Bugfix to CellRangerVDJWrapper when there are no passing g/d contigs

bbimber · bbimber · commit 1af53302b4f9 · 2024-08-25T06:33:04.000-07:00
diff --git a/tcrdb/src/org/labkey/tcrdb/pipeline/CellRangerVDJUtils.java b/tcrdb/src/org/labkey/tcrdb/pipeline/CellRangerVDJUtils.java
@@ -512,6 +512,12 @@ else if (discordantBarcodes.contains(barcode))
         for (File f : Arrays.asList(consensusFastaGD, allFastaGD))
         {
             _log.info("processing G/D FASTA: " + f.getPath());
+            if (!SequencePipelineService.get().hasMinLineCount(f, 2))
+            {
+                _log.info("too few lines, skipping FASTA:" + f.getPath());
+                continue;
+            }
+
             try (FastaDataLoader loader = new FastaDataLoader(f, false))
             {
                 loader.setCharacterFilter(new FastaLoader.UpperAndLowercaseCharacterFilter());

Original file line number	Diff line number	Diff line change
`@@ -512,6 +512,12 @@ else if (discordantBarcodes.contains(barcode))`
`512`	`512`	`for (File f : Arrays.asList(consensusFastaGD, allFastaGD))`
`513`	`513`	`{`
`514`	`514`	`_log.info("processing G/D FASTA: " + f.getPath());`
	`515`	`+ if (!SequencePipelineService.get().hasMinLineCount(f, 2))`
	`516`	`+ {`
	`517`	`+ _log.info("too few lines, skipping FASTA:" + f.getPath());`
	`518`	`+ continue;`
	`519`	`+ }`
	`520`	`+`
`515`	`521`	`try (FastaDataLoader loader = new FastaDataLoader(f, false))`
`516`	`522`	`{`
`517`	`523`	`loader.setCharacterFilter(new FastaLoader.UpperAndLowercaseCharacterFilter());`