Bugfix to merge lofreq VCFs

bbimber · bbimber · commit 1f5f4ce5c638 · 2020-07-21T09:16:24.000-07:00
diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/MergeLoFreqVcfHandler.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/MergeLoFreqVcfHandler.java
@@ -256,6 +256,13 @@ public void processFilesRemote(List<SequenceOutputFile> inputFiles, JobContext c
                                 continue;
                             }
 
+                            if (vc.getStart() > site.getRight())
+                            {
+                                ctx.getLogger().error("Site located after start: " + site.getRight());
+                                ctx.getLogger().error(vc.toStringWithoutGenotypes());
+                                ctx.getLogger().error(so.getFile().getPath());
+                            }
+
                             //NOTE: the start position of this SiteAndAlleles might differ from the VC
                             siteToAllele.get(key).addSite(vc);
                         }

Original file line number	Diff line number	Diff line change
`@@ -256,6 +256,13 @@ public void processFilesRemote(List<SequenceOutputFile> inputFiles, JobContext c`
`256`	`256`	`continue;`
`257`	`257`	`}`
`258`	`258`
	`259`	`+ if (vc.getStart() > site.getRight())`
	`260`	`+ {`
	`261`	`+ ctx.getLogger().error("Site located after start: " + site.getRight());`
	`262`	`+ ctx.getLogger().error(vc.toStringWithoutGenotypes());`
	`263`	`+ ctx.getLogger().error(so.getFile().getPath());`
	`264`	`+ }`
	`265`	`+`
`259`	`266`	`//NOTE: the start position of this SiteAndAlleles might differ from the VC`
`260`	`267`	`siteToAllele.get(key).addSite(vc);`
`261`	`268`	`}`