Another bugfix to bwa/bwa2 index folders

Author: bbimber

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

@@ -79,7 +79,7 @@ public interface ReferenceGenome extends Serializable
 
     /**
      * @param name The name used by the aligner to identify its cached directory
-     * @return The folder expected containing the cached index, which is not guarenteed to exist.  See AlignerIndexUtil for related methods.
+     * @return The folder expected containing the cached index, which is not guaranteed to exist.  See AlignerIndexUtil for related methods.
      */
     File getAlignerIndexDir(String name);
 

SequenceAnalysis/src/org/labkey/sequenceanalysis/run/alignment/BWAMem2Wrapper.java

@@ -53,6 +53,12 @@ public String getIndexCachedDirName(PipelineJob job)
         }
     }
 
+    @Override
+    protected String getIndexDirName()
+    {
+        return("bwamem2");
+    }
+
     public static class Provider extends AbstractAlignmentStepProvider<AlignmentStep>
     {
         public Provider()

SequenceAnalysis/src/org/labkey/sequenceanalysis/run/alignment/BWAMemWrapper.java

@@ -116,7 +116,7 @@ public void performMemAlignment(PipelineJob job, AlignmentOutputImpl output, Fil
         }
         appendThreads(job, bwaArgs);
 
-        bwaArgs.add("'" + new File(referenceGenome.getAlignerIndexDir("bwa"), FileUtil.getBaseName(referenceGenome.getWorkingFastaFile().getName()) + ".bwa.index").getPath() + "'");
+        bwaArgs.add("'" + new File(referenceGenome.getAlignerIndexDir(getIndexDirName()), FileUtil.getBaseName(referenceGenome.getWorkingFastaFile().getName()) + ".bwa.index").getPath() + "'");
         bwaArgs.add("'" + inputFastq1.getPath() + "'");
 
         if (inputFastq2 != null)

SequenceAnalysis/src/org/labkey/sequenceanalysis/run/alignment/BWAWrapper.java

@@ -151,7 +151,7 @@ public final AlignmentOutput performAlignment(Readset rs, List<File> inputFastqs
             File inputFastq2 = assertSingleFile(inputFastqs2);
 
             AlignmentOutputImpl output = new AlignmentOutputImpl();
-            AlignerIndexUtil.copyIndexIfExists(this.getPipelineCtx(), output, "bwa", referenceGenome);
+            AlignerIndexUtil.copyIndexIfExists(this.getPipelineCtx(), output, getIndexCachedDirName(getPipelineCtx().getJob()), referenceGenome);
 
             doPerformAlignment(output, inputFastq1, inputFastq2, outputDirectory, referenceGenome, basename, rs, readGroupId, platformUnit);
             output.addCommandsExecuted(getWrapper().getCommandsExecuted());
@@ -197,7 +197,7 @@ private File runBWAAln(PipelineJob job, ReferenceGenome referenceGenome, File in
         args.add("aln");
         appendThreads(job, args);
         args.addAll(bwaAlnArgs);
-        args.add(new File(referenceGenome.getAlignerIndexDir("bwa"), FileUtil.getBaseName(referenceGenome.getWorkingFastaFile().getName()) + ".bwa.index").getPath());
+        args.add(new File(referenceGenome.getAlignerIndexDir(getIndexDirName()), FileUtil.getBaseName(referenceGenome.getWorkingFastaFile().getName()) + ".bwa.index").getPath());
         args.add(inputFile.getPath());
 
         File output = new File(getOutputDir(inputFile), inputFile.getName() + ".sai");
@@ -230,12 +230,12 @@ protected void performBwaAlignment(PipelineJob job, AlignmentOutputImpl output,
             throw new PipelineJobException("Reference FASTA does not exist: " + referenceGenome.getWorkingFastaFile().getPath());
         }
 
-        File expectedIndex = new File(referenceGenome.getAlignerIndexDir("bwa"), FileUtil.getBaseName(referenceGenome.getWorkingFastaFile()) + ".bwa.index.sa");
+        File expectedIndex = new File(referenceGenome.getAlignerIndexDir(getIndexDirName()), FileUtil.getBaseName(referenceGenome.getWorkingFastaFile()) + ".bwa.index.sa");
         if (!expectedIndex.exists())
         {
             throw new PipelineJobException("Expected index does not exist: " + expectedIndex);
         }
-        args.add(new File(referenceGenome.getAlignerIndexDir("bwa"), FileUtil.getBaseName(referenceGenome.getWorkingFastaFile().getName()) + ".bwa.index").getPath());
+        args.add(new File(referenceGenome.getAlignerIndexDir(getIndexDirName()), FileUtil.getBaseName(referenceGenome.getWorkingFastaFile().getName()) + ".bwa.index").getPath());
 
         //add SAI
         args.add(sai1.getPath());
@@ -283,4 +283,9 @@ public File getExe()
     {
         return SequencePipelineService.get().getExeForPackage("BWAPATH", "bwa");
     }
+
+    protected String getIndexDirName()
+    {
+        return("bwa");
+    }
 }