[query][rfc-0008] permit more INFO and FORMAT array-fields with missing elements #13465
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CHANGELOG: Fixed hail-is#13346. Previously, when parsing VCFs, Hail failed on INFO or FORMAT fields with missing elements because the meaning of "." could be ambiguous. Hail now resovles the ambiguity, when possible, using the number of alleles. If the meaning is still ambiguous after considering the number of alleles, Hail uses a new `hl.import_vcf` parameter to resolve the ambiguity. See the `hl.import_vcf` docs for details. See hail-is/hail-rfcs#8 for details on the problem and the solution. I assessed the effect of removing the `array_elements_required=True` fast path by evaluating the following code against this PR's tip commit `cd06c248e4` and `0.2.120` (`f00f916faf`). I ran it three times per commit and report each individual time as well as the average. ``` In [1]: import hail as hl In [2]: %%time ...: mt = hl.import_vcf( ...: '/Users/dking/projects/hail-data/ALL.chr21.raw.HC.vcf.bgz' ...: ) ...: mt._force_count_rows() ``` | commit | run 1 (s) | run 2 (s) | run 3 (s) | average (s) | warm average (s) | |--------------------------|-----------|-----------|-----------|-------------|------------------| | `cd06c248e4` (this PR) | 116s | 80s | 77s | 91+-18 | 78.5 +- 1.5 | | `f00f916faf` (`0.2.120`) | 112s | 80s | 79s | 90+-15 | 79.5 +- 0.5 | This is what I expected. For a VCF with no ambiguity and few instances of ".", we've added a very minor amount of new work.
danking
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Need more thought. |
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CHANGELOG: Fixed #13346. Previously, when parsing VCFs, Hail failed on INFO or FORMAT fields with missing elements because the meaning of "." could be ambiguous. Hail now resovles the ambiguity, when possible, using the number of alleles. If the meaning is still ambiguous after considering the number of alleles, Hail uses a new
hl.import_vcfparameter to resolve the ambiguity. See thehl.import_vcfdocs for details.See hail-is/hail-rfcs#8 for details on the problem and the solution.
I assessed the effect of removing the
array_elements_required=Truefast path by evaluating the following code against this PR's tip commitcd06c248e4and0.2.120(f00f916faf). I ran it three times per commit and report each individual time as well as the average.cd06c248e4(this PR)f00f916faf(0.2.120)This is what I expected. For a VCF with no ambiguity and few instances of ".", we've added a very minor amount of new work.
Note that I had to specifically override the Number setting for certain FORMAT and INFO fields because they were set to
.in the benchmarked VCF. If this error appears in a 1KG VCF, it must be fairly common.