Support MINIMUM_DISTANCE for MarkDuplicatesWithMate

Author: bbimber

SequenceAnalysis/src/org/labkey/sequenceanalysis/run/bampostprocessing/MarkDuplicatesWithMateCigarStep.java

@@ -35,7 +35,8 @@ public static class Provider extends AbstractPipelineStepProvider<MarkDuplicates
         public Provider()
         {
             super("MarkDuplicatesWithMateCigarStep", "Mark Duplicates With Mate", "Picard", "This runs Picard tools MarkDuplicatesWithMateCigarStep command in order to mark and/or remove duplicate reads.  Unlike the original MarkDuplicates, this uses paired read information to more accurately detect true duplicates.  Please note this can have implications for downstream analysis, because reads marked as duplicates are frequently omitted.  This is often desired, but can be a problem for sequencing of PCR products.", Arrays.asList(
-                    ToolParameterDescriptor.createCommandLineParam(CommandLineParam.create("REMOVE_DUPLICATES"), "removeDuplicates", "Remove Duplicates", "If selected, duplicate reads will be removed, as opposed to flagged as duplicates.", "checkbox", null, null)
+                    ToolParameterDescriptor.createCommandLineParam(CommandLineParam.create("REMOVE_DUPLICATES"), "removeDuplicates", "Remove Duplicates", "If selected, duplicate reads will be removed, as opposed to flagged as duplicates.", "checkbox", null, null),
+                    ToolParameterDescriptor.createCommandLineParam(CommandLineParam.create("MINIMUM_DISTANCE"), "minimumDistance", "Minimum Distance", "The minimum distance to buffer records to account for clipping on the 5' end of the records.", "ldk-integerfield", null, null)
             ), null, "http://picard.sourceforge.net/command-line-overview.shtml");
         }
 
@@ -60,7 +61,6 @@ public Output processBam(Readset rs, File inputBam, ReferenceGenome referenceGen
 
         output.setBAM(getWrapper().executeCommand(inputBam, outputBam, getClientCommandArgs("=")));
 
-
         if (sortedBam.exists() && !sortedPreexisting)
         {
             output.addIntermediateFile(sortedBam);

jbrowse/src/org/labkey/jbrowse/JBrowseRoot.java

@@ -1440,6 +1440,7 @@ private List<JSONObject> processFile(ExpData data, File outDir, String featureNa
         {
             File temp = null;
             Set<String> nameAttrs = new HashSet<>();
+            nameAttrs.add("gene_id");
             nameAttrs.add("gene_name");
             nameAttrs.add("ncbi_geneid");
             nameAttrs.add("ensembl_geneid");