Issue 48029: Labkey Illumina Parsing pipeline is extremely slow (#108)

Author: labkey-jeckels

genotyping/src/org/labkey/genotyping/IlluminaFastqParser.java

@@ -135,13 +135,13 @@ public Map<Pair<Integer, Integer>, FileInfo> parseFastqFiles(PipelineJob job) th
                 // Copy to a temp file for parsing for perf reasons. See issue 48029
                 // Ideally we'd avoid the copy when the file is already on a local file system, but there's no
                 // good way to check if a file is truly local
-                tempFile = FileUtil.createTempFile(FileUtil.getBaseName(f), FileUtil.getExtension(f));
+                tempFile = FileUtil.createTempFile(FileUtil.getBaseName(f) + ".", "." + FileUtil.getExtension(f));
                 tempFile.deleteOnExit();
-                _logger.debug("Copying to temp file, size is " + f.length() + " bytes");
+                _logger.debug("Copying to temp file " + tempFile + ", size is " + f.length() + " bytes");
                 FileUtil.copyFile(f, tempFile);
 
                 _logger.info("Beginning to parse file: " + f.getName());
-                try (FastqReader reader = new FastqReader(f))
+                try (FastqReader reader = new FastqReader(tempFile))
                 {
                     File targetDir = f.getParentFile();
                     String fileName = f.getName();