Ensure CellRanger retains BAM when analyses are selected

Author: bbimber

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

@@ -707,7 +707,7 @@ private void alignSet(Readset rs, String basename, Map<ReadData, Pair<File, File
         {
             if (!SequencePipelineService.get().getSteps(getJob(), BamProcessingStep.class).isEmpty())
             {
-                throw new PipelineJobException("No BAM was created, but post-procesing steps were selected!");
+                throw new PipelineJobException("No BAM was created, but post-processing steps were selected!");
             }
 
             if (!SequencePipelineService.get().getSteps(getJob(), AnalysisStep.class).isEmpty())

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

@@ -107,7 +107,7 @@ public List<String> getProtocolActionNames()
         }
 
         @Override
-        public PipelineJob.Task createTask(PipelineJob job)
+        public PipelineJob.Task<?> createTask(PipelineJob job)
         {
             SequenceAnalysisTask task = new SequenceAnalysisTask(this, job);
             setJoin(true);
@@ -202,7 +202,7 @@ public RecordedActionSet run() throws PipelineJobException
 
             //find BAM
             List<? extends ExpData> datas = run.getInputDatas(SequenceAlignmentTask.FINAL_BAM_ROLE, ExpProtocol.ApplicationType.ExperimentRunOutput);
-            if (datas.size() > 0)
+            if (!datas.isEmpty())
             {
                 boolean found = false;
                 for (ExpData d : datas)
@@ -261,7 +261,7 @@ else if (!d.getFile().exists())
             else
             {
                 List<? extends ExpData> fastaDatas = run.getInputDatas(IndexOutputImpl.REFERENCE_DB_FASTA, null);
-                if (fastaDatas.size() > 0)
+                if (!fastaDatas.isEmpty())
                 {
                     for (ExpData d : fastaDatas)
                     {
@@ -289,7 +289,7 @@ else if (d.getFile().exists())
 
             //input FASTQs
             datas = run.getInputDatas(SequenceTaskHelper.FASTQ_DATA_INPUT_NAME, ExpProtocol.ApplicationType.ProtocolApplication);
-            if (datas.size() > 0)
+            if (!datas.isEmpty())
             {
                 for (ExpData d : datas)
                 {

jbrowse/src/client/JBrowse/utils.ts

@@ -80,7 +80,7 @@ export function passesSampleFilters(feature, sampleIDs){
 }
 
 export function isVariant(gt) {
-    return !(gt === "./." || gt === ".|." || gt === "0/0" || gt === "0|0")
+    return !(gt === "./." || gt === ".|." || gt === '.' || gt === "0/0" || gt === "0|0")
 }
 
 

singlecell/src/org/labkey/singlecell/run/CellRangerGexCountStep.java

@@ -31,6 +31,7 @@
 import org.labkey.api.sequenceanalysis.pipeline.AlignmentOutputImpl;
 import org.labkey.api.sequenceanalysis.pipeline.AlignmentStep;
 import org.labkey.api.sequenceanalysis.pipeline.AlignmentStepProvider;
+import org.labkey.api.sequenceanalysis.pipeline.AnalysisStep;
 import org.labkey.api.sequenceanalysis.pipeline.CommandLineParam;
 import org.labkey.api.sequenceanalysis.pipeline.IndexOutputImpl;
 import org.labkey.api.sequenceanalysis.pipeline.PipelineContext;
@@ -321,6 +322,12 @@ public boolean canAlignMultiplePairsAtOnce()
 
     private boolean shouldDiscardBam()
     {
+        // NOTE: if downstream analyses are selected, always keep BAM
+        if (!SequencePipelineService.get().getSteps(getPipelineCtx().getJob(), AnalysisStep.class).isEmpty())
+        {
+            return false;
+        }
+
         return !_alwaysRetainBam &&  getProvider().getParameterByName(AbstractAlignmentStepProvider.DISCARD_BAM).extractValue(getPipelineCtx().getJob(), getProvider(), getStepIdx(), Boolean.class, false);
     }