fix makefile variable name for reference genome and remove debug logs…

… from apply_bp2cm

Makefile

@@ -166,7 +166,7 @@ wgs_wild : $(CORRESP) $(SIZES) $(WGS)/variant/hap.wild.matrix
 bp2cm:
  # Compute coordinates of linkage map markers in new genome
  # Compute cM/BP ratio in each inter-marker interval
- bash src/convert_coord/bp2cm.sh -r $(OLDREF) -n $(REF) -o $(LINKMAP)/bp2cm/bp2cm.tsv \
+ bash src/convert_coord/bp2cm.sh -r $(OLD-REF) -n $(REF) -o $(LINKMAP)/bp2cm/bp2cm \
  -m $(LINKMAP)/linkage_markers.csv
  # Apply transformation to CSD dataset to get cM coordinates
  bash src/convert_coord/apply_bp2cm.sh $(ASSOC)/case_control/case_control_all.tsv \

src/convert_coord/apply_bp2cm.sh

@@ -53,15 +53,13 @@ while read -a hit; do
  # Position of SNP from start of interval
  from_start=$((bp - interv[1]))
  curr_cM=$(echo "$from_start * ${interv[3]} + $cum_cM" | bc -l)
- echo "CURR: $curr_cM"
  echo -e "${hit[*]}\t$curr_cM" >> "$out_hits"
  else
  # SNP not found, next read will not use this interval
  ((n_interv++))
  # Computing total cM in interval (cM/BP) * (end-start) 
  int_cM=$(echo "${interv[3]} * (${interv[2]} - ${interv[1]})")
  cum_cM=$(echo "$cum_cM + $int_cM" | bc -l)
- echo "NEXT"
  fi
  echo "$cum_cM"