Add reference arg to CollectInsertSizeMetrics

Author: bbimber

SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/PicardAlignmentMetricsHandler.java

@@ -258,7 +258,7 @@ public void processFilesRemote(List<SequenceOutputFile> inputFiles, JobContext c
                     File metricsFile = new File(ctx.getOutputDir(), FileUtil.getBaseName(o.getFile()) + ".insertsize.metrics");
                     File metricsHistogram = new File(ctx.getOutputDir(), FileUtil.getBaseName(o.getFile()) + ".insertsize.metrics.pdf");
                     CollectInsertSizeMetricsWrapper wrapper = new CollectInsertSizeMetricsWrapper(job.getLogger());
-                    wrapper.executeCommand(o.getFile(), metricsFile, metricsHistogram);
+                    wrapper.executeCommand(o.getFile(), metricsFile, metricsHistogram, ctx.getSequenceSupport().getCachedGenome(o.getLibrary_id()).getWorkingFastaFile());
                 }
 
                 if (runMarkDuplicates)

SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/AlignmentNormalizationTask.java

@@ -268,7 +268,7 @@ else if (step.expectToCreateNewBam())
                 getJob().setStatus(PipelineJob.TaskStatus.running, "CALCULATING INSERT SIZE METRICS");
                 File metricsFile2 = new File(finalDestination.getParentFile(), FileUtil.getBaseName(finalDestination) + ".insertsize.metrics");
                 File metricsHistogram = new File(finalDestination.getParentFile(), FileUtil.getBaseName(finalDestination) + ".insertsize.metrics.pdf");
-                if (new CollectInsertSizeMetricsWrapper(getJob().getLogger()).executeCommand(finalDestination, metricsFile2, metricsHistogram) != null)
+                if (new CollectInsertSizeMetricsWrapper(getJob().getLogger()).executeCommand(finalDestination, metricsFile2, metricsHistogram, referenceGenome.getWorkingFastaFile()) != null)
                 {
                     getTaskHelper().getFileManager().addOutput(metricsAction, "Insert Size Metrics File", metricsFile2);
                     getTaskHelper().getFileManager().addOutput(metricsAction, "Insert Size  Metrics Histogram", metricsHistogram);

SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/SequenceAlignmentTask.java

@@ -1014,7 +1014,7 @@ else if (step.expectToCreateNewBam())
                         File metricsFile2 = new File(renamedBam.getParentFile(), FileUtil.getBaseName(renamedBam) + ".insertsize.metrics");
                         File metricsHistogram = new File(renamedBam.getParentFile(), FileUtil.getBaseName(renamedBam) + ".insertsize.metrics.pdf");
                         CollectInsertSizeMetricsWrapper collectInsertSizeMetricsWrapper = new CollectInsertSizeMetricsWrapper(getJob().getLogger());
-                        if (collectInsertSizeMetricsWrapper.executeCommand(renamedBam, metricsFile2, metricsHistogram) != null)
+                        if (collectInsertSizeMetricsWrapper.executeCommand(renamedBam, metricsFile2, metricsHistogram, referenceGenome.getWorkingFastaFile()) != null)
                         {
                             getHelper().getFileManager().addOutput(metricsAction, "Insert Size Metrics File", metricsFile2);
                             getHelper().getFileManager().addOutput(metricsAction, "Insert Size Metrics Histogram", metricsHistogram);

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

@@ -156,15 +156,15 @@ private static String parseInsertMetrics(File inputFile, int minInsertSize) thro
         return null;
     }
 
-    private static String inferInsertSize(PipelineContext ctx, File bam, int minInsertSize) throws PipelineJobException
+    private static String inferInsertSize(PipelineContext ctx, File bam, File fasta, int minInsertSize) throws PipelineJobException
     {
         File expectedPicard = new File(bam.getParentFile(), FileUtil.getBaseName(bam.getName()) + ".insertsize.metrics");
         if (!expectedPicard.exists())
         {
             ctx.getLogger().debug("Unable to find insert metrics file, creating: " + expectedPicard.getPath());
             CollectInsertSizeMetricsWrapper wrapper = new CollectInsertSizeMetricsWrapper(ctx.getLogger());
             File histFile = new File(expectedPicard.getPath() + ".hist");
-            wrapper.executeCommand(bam, expectedPicard, histFile);
+            wrapper.executeCommand(bam, expectedPicard, histFile, fasta);
             histFile.delete();
 
             if (!expectedPicard.exists())
@@ -216,7 +216,7 @@ public static File runPindel(AnalysisOutputImpl output, PipelineContext ctx, Rea
         File pindelParams = new File(outDir, "pindelCfg.txt");
         try (CSVWriter writer = new CSVWriter(PrintWriters.getPrintWriter(pindelParams), '\t', CSVWriter.NO_QUOTE_CHARACTER))
         {
-            String insertSize = inferInsertSize(ctx, inputBam, minInsertSize);
+            String insertSize = inferInsertSize(ctx, inputBam, fasta, minInsertSize);
             writer.writeNext(new String[]{bamToUse.getPath(), insertSize, FileUtil.makeLegalName(rs.getName())});
         }
         catch (IOException e)

SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/CollectInsertSizeMetricsWrapper.java

@@ -20,7 +20,7 @@ public CollectInsertSizeMetricsWrapper(@Nullable Logger logger)
         super(logger);
     }
 
-    public File executeCommand(File inputFile, File outputFile, File histogramFile) throws PipelineJobException
+    public File executeCommand(File inputFile, File outputFile, File histogramFile, File fasta) throws PipelineJobException
     {
         getLogger().info("Running CollectInsertSizeMetrics: " + inputFile.getPath());
         File idx = SequenceAnalysisService.get().getExpectedBamOrCramIndex(inputFile);
@@ -39,6 +39,9 @@ public File executeCommand(File inputFile, File outputFile, File histogramFile)
         params.add("--OUTPUT");
         params.add(outputFile.getPath());
 
+        params.add("-R");
+        params.add(fasta.getPath());
+
         params.add("-H");
         params.add(histogramFile.getPath());