From a9a8b7ae21e32e966ac58f56f5d6b2fa354bef01 Mon Sep 17 00:00:00 2001
From: RosCraddock <109593931+RosCraddock@users.noreply.github.com>
Date: Mon, 21 Oct 2024 13:40:44 +0100
Subject: [PATCH 1/2] Allow AAP to be non integer

Changed integer to a float to allow decimal place on input e.g 0.5, 0.45 etc. Previously was forced on input to be an integer (then later turned into a float).
---
 MultiThreadIO.py | 11 +++++++----
 Pedigree.py      |  2 +-
 2 files changed, 8 insertions(+), 5 deletions(-)

diff --git a/MultiThreadIO.py b/MultiThreadIO.py
index 1088f10..c88b166 100644
--- a/MultiThreadIO.py
+++ b/MultiThreadIO.py
@@ -56,7 +56,7 @@ def split_by(array, step):
 
 
 
-def process_input_line(line, startsnp, stopsnp, dtype):
+def process_input_line(line, startsnp, stopsnp, dtype, nonInteger = False):
     parts = line.split(); 
     idx = parts[0]
     parts = parts[1:]
@@ -64,7 +64,10 @@ def process_input_line(line, startsnp, stopsnp, dtype):
     if startsnp is not None :
         parts = parts[startsnp : stopsnp + 1] #Offset 1 for id and 2 for id + include stopsnp
 
-    data=np.array([int(val) for val in parts], dtype = dtype)
+    if nonInteger :
+        data = np.array([val for val in parts], dtype=dtype)
+    else :
+        data = np.array([int(val) for val in parts], dtype = dtype)
 
     return (idx, data)
 
@@ -91,7 +94,7 @@ def process_input_line_plink(line, startsnp, stopsnp, dtype):
     return (idx, data)
 
 
-def readLines(fileName, startsnp, stopsnp, dtype, processor=process_input_line):
+def readLines(fileName, startsnp, stopsnp, dtype, processor=process_input_line, nonInteger = False):
     # print(f"Reading in file: {fileName}")
 
     try:
@@ -117,7 +120,7 @@ def readLines(fileName, startsnp, stopsnp, dtype, processor=process_input_line):
 
         if iothreads <= 1:
             for line in f:
-                output.append(processor(line, startsnp = startsnp, stopsnp = stopsnp, dtype = dtype))
+                output.append(processor(line, startsnp = startsnp, stopsnp = stopsnp, dtype = dtype, nonInteger = nonInteger))
 
     return output
 
diff --git a/Pedigree.py b/Pedigree.py
index 090f248..f42a852 100644
--- a/Pedigree.py
+++ b/Pedigree.py
@@ -942,7 +942,7 @@ def readInAAP(self, fileName):
         :param fileName: The file path
         :type fileName: str
         """        
-        data_list = MultiThreadIO.readLines(fileName, startsnp=None, stopsnp=None, dtype = np.int64)
+        data_list = MultiThreadIO.readLines(fileName, startsnp=None, stopsnp=None, dtype = np.float32, nonInteger = True)
 
         # flag of whether adding a default alternative allele probability
         default_aap = False

From e1fc6cf2b56572f391b70c5d56a827d0219d43f4 Mon Sep 17 00:00:00 2001
From: RosCraddock <109593931+RosCraddock@users.noreply.github.com>
Date: Tue, 22 Oct 2024 13:44:46 +0100
Subject: [PATCH 2/2] Removed nonInteger argument

---
 MultiThreadIO.py | 8 ++++----
 Pedigree.py      | 2 +-
 2 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/MultiThreadIO.py b/MultiThreadIO.py
index c88b166..2577944 100644
--- a/MultiThreadIO.py
+++ b/MultiThreadIO.py
@@ -56,7 +56,7 @@ def split_by(array, step):
 
 
 
-def process_input_line(line, startsnp, stopsnp, dtype, nonInteger = False):
+def process_input_line(line, startsnp, stopsnp, dtype):
     parts = line.split(); 
     idx = parts[0]
     parts = parts[1:]
@@ -64,7 +64,7 @@ def process_input_line(line, startsnp, stopsnp, dtype, nonInteger = False):
     if startsnp is not None :
         parts = parts[startsnp : stopsnp + 1] #Offset 1 for id and 2 for id + include stopsnp
 
-    if nonInteger :
+    if dtype in [np.float16, np.float32, np.float64] :
         data = np.array([val for val in parts], dtype=dtype)
     else :
         data = np.array([int(val) for val in parts], dtype = dtype)
@@ -94,7 +94,7 @@ def process_input_line_plink(line, startsnp, stopsnp, dtype):
     return (idx, data)
 
 
-def readLines(fileName, startsnp, stopsnp, dtype, processor=process_input_line, nonInteger = False):
+def readLines(fileName, startsnp, stopsnp, dtype, processor=process_input_line):
     # print(f"Reading in file: {fileName}")
 
     try:
@@ -120,7 +120,7 @@ def readLines(fileName, startsnp, stopsnp, dtype, processor=process_input_line,
 
         if iothreads <= 1:
             for line in f:
-                output.append(processor(line, startsnp = startsnp, stopsnp = stopsnp, dtype = dtype, nonInteger = nonInteger))
+                output.append(processor(line, startsnp = startsnp, stopsnp = stopsnp, dtype = dtype))
 
     return output
 
diff --git a/Pedigree.py b/Pedigree.py
index f42a852..339f97e 100644
--- a/Pedigree.py
+++ b/Pedigree.py
@@ -942,7 +942,7 @@ def readInAAP(self, fileName):
         :param fileName: The file path
         :type fileName: str
         """        
-        data_list = MultiThreadIO.readLines(fileName, startsnp=None, stopsnp=None, dtype = np.float32, nonInteger = True)
+        data_list = MultiThreadIO.readLines(fileName, startsnp=None, stopsnp=None, dtype = np.float32)
 
         # flag of whether adding a default alternative allele probability
         default_aap = False