Bugfix to GLNexus

Author: bbimber

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

@@ -221,6 +221,11 @@ public int getMaxRetries()
         return _maxRetries;
     }
 
+    public void setMaxRetries(int maxRetries)
+    {
+        _maxRetries = maxRetries;
+    }
+
     // NOTE: when running on a shared/cluster environment with multiple containers initializing concurrently, conflicts can result in these error codes.
     // As a convenience, build in auto-retry behavior if one of these occurs
     private final List<Integer> ALLOWABLE_FAIL_CODES = new UnmodifiableList<>(Arrays.asList(125, 127));

SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/GLNexusHandler.java

@@ -15,7 +15,6 @@
 import org.labkey.api.sequenceanalysis.SequenceAnalysisService;
 import org.labkey.api.sequenceanalysis.SequenceOutputFile;
 import org.labkey.api.sequenceanalysis.pipeline.AbstractParameterizedOutputHandler;
-import org.labkey.api.sequenceanalysis.pipeline.BcftoolsRunner;
 import org.labkey.api.sequenceanalysis.pipeline.PipelineOutputTracker;
 import org.labkey.api.sequenceanalysis.pipeline.ReferenceGenome;
 import org.labkey.api.sequenceanalysis.pipeline.SequenceAnalysisJobSupport;
@@ -25,9 +24,9 @@
 import org.labkey.api.sequenceanalysis.run.AbstractCommandWrapper;
 import org.labkey.api.sequenceanalysis.run.DockerWrapper;
 import org.labkey.api.util.FileType;
+import org.labkey.api.util.FileUtil;
 import org.labkey.api.writer.PrintWriters;
 import org.labkey.sequenceanalysis.SequenceAnalysisModule;
-import org.labkey.sequenceanalysis.run.util.BgzipRunner;
 import org.labkey.sequenceanalysis.util.SequenceUtil;
 
 import java.io.File;
@@ -172,7 +171,7 @@ else if (genomeIds.isEmpty())
             SAMSequenceDictionary dict = SAMSequenceDictionaryExtractor.extractDictionary(rg.getSequenceDictionary().toPath());
             for (SAMSequenceRecord r : dict.getSequences())
             {
-                File contigVcf = new File(ctx.getOutputDir(), basename + "." + r.getSequenceName() + ".vcf.gz");
+                File contigVcf = FileUtil.appendName(ctx.getOutputDir(), basename + "." + r.getSequenceName() + ".vcf.gz");
                 File contigVcfIdx = new File(contigVcf.getPath() + ".tbi");
                 File doneFile = new File(contigVcf.getPath() + ".done");
                 ctx.getFileManager().addIntermediateFile(contigVcf);
@@ -241,8 +240,9 @@ public void execute(List<File> inputGvcfs, File outputVcf, PipelineOutputTracker
             DockerWrapper wrapper = new DockerWrapper("ghcr.io/dnanexus-rnd/glnexus:" + binVersion, ctx.getLogger(), ctx);
             wrapper.setTmpDir(new File(SequencePipelineService.get().getJavaTempDir()));
             wrapper.setWorkingDir(ctx.getWorkingDirectory());
+            wrapper.setMaxRetries(0);
 
-            File bed = new File(ctx.getWorkingDirectory(), "contig.bed");
+            File bed = FileUtil.appendName(ctx.getWorkingDirectory(), "contig.bed");
             tracker.addIntermediateFile(bed);
             try (PrintWriter bedWriter = PrintWriters.getPrintWriter(bed))
             {
@@ -277,12 +277,10 @@ public void execute(List<File> inputGvcfs, File outputVcf, PipelineOutputTracker
                 dockerArgs.add(f.getPath());
             });
 
-            File bcftools = BcftoolsRunner.getBcfToolsPath();
-            File bgzip = BgzipRunner.getExe();
-            dockerArgs.add(" | " + bcftools.getPath() + " view | " + bgzip.getPath() + " -c > " + outputVcf.getPath());
+            dockerArgs.add(" | bcftools view | bgzip -f -c > " + outputVcf.getPath());
 
             // Command will fail if this exists:
-            File dbDir = new File (ctx.getWorkingDirectory(), "GLnexus.DB");
+            File dbDir = FileUtil.appendName(ctx.getWorkingDirectory(), "GLnexus.DB");
             tracker.addIntermediateFile(dbDir);
             if (dbDir.exists())
             {
@@ -296,6 +294,10 @@ public void execute(List<File> inputGvcfs, File outputVcf, PipelineOutputTracker
                     throw new PipelineJobException(e);
                 }
             }
+            else
+            {
+                getLogger().debug("GLnexus.DB does not exist: " + dbDir.getPath());
+            }
 
             wrapper.executeWithDocker(dockerArgs, ctx.getWorkingDirectory(), tracker, inputGvcfs);
 

jbrowse/src/org/labkey/jbrowse/model/JsonFile.java

@@ -1,5 +1,8 @@
 package org.labkey.jbrowse.model;
 
+import htsjdk.samtools.BAMIndexer;
+import htsjdk.samtools.SamReader;
+import htsjdk.samtools.SamReaderFactory;
 import htsjdk.samtools.util.FileExtensions;
 import htsjdk.tribble.bed.BEDCodec;
 import htsjdk.tribble.gff.Gff3Codec;
@@ -931,6 +934,25 @@ public File prepareResource(User u, Logger log, boolean throwIfNotPrepared, bool
                 {
                     SequenceAnalysisService.get().ensureBamOrCramIdx(targetFile, log, false);
                 }
+                else if (TRACK_TYPES.bam.getFileType().isType(targetFile))
+                {
+                    if (targetFile.length() < 5e6)
+                    {
+                        log.debug("Creating BAM index: " + targetFile.getPath());
+                        try (SamReader samReader = SamReaderFactory.make().open(targetFile.toPath()))
+                        {
+                            BAMIndexer.createIndex(samReader, fileIdx);
+                        }
+                        catch (IOException e)
+                        {
+                            throw new PipelineJobException(e);
+                        }
+                    }
+                    else
+                    {
+                        log.debug("BAM lacks an index but is too large to auto-create: " + targetFile.length());
+                    }
+                }
             }
         }