Barcoding bugfixes

Author: bbimber

singlecell/src/org/labkey/singlecell/CellHashingServiceImpl.java

@@ -226,14 +226,7 @@ public void prepareHashingAndCiteSeqFilesIfNeeded(File sourceDir, PipelineJob jo
                         TableSelector ts = new TableSelector(sequenceOutputs, filter, new org.labkey.api.data.Sort("-rowid"));
                         if (!ts.exists())
                         {
-                            if (failIfNoHashing)
-                            {
-                                throw new IllegalArgumentException("Unable to find existing count matrix for hashing readset: " + hashingReadsetId);
-                            }
-                            else
-                            {
-                                job.getLogger().info("Count matrix not found for readset: " + hashingReadsetId);
-                            }
+                            throw new IllegalArgumentException("Unable to find existing count matrix for hashing readset: " + hashingReadsetId);
                         }
                         else
                         {
@@ -275,14 +268,7 @@ else if (distinctHTOs.size() == 1)
                     TableSelector ts = new TableSelector(sequenceOutputs, filter, new org.labkey.api.data.Sort("-rowid"));
                     if (!ts.exists())
                     {
-                        if (failIfNoHashing)
-                        {
-                            throw new IllegalArgumentException("Unable to find existing count matrix for CITE-seq readset: " + citeseqReadsetId);
-                        }
-                        else
-                        {
-                            job.getLogger().info("Count matrix not found for readset: " + citeseqReadsetId);
-                        }
+                        throw new IllegalArgumentException("Unable to find existing count matrix for CITE-seq readset: " + citeseqReadsetId);
                     }
                     else
                     {

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

@@ -167,9 +167,9 @@ else if (rs.getApplication().equals("CITE-Seq"))
 
             //https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/feature-bc-analysis
             File libraryCsv = new File(ctx.getOutputDir(), "libraries.csv");
-            try (CSVWriter writer = new CSVWriter(PrintWriters.getPrintWriter(libraryCsv), ','))
+            try (CSVWriter writer = new CSVWriter(PrintWriters.getPrintWriter(libraryCsv), ',', CSVWriter.NO_QUOTE_CHARACTER))
             {
-                writer.writeNext(new String[]{"fastqs", "sample", "librarytype"});
+                writer.writeNext(new String[]{"fastqs", "sample", "library_type"});
                 writer.writeNext(new String[]{wrapper.getLocalFastqDir(ctx.getOutputDir()).getPath(), wrapper.makeLegalSampleName(rs.getName()), "Antibody Capture"});
             }
             catch (IOException e)
@@ -308,7 +308,7 @@ private File makeDummyIndex(JobContext ctx) throws PipelineJobException
         private File createFeatureRefForCiteSeq(File outputDir, File adtWhitelist) throws PipelineJobException
         {
             File featuresCsv = new File(outputDir, "adtFeatureRef.csv");
-            try (CSVReader reader = new CSVReader(Readers.getReader(adtWhitelist), '\t'); CSVWriter writer = new CSVWriter(PrintWriters.getPrintWriter(featuresCsv), ','))
+            try (CSVReader reader = new CSVReader(Readers.getReader(adtWhitelist), '\t'); CSVWriter writer = new CSVWriter(PrintWriters.getPrintWriter(featuresCsv), ',', CSVWriter.NO_QUOTE_CHARACTER))
             {
                 writer.writeNext(new String[]{"id", "name", "read", "pattern", "sequence", "feature_type"});
 
@@ -335,7 +335,7 @@ private File createFeatureRefForCiteSeq(File outputDir, File adtWhitelist) throw
         private File createFeatureRefForHashing(File outputDir, File hashingWhitelist) throws PipelineJobException
         {
             File featuresCsv = new File(outputDir, "hashingFeatureRef.csv");
-            try (CSVReader reader = new CSVReader(Readers.getReader(hashingWhitelist), ',');CSVWriter writer = new CSVWriter(PrintWriters.getPrintWriter(featuresCsv), ','))
+            try (CSVReader reader = new CSVReader(Readers.getReader(hashingWhitelist), ',');CSVWriter writer = new CSVWriter(PrintWriters.getPrintWriter(featuresCsv), ',', CSVWriter.NO_QUOTE_CHARACTER))
             {
                 writer.writeNext(new String[]{"id", "name", "read", "pattern", "sequence", "feature_type"});
                 String[] line;