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ah update array extract tool #6827

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merged 2 commits into from
Sep 18, 2020
Merged

ah update array extract tool #6827

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8853098
remove compressed data, change GT to single char
ahaessly Sep 16, 2020
30bab6d
updated from PR feedback
ahaessly Sep 17, 2020
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22 changes: 19 additions & 3 deletions src/main/java/org/broadinstitute/hellbender/tools/variantdb/arrays/ArrayExtractCohort.java
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Original file line number Diff line number Diff line change
Expand Up @@ -57,8 +57,8 @@ public enum QueryMode {
private String projectID = null;

@Argument(
fullName = "sample-info-table",
doc = "Fully qualified name of a bigquery table containing a single column `sample` that describes the full list of samples to evoque",
fullName = "cohort-sample-table",
doc = "Fully qualified name of a bigquery table containing the sample_id and sample_name for the samples in the cohort you are extracting ",
optional = true
)
private String sampleTableName = null;
Expand Down Expand Up @@ -98,6 +98,12 @@ public enum QueryMode {
)
private String cohortTable = null;

@Argument(
fullName = "gt-only",
doc = "If true, only get the genotype info. Otherwise include NORMX, NORMY, BAF, and LRR",
optional = true)
private boolean gtDataOnly = false;

@Argument(
fullName = "use-compressed-data",
doc = "If true, use bit-packed fields for data",
Expand All @@ -117,6 +123,14 @@ public enum QueryMode {
)
private int localSortMaxRecordsInRam = DEFAULT_LOCAL_SORT_MAX_RECORDS_IN_RAM;

// TODO remove before production
@Argument(
fullName = "use-legacy-gt-encoding",
doc = "If the GT encodoing was AA, AB, BB",
optional = true
)
private Boolean useLegacyGTEncoding = false;

@Override
public boolean requiresReference() {
return true;
Expand Down Expand Up @@ -170,12 +184,14 @@ protected void onStartup() {
sampleIdMap,
probeIdMap,
cohortTable,
gtDataOnly,
minProbeId,
maxProbeId,
localSortMaxRecordsInRam,
useCompressedData,
printDebugInformation,
progressMeter);
progressMeter,
useLegacyGTEncoding);
vcfWriter.writeHeader(header);
}

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