From 4bacbfad7d0732ed5f45ae648170155113255e9b Mon Sep 17 00:00:00 2001
From: Rachel Colquhoun <rachel.colquhoun@ed.ac.uk>
Date: Thu, 17 Jun 2021 14:59:03 +0100
Subject: [PATCH 1/4] #215

---
 pangolin/scripts/pangolearn.smk | 1 +
 1 file changed, 1 insertion(+)

diff --git a/pangolin/scripts/pangolearn.smk b/pangolin/scripts/pangolearn.smk
index 8dd69fa..d2361fb 100644
--- a/pangolin/scripts/pangolearn.smk
+++ b/pangolin/scripts/pangolearn.smk
@@ -175,6 +175,7 @@ rule scorpio:
         -i {input.fasta:q} \
         -o {output.report:q} \
         -t {workflow.cores} \
+        --output-counts \
         --long &> {log:q}
         """
 

From e8478d8f9dcdf9023fa2286dc546fb8385ed8a7e Mon Sep 17 00:00:00 2001
From: aineniamh <aine.otoole@ed.ac.uk>
Date: Sun, 20 Jun 2021 10:19:31 +0100
Subject: [PATCH 2/4] patch for art's tweet about slashes breaking paths

---
 pangolin/__init__.py            | 2 +-
 pangolin/scripts/pangolearn.smk | 7 ++++---
 2 files changed, 5 insertions(+), 4 deletions(-)

diff --git a/pangolin/__init__.py b/pangolin/__init__.py
index bdaa721..e3e659f 100644
--- a/pangolin/__init__.py
+++ b/pangolin/__init__.py
@@ -1,5 +1,5 @@
 _program = "pangolin"
-__version__ = "3.1.3"
+__version__ = "3.1.4"
 
 __all__ = ["pangolearn",
     "utils"]
diff --git a/pangolin/scripts/pangolearn.smk b/pangolin/scripts/pangolearn.smk
index d2361fb..e915a58 100644
--- a/pangolin/scripts/pangolearn.smk
+++ b/pangolin/scripts/pangolearn.smk
@@ -226,9 +226,10 @@ rule generate_report:
                             scorpio_lineage = new_row["scorpio_call"].split("+")[0].split("-like")[0]
                         expanded_scorpio_lineage = expand_alias(scorpio_lineage, alias_dict)
                         expanded_pango_lineage = expand_alias(row['lineage'], alias_dict)
-                        if expanded_scorpio_lineage and expanded_pango_lineage and not expanded_pango_lineage.startswith(expanded_scorpio_lineage):
-                            new_row["note"] += f'; scorpio replaced lineage assignment {row["lineage"]}'
-                            new_row['lineage'] = scorpio_lineage
+                        if '/' not in scorpio_lineage:
+                            if expanded_scorpio_lineage and expanded_pango_lineage and not expanded_pango_lineage.startswith(expanded_scorpio_lineage):
+                                new_row["note"] += f'; scorpio replaced lineage assignment {row["lineage"]}'
+                                new_row['lineage'] = scorpio_lineage
 
                     writer.writerow(new_row)
 

From 05e88ee8108784fc7c3c514620b811a463e4f00c Mon Sep 17 00:00:00 2001
From: Rachel Colquhoun <rachel.colquhoun@ed.ac.uk>
Date: Wed, 23 Jun 2021 14:19:06 +0100
Subject: [PATCH 3/4] use scorpio mrca_lineage and --pangolin mode to make more
 robust

---
 pangolin/scripts/pangolearn.smk | 11 +++--------
 1 file changed, 3 insertions(+), 8 deletions(-)

diff --git a/pangolin/scripts/pangolearn.smk b/pangolin/scripts/pangolearn.smk
index e915a58..c8e5b64 100644
--- a/pangolin/scripts/pangolearn.smk
+++ b/pangolin/scripts/pangolearn.smk
@@ -176,6 +176,7 @@ rule scorpio:
         -o {output.report:q} \
         -t {workflow.cores} \
         --output-counts \
+        --pangolin \
         --long &> {log:q}
         """
 
@@ -220,10 +221,7 @@ rule generate_report:
                         new_row["scorpio_conflict"] = scorpio_call_info["conflict"]
                         new_row["note"] = f'scorpio call: Alt alleles {scorpio_call_info["alt_count"]}; Ref alleles {scorpio_call_info["ref_count"]}; Amb alleles {scorpio_call_info["ambig_count"]}'
 
-                        if "(" in new_row["scorpio_call"]:
-                            scorpio_lineage = new_row["scorpio_call"].split("(")[1].split("+")[0].split("-like")[0]
-                        else:
-                            scorpio_lineage = new_row["scorpio_call"].split("+")[0].split("-like")[0]
+                        scorpio_lineage = scorpio_call_info["mrca_lineage"]
                         expanded_scorpio_lineage = expand_alias(scorpio_lineage, alias_dict)
                         expanded_pango_lineage = expand_alias(row['lineage'], alias_dict)
                         if '/' not in scorpio_lineage:
@@ -347,10 +345,7 @@ rule usher_to_report:
                         scorpio_conflict = scorpio_call_info["conflict"]
                         note = f'scorpio call: Alt alleles {scorpio_call_info["alt_count"]}; Ref alleles {scorpio_call_info["ref_count"]}; Amb alleles {scorpio_call_info["ambig_count"]}'
 
-                        if "(" in scorpio_call:
-                            scorpio_lineage = scorpio_call.split("(")[1].split("+")[0].split("-like")[0]
-                        else:
-                            scorpio_lineage = scorpio_call.split("+")[0].split("-like")[0]
+                        scorpio_lineage = scorpio_call_info["mrca_lineage"]
                         expanded_scorpio_lineage = expand_alias(scorpio_lineage, alias_dict)
                         expanded_pango_lineage = expand_alias(lineage, alias_dict)
                         if expanded_scorpio_lineage and expanded_pango_lineage and not expanded_pango_lineage.startswith(expanded_scorpio_lineage):

From 4fdad9986a211722a11e85da04954d42f31f9c07 Mon Sep 17 00:00:00 2001
From: Rachel Colquhoun <rachel.colquhoun@ed.ac.uk>
Date: Wed, 23 Jun 2021 20:40:59 +0100
Subject: [PATCH 4/4] update init if accept PR

---
 pangolin/__init__.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pangolin/__init__.py b/pangolin/__init__.py
index e3e659f..70320d6 100644
--- a/pangolin/__init__.py
+++ b/pangolin/__init__.py
@@ -1,5 +1,5 @@
 _program = "pangolin"
-__version__ = "3.1.4"
+__version__ = "3.1.5"
 
 __all__ = ["pangolearn",
     "utils"]