Remove pet code from CreateVariantIngestFiles and friends [VS-375] #7773
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mcovarr
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RoriCremer
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Apr 13, 2022
| @@ -123,7 +123,7 @@ task CheckForDuplicateData { | |||
| # check the INFORMATION_SCHEMA.PARTITIONS table to see if any of input sample names/ids have data loaded into their partitions | |||
| # this returns the list of sample names that do already have data loaded | |||
| echo "WITH items as (SELECT s.sample_id, s.sample_name, s.is_loaded, s.withdrawn FROM \`${TEMP_TABLE}\` t left outer join \`${SAMPLE_INFO_TABLE}\` s on (s.sample_name = t.sample_name)) " >> query.sql | |||
| echo "SELECT i.sample_name FROM \`${INFO_SCHEMA_TABLE}\` p JOIN items i ON (p.partition_id = CAST(i.sample_id AS STRING)) WHERE p.total_logical_bytes > 0 AND (table_name like 'ref_ranges_%' OR table_name like 'vet_%' OR table_name like 'pet_%')" >> query.sql | |||
| echo "SELECT i.sample_name FROM \`${INFO_SCHEMA_TABLE}\` p JOIN items i ON (p.partition_id = CAST(i.sample_id AS STRING)) WHERE p.total_logical_bytes > 0 AND (table_name like 'ref_ranges_%' OR table_name like 'vet_%')" >> query.sql | |||
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outside the scope of this pr---but this might be a good place to collect info on which samples have been loaded into just the vet or just re_ranges
RoriCremer
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Apr 13, 2022
| if (enablePet || enableReferenceRanges) { | ||
| refCreator = new RefCreator(sampleIdentifierForOutputFileName, sampleId, tableNumber, seqDictionary, gqStateToIgnore, dropAboveGqThreshold, outputDir, outputType, enablePet, enableReferenceRanges, projectID, datasetName); | ||
| if (enableReferenceRanges) { | ||
| //noinspection ConstantConditions |
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I was going to complain, but we do this for the VET as well.!??!...seems like unneeded complexity esp since it's also a param
RoriCremer
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Apr 13, 2022
| @@ -279,12 +258,10 @@ public void apply(final VariantContext variant, final ReadsContext readsContext, | |||
| refCreator.apply(variant, intervalsToWrite); | |||
| } | |||
| } catch (IOException ioe) { | |||
| throw new GATKException("Error writing PET", ioe); | |||
| throw new GATKException("Error writing reference ranges", ioe); | |||
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and here, are we then assuming enableReferenceRanges is true?
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Good catch, it looks like there should be an if here like the one for vet on line 250.
RoriCremer
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Apr 13, 2022
| @@ -35,8 +32,8 @@ | |||
| * Ingest variant walker | |||
| */ | |||
| @CommandLineProgramProperties( | |||
| summary = "Exome and Genome Ingest tool for the Joint Genotyping in Big Query project", | |||
| oneLineSummary = "Ingest tool for BQJG", | |||
| summary = "Exome and Genome Ingest tool for the Genomic Variant Store in Big Query project", | |||
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nit: we could drop the "in Big Query project"
RoriCremer
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Apr 13, 2022
| shortName = "ep", | ||
| doc = "write pet data", | ||
| optional = true) | ||
| public boolean enablePet = true; |
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since we from the default as true here, maybe we make it default to true on ref ranges above?
RoriCremer
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Apr 13, 2022
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