Fix NPE

Author: bbimber

SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/LofreqAnalysis.java

@@ -230,6 +230,7 @@ public Output performAnalysisPerSampleRemote(Readset rs, File inputBam, Referenc
         int gapIntervals = 0;
         double avgDepth;
 
+        //TODO: rescue pindel?
         File mask = new File(outputDir, "mask.bed");
         Map<String, Integer> gatkDepth = new HashMap<>();
         try (CSVReader reader = new CSVReader(Readers.getReader(coverageOut), '\t');CSVWriter writer = new CSVWriter(IOUtil.openFileForBufferedUtf8Writing(mask), '\t', CSVWriter.NO_QUOTE_CHARACTER))
@@ -449,6 +450,7 @@ public Output performAnalysisPerSampleRemote(Readset rs, File inputBam, Referenc
                 }
             }
 
+            getPipelineCtx().getLogger().info("Total consensus pindel variants: " + totalPindelConsensusVariants);
             if (totalPindelConsensusVariants == 0)
             {
                 getPipelineCtx().getLogger().info("deleting empty pindel VCF: " + pindelVcf.getPath());

SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/PindelAnalysis.java

@@ -492,9 +492,9 @@ public static File createVcf(File pindelOutput, File vcfOutput, ReferenceGenome
                 }
 
                 double eventCoverage = 0.0;
-                if (StringUtils.trimToNull(line[11]) != null)
+                if (StringUtils.trimToNull(line[10]) != null)
                 {
-                    eventCoverage = Double.parseDouble(line[11]);
+                    eventCoverage = Double.parseDouble(line[10]);
                 }
 
                 if (("D".equals(line[0]) || "S".equals(line[0])) && eventCoverage > settings.MAX_DEL_EVENT_COVERAGE)