Fix build

Author: bbimber

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

@@ -46,7 +46,7 @@ public File executeCommand(File file) throws PipelineJobException
         return output;
     }
 
-    private List<String> getParams(File file)
+    private List<String> getParams(File file) throws PipelineJobException
     {
         List<String> params = getBaseArgs();
 

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

@@ -39,7 +39,7 @@ public File execute(File file, Double pctRetained) throws PipelineJobException
 
     }
 
-    private List<String> getParams(File file, Double pctRetained)
+    private List<String> getParams(File file, Double pctRetained) throws PipelineJobException
     {
         List<String> params = getBaseArgs();
         params.add("--INPUT");

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

@@ -54,7 +54,7 @@ protected String getToolName()
         return "FastqToSam";
     }
 
-    private List<String> getParams(File file, File file2, SAMFileHeader.SortOrder sortOrder, @Nullable SAMReadGroupRecord rg)
+    private List<String> getParams(File file, File file2, SAMFileHeader.SortOrder sortOrder, @Nullable SAMReadGroupRecord rg) throws PipelineJobException
     {
         List<String> params = getBaseArgs();
 

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

@@ -111,7 +111,7 @@ public File execute(List<File> files, @Nullable File outputPath, boolean deleteO
         return output;
     }
 
-    private List<String> getParams(File outputPath, List<File> files)
+    private List<String> getParams(File outputPath, List<File> files) throws PipelineJobException
     {
         List<String> params = getBaseArgs();
 

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

@@ -44,7 +44,7 @@ else if (deleteInput)
         return outputFile;
     }
 
-    private List<String> getParams(File inputFile, File outputFile)
+    private List<String> getParams(File inputFile, File outputFile) throws PipelineJobException
     {
         List<String> params = getBaseArgs();
 

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

@@ -89,7 +89,7 @@ public Pair<File, File> executeCommand(File file, String outputName1, @Nullable
         return Pair.of(output, output2);
     }
 
-    private List<String> getBaseParams(File file)
+    private List<String> getBaseParams(File file) throws PipelineJobException
     {
         List<String> params = getBaseArgs();
         params.add("--INPUT");