Add filtering to ExtractCohort #6971
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kcibul
approved these changes
Nov 19, 2020
| @@ -46,6 +55,17 @@ protected void onStartup() { | |||
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| VCFHeader header = CommonCode.generateVcfHeader(sampleNames, reference.getSequenceDictionary()); | |||
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| if (minLocation == null && maxLocation == null && hasUserSuppliedIntervals()) { | |||
| fullName = "filter-set-name", | ||
| doc = "Name in filter_set_name column of filtering table to use. Which training set should be applied in extract." | ||
| ) | ||
| private String nameOfFilterSet = null; |
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perhaps filterSetName instead
| @@ -85,7 +86,8 @@ public ExtractCohortEngine(final String projectID, | |||
| final double vqsLodSNPThreshold, | |||
| final double vqsLodINDELThreshold, | |||
| final ProgressMeter progressMeter, | |||
| final ExtractCohort.QueryMode queryMode) { | |||
| final ExtractCohort.QueryMode queryMode, | |||
| final String nameOfFilterSet) { | |||
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perhaps filterSetName instead
| final String rowRestrictionWithFilterSetName = rowRestriction + " AND " + SchemaUtils.FILTER_SET_NAME + " = '" + nameOfFilterSet + "'"; | ||
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| final StorageAPIAvroReader filteringTableAvroReader = new StorageAPIAvroReader(filteringTableRef, rowRestrictionWithFilterSetName, projectID); | ||
| final HashMap<Locatable, HashMap<Allele, HashMap<Allele, Double>>> fullVqsLodMap = new HashMap<>(); |
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might be good to have a comment about what each of these alleles are? is the first allele reference and the second is the alternate?
| final String yng = queryRow.get("yng_status").toString(); | ||
| final Allele ref = Allele.create(queryRow.get("ref").toString(), true); | ||
| final Allele alt = Allele.create(queryRow.get("alt").toString(), false); | ||
| final Locatable locatable = new SimpleInterval(contig, currentPosition, currentPosition); |
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instead of locatable, could we just leave it as location since we'll have that when we try to lookup in this table? (ie coming out of the extract BQ?)
| } | ||
| final VariantContext filteredVC = builder.make(); | ||
| return filteredVC; | ||
| } | ||
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| private <T> LinkedHashMap<Allele, T> remapAllelesInMap(VariantContext vc, HashMap<Allele, HashMap<Allele, T>> datamap, T emptyVal) { |
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A comment for what this does would be great, since even reading it... I'm not sure!
kcibul
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* adding filtering to extractCohort * addressing comments
kcibul
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* adding filtering to extractCohort * addressing comments
Marianie-Simeon
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* adding filtering to extractCohort * addressing comments
kcibul
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* adding filtering to extractCohort * addressing comments
mmorgantaylor
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* adding filtering to extractCohort * addressing comments
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I think this is ready for initial review while I start testing it on larger scale data. I've left adding in the full VQSR tranche filtering as TODOs for now.