From e3471dc4b0583f1ffdfb7eefeda74a3efe9302aa Mon Sep 17 00:00:00 2001
From: pbashyal-nmdp <pbashyal@nmdp.org>
Date: Tue, 7 Dec 2021 14:10:58 -0600
Subject: [PATCH 1/3] Remove remove_invalid arg from ARD

---
 scripts/pyard-reduce-csv | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/scripts/pyard-reduce-csv b/scripts/pyard-reduce-csv
index 59e453c..a0c6bc6 100755
--- a/scripts/pyard-reduce-csv
+++ b/scripts/pyard-reduce-csv
@@ -170,7 +170,7 @@ if __name__ == '__main__':
         sys.exit(1)
 
     # Instantiate py-ard object with the latest
-    ard = pyard.ARD(remove_invalid=False)
+    ard = pyard.ARD()
 
     # Read the Input File
     # Read only the columns to be saved.

From 4ec4cc460842a929941f64577295323167e64622 Mon Sep 17 00:00:00 2001
From: pbashyal-nmdp <pbashyal@nmdp.org>
Date: Tue, 7 Dec 2021 14:12:12 -0600
Subject: [PATCH 2/3] =?UTF-8?q?Bump=20version:=200.6.9=20=E2=86=92=200.6.1?=
 =?UTF-8?q?0?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

---
 pyard/__init__.py | 2 +-
 setup.cfg         | 2 +-
 setup.py          | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/pyard/__init__.py b/pyard/__init__.py
index a419903..59b08c1 100644
--- a/pyard/__init__.py
+++ b/pyard/__init__.py
@@ -24,4 +24,4 @@
 from .pyard import ARD
 
 __author__ = """NMDP Bioinformatics"""
-__version__ = '0.6.9'
+__version__ = '0.6.10'
diff --git a/setup.cfg b/setup.cfg
index 9917d39..979da02 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.6.9
+current_version = 0.6.10
 commit = True
 tag = True
 
diff --git a/setup.py b/setup.py
index f3cc342..bf86ec5 100644
--- a/setup.py
+++ b/setup.py
@@ -42,7 +42,7 @@
 
 setup(
     name='py-ard',
-    version='0.6.9',
+    version='0.6.10',
     description="ARD reduction for HLA with Python",
     long_description=readme + '\n\n' + history,
     author="CIBMTR",

From e329e5e39ed21147e8fd1e9f07ceb593363b445c Mon Sep 17 00:00:00 2001
From: pbashyal-nmdp <pbashyal@nmdp.org>
Date: Fri, 10 Dec 2021 15:30:06 -0600
Subject: [PATCH 3/3] Batch Reduce fixes:     - Fix serology check     - Fix
 issue with P groups     - A new flag `convert_v2_to_v3` to convert v2 to v3
 but not reduce.

---
 extras/reduce_conf.json  |  1 +
 scripts/pyard-reduce-csv | 29 ++++++++++++++++++++++-------
 2 files changed, 23 insertions(+), 7 deletions(-)

diff --git a/extras/reduce_conf.json b/extras/reduce_conf.json
index a219e94..6c4e737 100644
--- a/extras/reduce_conf.json
+++ b/extras/reduce_conf.json
@@ -30,6 +30,7 @@
   "apply_compression": "gzip",
   "reduce_serology": false,
   "reduce_v2": true,
+  "convert_v2_to_v3": false,
   "reduce_3field": true,
   "reduce_P": true,
   "reduce_XX": false,
diff --git a/scripts/pyard-reduce-csv b/scripts/pyard-reduce-csv
index a0c6bc6..40ab179 100755
--- a/scripts/pyard-reduce-csv
+++ b/scripts/pyard-reduce-csv
@@ -40,8 +40,7 @@ import pyard.drbx as drbx
 
 
 def is_serology(allele: str) -> bool:
-    if len(allele.split(':')) == 1:
-        return True
+    return ard.is_serology(allele)
 
 
 def is_3field(allele: str) -> bool:
@@ -52,7 +51,11 @@ def is_P(allele: str) -> bool:
     if allele.endswith('P'):
         fields = allele.split(':')
         if len(fields) == 2:  # Ps are 2 fields
-            return fields[0].isdigit() and fields[0].isdigit()
+            # Check both fields are digits only
+            # Eg: A*02:01P
+            # Check last 2 digits of first field: 02 is numeric 
+            # Check digits of seconds field: 01 is numeric
+            return fields[0][-2:].isdigit() and fields[1][:-1].isdigit()
     return False
 
 
@@ -83,6 +86,11 @@ def should_be_reduced(allele, locus_allele):
     return False
 
 
+def remove_locus_name(reduced_allele):
+    return "/".join(map(lambda a: a.split('*')[1],
+                        reduced_allele.split('/')))
+
+
 def reduce(allele, locus, column_name):
     # Does the allele name have the locus in it ?
     if allele == '':
@@ -111,16 +119,23 @@ def reduce(allele, locus, column_name):
             if ard_config["keep_locus_in_allele_name"]:
                 allele = reduced_allele
             else:
-                allele = "/".join(map(lambda a: a.split('*')[1],
-                                      reduced_allele.split('/')))
+                allele = remove_locus_name(reduced_allele)
         else:
             if verbose:
                 print(f"Failed to reduce {locus_allele}")
-
         if verbose:
             print(f"\t{locus_allele} => {allele}")
     else:
-        if ard_config["keep_locus_in_allele_name"]:
+        if ard_config['convert_v2_to_v3']:
+            if ard.is_v2(locus_allele):
+                v3_allele = ard.v2_to_v3(locus_allele)
+                if not ard_config["keep_locus_in_allele_name"]:
+                    allele = remove_locus_name(v3_allele)
+                else:
+                    allele = v3_allele
+                if verbose:
+                    print(f"\t{locus_allele} => {allele}")
+        elif ard_config["keep_locus_in_allele_name"]:
             allele = locus_allele
 
     return allele