From bc15752602b333778fa185ba5a239e5eb49fa057 Mon Sep 17 00:00:00 2001
From: ajw2329 <ajw2329@gmail.com>
Date: Wed, 13 Mar 2024 23:11:32 -0700
Subject: [PATCH 1/2] Change HS (haplotype) field from Integer to character in
 VCFs heterogenesis_varincorp.py

Haplotypes are represented by the HS field in the VCFs generated by Heterogenesis, and are indicated by letters A, B . .  Currently, the VCF header specifies that this field is numeric.  This causes certain VCF parsers to fail to correctly read the HS field.
---
 heterogenesis_varincorp.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/heterogenesis_varincorp.py b/heterogenesis_varincorp.py
index e5c0dcb..97ce667 100644
--- a/heterogenesis_varincorp.py
+++ b/heterogenesis_varincorp.py
@@ -146,7 +146,7 @@ def writevcffile(directory,prefix,clo,combvcfs,prochro):
             file.write('##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of Samples With Data">\n')
             file.write('##FORMAT=<ID=AF,Number=A,Type=Float,Description="Alt allele frequency">\n')
             file.write('##FORMAT=<ID=TC,Number=1,Type=Integer,Description="Total copies of alt allele">\n')
-            file.write('##FORMAT=<ID=HS,Number=1,Type=Integer,Description="Haplotypes">\n')
+            file.write('##FORMAT=<ID=HS,Number=1,Type=Character,Description="Haplotypes">\n')
             file.write('##FORMAT=<ID=HC,Number=.,Type=Integer,Description="Total copies of alt allele per haplotype">\n')
             file.write('##FORMAT=<ID=CN,Number=2,Type=Integer,Description="Copy number at position">\n')
             file.write('#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\t'+clo+'\n')

From a797f38690a1f3f4a26c5b8794d89eed2d97ee05 Mon Sep 17 00:00:00 2001
From: ajw2329 <ajw2329@gmail.com>
Date: Mon, 10 Mar 2025 21:09:27 -0700
Subject: [PATCH 2/2] Update heterogenesis_varincorp.py -- augment
 substitutions with all IUPAC codes

---
 heterogenesis_varincorp.py | 24 ++++++++++++++++++++----
 1 file changed, 20 insertions(+), 4 deletions(-)

diff --git a/heterogenesis_varincorp.py b/heterogenesis_varincorp.py
index 97ce667..cac2c1d 100644
--- a/heterogenesis_varincorp.py
+++ b/heterogenesis_varincorp.py
@@ -252,10 +252,26 @@ def invert(forward):
                 substitutions['g']='c'
                 substitutions['N']='N'
                 substitutions['n']='n'
-                substitutions['R']='R'
-                substitutions['r']='r'
-                substitutions['M']='M'
-                substitutions['m']='m'
+                substitutions['R']='Y'
+                substitutions['Y']='R'
+                substitutions['y']='r'
+                substitutions['r']='y'
+                substitutions['S']='S'
+                substitutions['s']='s'
+                substitutions['W']='W'
+                substitutions['w']='w'
+                substitutions['K']='M'
+                substitutions['M']='K'
+                substitutions['k']='m'
+                substitutions['m']='k'
+                substitutions['B']='V'
+                substitutions['V']='B'
+                substitutions['b']='v'
+                substitutions['v']='b'
+       	       	substitutions['D']='H'
+       	       	substitutions['H']='D'
+       	       	substitutions['d']='h'
+       	       	substitutions['h']='d'
                 for i in forward[::-1]:
                     reverse.append(substitutions[i])
                 return reverse