
  • test_map_brca1_snp1kg (30 seconds)
  • test_map_brca1_snp1kg_mpmap (31 seconds)
  • test_map_mhc_primary (31 seconds)
  • test_map_mhc_snp1kg (32 seconds)
  • test_sim_mhc_cactus (29 seconds)
  • test_sim_mhc_snp1kg (28 seconds)
  • test_sim_mhc_snp1kg_mpmap (26 seconds)
  • test_call_chr21_snp1kg (39 seconds)
  • test_sim_chr21_snp1kg_trained (32 seconds)
  • test_sim_yeast_cactus (28 seconds)

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