Bugfix Tag-PCR summary

bbimber · bbimber · commit ef522ad897bc · 2020-03-03T15:18:37.000-08:00
diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/preprocessing/TagPcrSummaryStep.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/preprocessing/TagPcrSummaryStep.java
@@ -158,6 +158,7 @@ public Output performAnalysisPerSampleRemote(Readset rs, File inputBam, Referenc
             if (totalReads > 0)
             {
                 hitRate = Integer.parseInt(metricMap.get("NumReadsSpanningJunction")) / (double) totalReads;
+                getPipelineCtx().getLogger().info("hit rate: " + hitRate);
             }
         }
         else
@@ -172,7 +173,7 @@ public Output performAnalysisPerSampleRemote(Readset rs, File inputBam, Referenc
                 referenceGenome.getGenomeId(),
                 "Reads: " + metricMap.get("NumReadsSpanningJunction") +
                         "\nJunction hit rate (of alignments): " + pf.format(Double.parseDouble(metricMap.get("PctReadsSpanningJunction")) +
-                        (hitRate == null ? "" : "\nJunction hit rate (of total reads): ") + pf.format(hitRate) +
+                        (hitRate == null ? "" : "\nJunction hit rate (of total reads): " + pf.format(hitRate)) +
                         "\nIntegration Sites: " + metricMap.get("TotalIntegrationSitesOutput") +
                         "\nAlignments Matching Insert: " + metricMap.get("FractionPrimaryAlignmentsMatchingInsert")
 

Original file line number	Diff line number	Diff line change
`@@ -158,6 +158,7 @@ public Output performAnalysisPerSampleRemote(Readset rs, File inputBam, Referenc`
`158`	`158`	`if (totalReads > 0)`
`159`	`159`	`{`
`160`	`160`	`hitRate = Integer.parseInt(metricMap.get("NumReadsSpanningJunction")) / (double) totalReads;`
	`161`	`+ getPipelineCtx().getLogger().info("hit rate: " + hitRate);`
`161`	`162`	`}`
`162`	`163`	`}`
`163`	`164`	`else`
`@@ -172,7 +173,7 @@ public Output performAnalysisPerSampleRemote(Readset rs, File inputBam, Referenc`
`172`	`173`	`referenceGenome.getGenomeId(),`
`173`	`174`	`"Reads: " + metricMap.get("NumReadsSpanningJunction") +`
`174`	`175`	`"\nJunction hit rate (of alignments): " + pf.format(Double.parseDouble(metricMap.get("PctReadsSpanningJunction")) +`
`175`		`- (hitRate == null ? "" : "\nJunction hit rate (of total reads): ") + pf.format(hitRate) +`
	`176`	`+ (hitRate == null ? "" : "\nJunction hit rate (of total reads): " + pf.format(hitRate)) +`
`176`	`177`	`"\nIntegration Sites: " + metricMap.get("TotalIntegrationSitesOutput") +`
`177`	`178`	`"\nAlignments Matching Insert: " + metricMap.get("FractionPrimaryAlignmentsMatchingInsert")`
`178`	`179`