move gap limit handling to scfmap file

src/scripts/bam_rename.py

@@ -4,8 +4,6 @@
 import fasta_util as seq
 import re
 
-MAX_GAP_SIZE=100000
-
 # rename a bam based on the input scfmap and tig name mapping files
 # in the case of scaffolds, offset the start coordinate by the start of the sequence in the scaffold
 #
@@ -56,9 +54,7 @@
    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)
-         offset += int(tuned_numn)
+         offset += int(numn[1])
       elif piece in lens:
          offsets[names[piece]] = offset
          #sys.stderr.write("The offset for %s is %s\n"%(names[piece], offset))

src/scripts/fasta_combine.py

@@ -6,9 +6,6 @@
 
 import fasta_util as seq
 
-#TODO: constant to verkko.yml_sample
-MAX_GAP_SIZE     = 100000
-
 mode             = None
 output_name      = None
 namedict         = dict()
@@ -90,12 +87,10 @@
     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(tuned_numn)
+        seq += "N" * int(numn[1])
       elif piece in pieces:
         seq += pieces[piece]
       elif seq:

src/scripts/get_layout_from_mbg.py

@@ -17,6 +17,7 @@
 layout_output = sys.argv[6]
 layscf_output = sys.argv[7]
 
+MAX_GAP_SIZE = 100000
 min_contig_no_trim = 500000
 min_read_len_fraction = 0.5
 min_read_fromend_fraction = min_read_len_fraction/1.5
@@ -255,7 +256,8 @@ def get_exact_match_length(clusters):
 			#pp is either path without gaps or gap. In latest case do nothing
 			gp = re.match(r"\[(N\d+N)(?:[^\]]+){0,1}\]", pp)
 			if gp:
-				contig_pieces[fullname].append("[" + gp.group(1) + "]")
+				tuned_numn = min(round(int(gp.group(1)[1:-1]) * 1.5), MAX_GAP_SIZE)
+				contig_pieces[fullname].append("[N" + str(tuned_numn) + "N]")
 				continue
 
 			pieceid = pieceid + 1