--- a/find_str.py	Wed Jul 17 06:19:22 2024 +0000
+++ b/find_str.py	Wed Jul 17 07:40:00 2024 +0000
@@ -23,8 +23,7 @@
         specific = args.specific.upper().split(",")
     fa = Fastx(args.fasta, uppercase=True)
     for name, seq in fa:
-        if args.specific:
-            ssrs = pytrf.STRFinder(
+        for ssr in pytrf.STRFinder(
                 name,
                 seq,
                 args.monomin,
@@ -33,29 +32,17 @@
                 args.tetramin,
                 args.pentamin,
                 args.hexamin,
-            )
-        else:
-            ssrs = pytrf.STRFinder(
-                name,
-                seq,
-                args.monomin,
-                args.dimin,
-                args.trimin,
-                args.tetramin,
-                args.pentamin,
-                args.hexamin,
-            )
-        for ssr in ssrs:
+            ):
             row = (
                 ssr.chrom,
-                ssr.start - 1,
+                ssr.start,
                 ssr.end,
                 ssr.motif,
                 ssr.repeat,
                 ssr.length,
             )
             # pytrf reports a 1 based start position so start-1 fixes the bed interval lengths
-            if args.specific and ssr.motif in specific and ssr.repeat >= args.minreps:
+            if args.specific and ssr.motif in specific:
                 bed.append(row)
             elif args.mono and len(ssr.motif) == 1:
                 bed.append(row)