Bugfix to SRA fastq validation

bbimber · bbimber · commit f217864766f1 · 2022-04-02T13:16:38.000-07:00
diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/RestoreSraDataHandler.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/RestoreSraDataHandler.java
@@ -391,7 +391,7 @@ public void processFilesRemote(List<Readset> readsets, JobContext ctx) throws Un
                     FastqDumpWrapper wrapper = new FastqDumpWrapper(ctx.getLogger());
                     Pair<File, File> files = wrapper.downloadSra(accession, ctx.getOutputDir());
 
-                    long lines1 = SequenceUtil.getLineCount(files.first);
+                    long lines1 = SequenceUtil.getLineCount(files.first) / 4;
                     ctx.getJob().getLogger().debug("Reads in " + files.first.getName() + ": " + lines1);
                     if (lines1 != accessionToReads.get(accession))
                     {
@@ -400,7 +400,7 @@ public void processFilesRemote(List<Readset> readsets, JobContext ctx) throws Un
 
                     if (files.second != null)
                     {
-                        long lines2 = SequenceUtil.getLineCount(files.second);
+                        long lines2 = SequenceUtil.getLineCount(files.second) / 4;
                         ctx.getJob().getLogger().debug("Reads in " + files.second.getName() + ": " + lines2);
                         if (lines2 != accessionToReads.get(accession))
                         {

Original file line number	Diff line number	Diff line change
`@@ -391,7 +391,7 @@ public void processFilesRemote(List<Readset> readsets, JobContext ctx) throws Un`
`391`	`391`	`FastqDumpWrapper wrapper = new FastqDumpWrapper(ctx.getLogger());`
`392`	`392`	`Pair<File, File> files = wrapper.downloadSra(accession, ctx.getOutputDir());`
`393`	`393`
`394`		`- long lines1 = SequenceUtil.getLineCount(files.first);`
	`394`	`+ long lines1 = SequenceUtil.getLineCount(files.first) / 4;`
`395`	`395`	`ctx.getJob().getLogger().debug("Reads in " + files.first.getName() + ": " + lines1);`
`396`	`396`	`if (lines1 != accessionToReads.get(accession))`
`397`	`397`	`{`
`@@ -400,7 +400,7 @@ public void processFilesRemote(List<Readset> readsets, JobContext ctx) throws Un`
`400`	`400`
`401`	`401`	`if (files.second != null)`
`402`	`402`	`{`
`403`		`- long lines2 = SequenceUtil.getLineCount(files.second);`
	`403`	`+ long lines2 = SequenceUtil.getLineCount(files.second) / 4;`
`404`	`404`	`ctx.getJob().getLogger().debug("Reads in " + files.second.getName() + ": " + lines2);`
`405`	`405`	`if (lines2 != accessionToReads.get(accession))`
`406`	`406`	`{`