Soften some penalties

enormandeau · Apr 21, 2023 · 5134153 · 5134153
1 parent 0bc2bf6
commit 5134153
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Showing 2 changed files with 5 additions and 5 deletions.
diff --git a/01_scripts/06_score_markers.py b/01_scripts/06_score_markers.py
@@ -71,7 +71,7 @@
                 # More than 10% difference to reference genome
                 if int(NumDiff) > 0.10 * len(Sequence):
                     penalties.append("D")
-                    score -= 0.5
+                    score -= 0.4
 
                 else:
                     penalties.append("d")
@@ -83,7 +83,7 @@
                 # Maximum 20% softclip that are not Ns
                 if (int(Softclip) - int(NumNs)) > 0.10 * len(Sequence):
                     penalties.append("S")
-                    score -= 0.5
+                    score -= 0.4
 
                 else:
                     penalties.append("s")
@@ -95,11 +95,11 @@
                 # Match plus softclip and Ns are not at least 80% of sequence
                 if (int(Match) + int(Softclip) + int(NumNs)) < 0.8 * len(Sequence):
                     penalties.append("p")
-                    score -= 0.3
+                    score -= 0.2
 
                 else:
                     penalties.append("P")
-                    score -= 0.5
+                    score -= 0.4
 
             if not penalties:
                 penalties.append(".")

diff --git a/README.md b/README.md
@@ -10,7 +10,7 @@ and then call and filter the loci.
 
 In the process, a proportion of the loci are inevitably lost. However, the
 transferred proportion is very high for genomes with low duplication content and
-when both genome versions are similar. Our test run on real data gives a 99.83%
+when both genome versions are similar. Our test run on real data gives a 99.87%
 transfers rate.
 
 **NOTE**: Although SNPLift was designed primarily for VCFs containing SNP data,