Merge pull request #16803 from mvdbeek/pysam_to_string_fix

Use AlignedSegment.to_string
galaxyproject · Oct 7, 2023 · d4b25fb · d4b25fb
2 parents a23c217 + 48dcf86
commit d4b25fb
Showing 1 changed file with 2 additions and 2 deletions.
diff --git a/lib/galaxy/datatypes/binary.py b/lib/galaxy/datatypes/binary.py
@@ -664,9 +664,9 @@ def get_chunk(self, trans, dataset: HasFileName, offset: int = 0, ck_size: Optio
                             break
 
                         offset = bamfile.tell()
-                        bamline = alignment.tostring(bamfile)
+                        bamline = alignment.to_string()
                         # With multiple tags, Galaxy would display each as a separate column
-                        # because the 'tostring()' function uses tabs also between tags.
+                        # because the 'to_string()' function uses tabs also between tags.
                         # Below code will turn these extra tabs into spaces.
                         n_tabs = bamline.count("\t")
                         if n_tabs > 11: