Add logging

bbimber · bbimber · commit c515cb4c855a · 2021-08-24T13:39:43.000-07:00
diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/preprocessing/TagPcrSummaryStep.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/preprocessing/TagPcrSummaryStep.java
@@ -165,12 +165,21 @@ public Output performAnalysisPerSampleRemote(Readset rs, File inputBam, Referenc
         {
             primerTable = new File(outputDir, basename + ".primers.txt");
         }
+        else
+        {
+            getPipelineCtx().getLogger().info("will not design primers")
+        }
 
         File genbank = null;
         if (outputGenbank)
         {
             genbank = new File(outputDir, basename + ".sites.gb");
         }
+        else
+        {
+            getPipelineCtx().getLogger().info("will not output genbank file")
+        }
+
         File metrics = getMetricsFile(inputBam, outputDir);
 
         List<String> extraArgs = new ArrayList<>(getClientCommandArgs());

Original file line number	Diff line number	Diff line change
`@@ -165,12 +165,21 @@ public Output performAnalysisPerSampleRemote(Readset rs, File inputBam, Referenc`
`165`	`165`	`{`
`166`	`166`	`primerTable = new File(outputDir, basename + ".primers.txt");`
`167`	`167`	`}`
	`168`	`+ else`
	`169`	`+ {`
	`170`	`+ getPipelineCtx().getLogger().info("will not design primers")`
	`171`	`+ }`
`168`	`172`
`169`	`173`	`File genbank = null;`
`170`	`174`	`if (outputGenbank)`
`171`	`175`	`{`
`172`	`176`	`genbank = new File(outputDir, basename + ".sites.gb");`
`173`	`177`	`}`
	`178`	`+ else`
	`179`	`+ {`
	`180`	`+ getPipelineCtx().getLogger().info("will not output genbank file")`
	`181`	`+ }`
	`182`	`+`
`174`	`183`	`File metrics = getMetricsFile(inputBam, outputDir);`
`175`	`184`
`176`	`185`	`List<String> extraArgs = new ArrayList<>(getClientCommandArgs());`