Merge pull request #126 from CCBR/iss-122

concatenate reference files without using excessive memory
CCBR · Nov 5, 2024 · e5360b6 · e5360b6
2 parents 0019fb5 + ba08780
commit e5360b6
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -7,6 +7,7 @@
 - Update docker containers to set `$PYTHONPATH`. (#119, #125, @kelly-sovacool)
   - Otherwise, this environment variable can be carried over and cause package conflicts when singularity is not run with `-C`.
 - Fix `reconfig` to correctly replace variables in the config file. (#121, @kelly-sovacool)
+- Prevent using excessive memory when copying reference files. (#126, @kelly-sovacool)
 
 ## CHARLIE 0.11.0
 

diff --git a/workflow/rules/init.smk b/workflow/rules/init.smk
@@ -53,9 +53,8 @@ def append_files_in_list(flist, ofile):
         with open(ofile, "w") as outfile:
             for fname in flist:
                 with open(fname) as infile:
-                    l = infile.read()
-                    l = l.strip()
-                    outfile.write("%s\n" % (l))
+                    for line in infile:
+                        outfile.write(line)
     return True