Fix to fileSource required for indexing bug

bbimber · bbimber · commit 43f46037642e · 2026-02-05T09:43:16.000-08:00
diff --git a/jbrowse/src/org/labkey/jbrowse/model/JsonFile.java b/jbrowse/src/org/labkey/jbrowse/model/JsonFile.java
@@ -939,7 +939,7 @@ else if (TRACK_TYPES.bam.getFileType().isType(targetFile))
                     if (targetFile.length() < 5e6)
                     {
                         log.debug("Creating BAM index: " + targetFile.getPath());
-                        try (SamReader samReader = SamReaderFactory.make().open(targetFile.toPath()))
+                        try (SamReader samReader = SamReaderFactory.makeDefault().enable(SamReaderFactory.Option.INCLUDE_SOURCE_IN_RECORDS).open(targetFile.toPath()))
                         {
                             BAMIndexer.createIndex(samReader, fileIdx);
                         }

Original file line number	Diff line number	Diff line change
`@@ -939,7 +939,7 @@ else if (TRACK_TYPES.bam.getFileType().isType(targetFile))`
`939`	`939`	`if (targetFile.length() < 5e6)`
`940`	`940`	`{`
`941`	`941`	`log.debug("Creating BAM index: " + targetFile.getPath());`
`942`		`- try (SamReader samReader = SamReaderFactory.make().open(targetFile.toPath()))`
	`942`	`+ try (SamReader samReader = SamReaderFactory.makeDefault().enable(SamReaderFactory.Option.INCLUDE_SOURCE_IN_RECORDS).open(targetFile.toPath()))`
`943`	`943`	`{`
`944`	`944`	`BAMIndexer.createIndex(samReader, fileIdx);`
`945`	`945`	`}`