Allow GenotypeGVCFs to be run on multiple inputs using a three-pass approach

Author: bbimber

SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/run/DISCVRSeqRunner.java

@@ -39,7 +39,7 @@ protected File getJar()
 
     }
 
-    protected List<String> getBaseArgs(String toolName)
+    public List<String> getBaseArgs(String toolName)
     {
         List<String> args = new ArrayList<>();
         args.add(SequencePipelineService.get().getJava8FilePath());

SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisController.java

@@ -3690,6 +3690,7 @@ public void export(ExportSequenceFilesForm form, HttpServletResponse response, B
 
             Set<File> files = new HashSet<>();
             FileType bamFileType = new FileType("bam");
+            FileType cramFileType = new FileType("cram");
             FileType fastaFileType = new FileType("fasta", FileType.gzSupportLevel.SUPPORT_GZ);
             FileType gzFileType = new FileType("gz");
             for (int id : form.getDataIds())
@@ -3710,6 +3711,14 @@ public void export(ExportSequenceFilesForm form, HttpServletResponse response, B
                         files.add(index);
                     }
                 }
+                if (cramFileType.isType(data.getFile()))
+                {
+                    File index = new File(data.getFile() + ".crai");
+                    if (index.exists())
+                    {
+                        files.add(index);
+                    }
+                }
                 else if (fastaFileType.isType(data.getFile()))
                 {
                     File index = new File(data.getFile() + ".fai");

SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisMaintenanceTask.java

@@ -459,6 +459,7 @@ private void deleteFile(File f, Logger log) throws IOException
     }
 
     private static FileType _bamFileType = new FileType("bam");
+    private static FileType _cramFileType = new FileType("cram");
     private static FileType _vcfFileType = new FileType("vcf", FileType.gzSupportLevel.SUPPORT_GZ);
     private static FileType _bedFileType = new FileType("bed");
 
@@ -474,6 +475,10 @@ public static List<String> getAssociatedFiles(File f, boolean includeGz)
         {
             ret.add(f.getName() + ".bai");
         }
+        else if (_cramFileType.isType(f))
+        {
+            ret.add(f.getName() + ".crai");
+        }
         else if (_vcfFileType.isType(f))
         {
             ret.add(f.getName() + ".tbi");