Fix evaluate mode: don't RC reverse primer before storing

The previous fix reverse-complemented the user-provided reverse primer,
causing it to align with orientation 0 instead of 16. This made
prepare-input find zero reverse primers, producing an empty .eval file
and no .eval.full, which broke export-report.

Store the reverse primer as-is (5'→3') to match the generate command
convention. bowtie2 will RC it during alignment, giving orientation 16
as prepare-input expects.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

Author: kbryanhsu

workflows/Snakefile.example

@@ -373,16 +373,15 @@ rule prepare_pset_fasta:
             shutil.copyfile(src, out)
 
         # case 2: direct for / rev → generate
-        # The reverse primer must be stored as RC to match the convention
-        # used by the 'generate' command (tiled from the RC of the target).
+        # Store primers as-is (5'→3') to match the convention used by the
+        # 'generate' command.  bowtie2 will RC the reverse primer during
+        # alignment, producing orientation flag 16 as prepare-input expects.
         else:
             for_seq = config["for"]
             rev_seq = config["rev"]
-            comp = str.maketrans("ACGTacgt", "TGCAtgca")
-            rev_seq_rc = rev_seq.translate(comp)[::-1]
 
             with open(out, "w") as f:
-                f.write(f">1_for\n{for_seq}\n>1_rev\n{rev_seq_rc}\n")
+                f.write(f">1_for\n{for_seq}\n>1_rev\n{rev_seq}\n")
 
         ids = check_ids(out)
 

workflows/Snakefile.template

@@ -373,16 +373,15 @@ rule prepare_pset_fasta:
             shutil.copyfile(src, out)
 
         # case 2: direct for / rev → generate
-        # The reverse primer must be stored as RC to match the convention
-        # used by the 'generate' command (tiled from the RC of the target).
+        # Store primers as-is (5'→3') to match the convention used by the
+        # 'generate' command.  bowtie2 will RC the reverse primer during
+        # alignment, producing orientation flag 16 as prepare-input expects.
         else:
             for_seq = config["for"]
             rev_seq = config["rev"]
-            comp = str.maketrans("ACGTacgt", "TGCAtgca")
-            rev_seq_rc = rev_seq.translate(comp)[::-1]
 
             with open(out, "w") as f:
-                f.write(f">1_for\n{for_seq}\n>1_rev\n{rev_seq_rc}\n")
+                f.write(f">1_for\n{for_seq}\n>1_rev\n{rev_seq}\n")
 
         ids = check_ids(out)