Fix error in several BAM processing steps that did not specify their output BAM

Author: bbimber

SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/pipeline/BamProcessingStep.java

@@ -29,6 +29,16 @@ public interface BamProcessingStep extends PipelineStep
 {
     public BamProcessingStep.Output processBam(Readset rs, File inputBam, ReferenceGenome referenceGenome, File outputDirectory) throws PipelineJobException;
 
+    /**
+     * The BamProcessingStep must call Output.setBam() to explicitly specify the modified file.  This method exists as a check
+     * to prevent the developer from forgetting this.  Unless this is overridden, the pipeline will error if the original BAM is returned
+     * instead.
+     */
+    default boolean expectToCreateNewBam()
+    {
+        return true;
+    }
+
     public static interface Output extends PipelineStepOutput
     {
         /**

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

@@ -172,6 +172,10 @@ public RecordedActionSet run() throws PipelineJobException
                         {
                             bam = output.getBAM();
                         }
+                        else if (step.expectToCreateNewBam())
+                        {
+                            throw new PipelineJobException("The BAM processing step should have created a new BAM, no BAM was specified. This is possible a coding error on this step");
+                        }
                         getJob().getLogger().info("\ttotal alignments in processed BAM: " + SequenceUtil.getAlignmentCount(bam));
 
                         action.setEndTime(new Date());

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

@@ -714,6 +714,10 @@ private void alignSet(Readset rs, String basename, Map<ReadData, Pair<File, File
                         //getJob().getLogger().info("\ttotal alignments in processed BAM: " + SequenceUtil.getAlignmentCount(bam));
                         getJob().getLogger().info("\tfile size: " + FileUtils.byteCountToDisplaySize(bam.length()));
                     }
+                    else if (step.expectToCreateNewBam())
+                    {
+                        throw new PipelineJobException("The BAM processing step should have created a new BAM, no BAM was specified. This is possible a coding error on this step");
+                    }
                     else
                     {
                         getJob().getLogger().info("no BAM created by step, using output from previous step");

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

@@ -140,6 +140,8 @@ public Output processBam(Readset rs, File inputBam, ReferenceGenome referenceGen
 
             getWrapper().execute(inputBam, referenceGenome.getWorkingFastaFile(), outputBam, knownVariants);
 
+            output.setBAM(outputBam);
+
             return output;
         }
     }

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

@@ -110,6 +110,7 @@ public Output processBam(Readset rs, File inputBam, ReferenceGenome referenceGen
             getWrapper().execute(inputBam, referenceGenome.getWorkingFastaFile(), bedFile, outputBam, reportFile);
 
             output.addSequenceOutput(reportFile, rs.getName() + ": alignment clipping report", "Alignment Clipping Report", rs.getReadsetId(), null, referenceGenome.getGenomeId(), null);
+            output.setBAM(outputBam);
 
             return output;
         }