add initial notebook copy pasta #8008
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Additional details and impacted files@@ Coverage Diff @@
## ah_var_store #8008 +/- ##
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Coverage ? 86.243%
Complexity ? 35196
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Files ? 2173
Lines ? 165004
Branches ? 17792
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Hits ? 142304
Misses ? 16373
Partials ? 6327 |
| # copy the reference data to set in hail | ||
| # gsutil -m cp 'gs://hail-common/references/Homo_sapiens_assembly38.fasta.gz' . | ||
| # gsutil -m cp 'gs://hail-common/references/Homo_sapiens_assembly38.fasta.fai' . | ||
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This is not necessary, the add_sequence call on lines 87/88 reads the references from GCS directly.
| # copy the reference data to set in hail | |
| # gsutil -m cp 'gs://hail-common/references/Homo_sapiens_assembly38.fasta.gz' . | |
| # gsutil -m cp 'gs://hail-common/references/Homo_sapiens_assembly38.fasta.fai' . |
| # gsutil -m cp 'gs://hail-common/references/Homo_sapiens_assembly38.fasta.gz' . | ||
| # gsutil -m cp 'gs://hail-common/references/Homo_sapiens_assembly38.fasta.fai' . | ||
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| ## Now RESTART the Kernal |
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Not necessary to restart the kernel in the notebook when working from the terminal, which is the expectation per lines 68-69.
| ## Now RESTART the Kernal |
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| ## * Replace LGT with GT ( for easier calculations later ) | ||
| filtered_vd = filtered_vds.variant_data | ||
| filtered_vd = filtered_vd.annotate_entries(GT=hl.vds.lgt_to_gt(filtered_vd.LGT, filtered_vd.LA) ) | ||
| filtered_vds = hl.vds.VariantDataset(filtered_vds.reference_data, filtered_vd) |
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It doesn't look like filtered_vds needs to be assigned here, it's never read before being reassigned on line 125.
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I liked the logic of it there, but you are right that it's overkill
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| ## * Respect the FT flag by setting all failing GTs to a no call | ||
| # TODO We dont seem to be using the dense matrix table here (TODO do we need to?) | ||
| filtered_vd = filtered_vd.annotate_entries(GT=hl.or_missing(hl.coalesce(filtered_vd.FT, True), filtered_vd.GT)) |
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This could use a comment for us non Hail wizards. 🙂 My (possibly incorrect) interpretation, working inside out:
coalesce returns the first non-missing value, so I think this is saying to return filtered_vt.FT if it is non-missing, otherwise True.
or_missing takes as its first argument a boolean predicate which if true returns the second argument, otherwise missing.
Putting it together:
filtered_vd.FT is True ⇒ GT keeps its current value
filtered_vd.FT is False ⇒ GT assigned missing
filtered_vd.FT is missing ⇒ GT keeps its current value
which actually doesn't seem right... 🤔 should this be ~filtered_vd.FT to keep GT if the filter is True?
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It does (and should) keep GT if the filter is True
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yeah I need to reverse the logic in my brain for how this works in Hail; work in progress... 🙂
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I just keep reciting "filter false is filter fail"
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