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Reflect rename of TagPcrSummary tool
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SequenceAnalysis/src/org/labkey/sequenceanalysis/run/preprocessing/TagPcrSummaryStep.java

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -69,7 +69,7 @@ public static class Provider extends AbstractAnalysisStepProvider<TagPcrSummaryS
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{
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public Provider()
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{
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super("Tag-PCR", "Tag-PCR Integration Sites", null, "This will produce a table summarizing unique alignments in this BAM. It was originally created to summarize genomic insertions.", Arrays.asList(
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super("Tag-PCR", "Map Integration Sites", null, "This will produce a table summarizing unique genome/transgene junctions using a BAM.", Arrays.asList(
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ToolParameterDescriptor.create(OUTPUT_GENBANK, "Create Genbank Output", "If selected, this will output a genbank file summarizing amplicons and primers", "checkbox", new JSONObject(){{
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put("checked", true);
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}}, true),
@@ -349,7 +349,7 @@ public void execute(File bamFile, File referenceFasta, File outputTable, @Nullab
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List<String> args = new ArrayList<>();
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args.addAll(getBaseArgs());
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args.add("TagPcrSummary");
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args.add("IntegrationSiteMapper");
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args.add("--bam");
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args.add(bamFile.getPath());

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