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Update mGAP steps to use sites-only VCF, not full VCF
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-2
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mGAP/src/org/labkey/mgap/pipeline/mGapReleaseAlleleFreqStep.java

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -43,7 +43,7 @@ public Provider()
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ToolParameterDescriptor.createExpDataParam(REF_VCF, "mGAP Release", "The mGAP release VCF to use for annotation", "sequenceanalysis-sequenceoutputfileselectorfield", new JSONObject()
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{{
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put("allowBlank", false);
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put("category", "mGAP Release");
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put("category", "mGAP Release: Sites Only:");
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put("performGenomeFilter", false);
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put("doNotIncludeInTemplates", true);
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}}, null)

mGAP/src/org/labkey/mgap/pipeline/mGapReleaseComparisonStep.java

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -46,7 +46,7 @@ public Provider()
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ToolParameterDescriptor.createExpDataParam(REF_VCF, "mGAP Release", "The mGAP release VCF to use for comparison", "sequenceanalysis-sequenceoutputfileselectorfield", new JSONObject()
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{{
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put("allowBlank", false);
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put("category", "mGAP Release");
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put("category", "mGAP Release: Sites Only");
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put("performGenomeFilter", false);
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put("doNotIncludeInTemplates", true);
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}}, null)

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