array cohort extract #6666
array cohort extract #6666
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is this static block a place holder for something?
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| private static final Logger logger = LogManager.getLogger(ExtractCohortEngine.class); |
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change to to match class name
| * This value is used to construct the genotype information of those missing samples | ||
| * when they are merged together into a {@link VariantContext} object | ||
| */ | ||
| public static int MISSING_CONF_THRESHOLD = 60; |
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i think we can remove this
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| final String contig = probeInfo.contig; | ||
| final long position = probeInfo.position; | ||
| final Allele refAllele = Allele.create(refSource.queryAndPrefetch(contig, position, position).getBaseString(), true); |
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i wonder if it would be easier to get the ref allele from the probe_info table - since we already use it. and then we might not need the reference as an input?
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Something to think about, although we still need the reference when we initialize the vcf writer to get the sequence dictionary for the header
| private void finalizeCurrentVariant(final List<VariantContext> unmergedCalls, final Set<String> currentVariantSamplesSeen, final String contig, final long start, final Allele refAllele) { | ||
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| // TODO: this is where we infer missing data points... once we know what we want to drop | ||
| // final Set<String> samplesNotEncountered = Sets.difference(sampleNames, currentVariantSamplesSeen); |
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do you think we are going to be dropping something we aren't already?
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maybe... we need to dig into more data, and when we get to imputed data I think we will
| lrr = data.lrr; | ||
| baf = data.baf; | ||
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| // Genotype -- what about no-call? |
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is no-call the same as missing? there is a enum value for MISSING.
and if you mean how do you represent a missing allele in the genotype, there is a constant for that. i think it's Genotype.NO_CALL
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| // TODO: constantize | ||
| try { |
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i think you can use the constants from the RawArrayFieldEnum
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yeah I think these might all go away once we're storing compressed data so I didn't think too much about it
| // Get the query string: | ||
| final String sampleListQueryString = | ||
| "SELECT probeId, Name, Chr, Position, Ref, AlleleA, AlleleB" + | ||
| " FROM `" + fqProbeTableName + "`"; |
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we could add a constant in ProbeInfoSchema for the list of field to get for extract. still need to figure out a package structure that makes sense since right now that class is in ingest
| this.alleleA = alleleA; | ||
| this.alleleB = alleleB; | ||
| } | ||
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i can merge the ProbeInfo class under ingest with this one
| // Order is critical here, the ordinal is the int encoding | ||
| AA,AB, BB, NO_CALL | ||
| } | ||
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again, i think we should merge this with the enum in the ingest code (i can do this after the PR is merged)
* array cohort extract * roundtripping with binary compression * PR comments
* array cohort extract * roundtripping with binary compression * PR comments
* array cohort extract * roundtripping with binary compression * PR comments
* array cohort extract * roundtripping with binary compression * PR comments
* array cohort extract * roundtripping with binary compression * PR comments
* array cohort extract * roundtripping with binary compression * PR comments
* array cohort extract * roundtripping with binary compression * PR comments
* array cohort extract * roundtripping with binary compression * PR comments
* array cohort extract * roundtripping with binary compression * PR comments
* array cohort extract * roundtripping with binary compression * PR comments
* array cohort extract * roundtripping with binary compression * PR comments
* array cohort extract * roundtripping with binary compression * PR comments
* array cohort extract * roundtripping with binary compression * PR comments
* array cohort extract * roundtripping with binary compression * PR comments
* array cohort extract * roundtripping with binary compression * PR comments
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