[query] resolve VCF array field ambiguity #8
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patrick-schultz
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Aug 18, 2023
rfc/0008-template.rst
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| 2. Add ``disambiguate_single_dot: Dict[str, Callable[[Expression], Expression]]`` which, for each | ||
| INFO field f, accepts a row at which field f was "." and returns a value for field f. The value | ||
| of other fields with a "." in this row is unspecified. |
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Can you flesh this out a bit? I didn't understand on my first reading. Offline, we also discussed specifying the argument to the Callable to be a struct containing the entire current row, but with all fields in disambiguate_single_dot missing.
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Aug 21, 2023
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CHANGELOG: Fixed hail-is#13346. Previously, when parsing VCFs, Hail failed on INFO 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.
danking
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Aug 21, 2023
CHANGELOG: Fixed hail-is#13346. Previously, when parsing VCFs, Hail failed on INFO 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.
danking
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Aug 21, 2023
CHANGELOG: Fixed hail-is#13346. Previously, when parsing VCFs, Hail failed on INFO 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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to danking/hail
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Aug 21, 2023
CHANGELOG: Fixed hail-is#13346. Previously, when parsing VCFs, Hail failed on INFO 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
pushed a commit
to danking/hail
that referenced
this pull request
Aug 21, 2023
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
pushed a commit
to danking/hail
that referenced
this pull request
Aug 21, 2023
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.
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