From 613634b2006768eea96d02c041264121e71fe46a Mon Sep 17 00:00:00 2001
From: Dmitry Antipov <dmitrij.antipov@gmail.com>
Date: Fri, 16 Aug 2024 15:59:26 -0400
Subject: [PATCH] tuning gap size

---
 src/scripts/fasta_combine.py | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/src/scripts/fasta_combine.py b/src/scripts/fasta_combine.py
index cb7fd297..e2b9e850 100755
--- a/src/scripts/fasta_combine.py
+++ b/src/scripts/fasta_combine.py
@@ -6,6 +6,9 @@
 
 import fasta_util as seq
 
+#TODO: constant to verkko.yml_sample
+MAX_GAP_SIZE     = 100000
+
 mode             = None
 output_name      = None
 namedict         = dict()
@@ -86,12 +89,13 @@
     prev = ""
     for piece in scfmap[clist]:
       numn = re.match(r"\[N(\d+)N]", piece)
-
       if numn:
+        #1.5 - approximation for hpc->non-hpc transformation. 
+        tuned_numn = min(round(int(numn[1]) * 1.5), MAX_GAP_SIZE)
         if not seq:
            print(f"ERROR:piece {prev} missing from gapped contig {clist}.", file=sys.stderr)
            sys.exit(1)
-        seq += "N" * int(numn[1])
+        seq += "N" * int(tuned_numn)
       elif piece in pieces:
         seq += pieces[piece]
       elif seq: