1 files changed, 0 insertions, 31 deletions
diff --git a/biology/haplohseq/files/patch-scripts_simple__phaser.py b/biology/haplohseq/files/patch-scripts_simple__phaser.py
deleted file mode 100644
index c6c5941ee00d..000000000000
--- a/biology/haplohseq/files/patch-scripts_simple__phaser.py
+++ /dev/null
@@ -1,31 +0,0 @@
---- scripts/simple_phaser.py.orig	2021-01-23 17:25:56 UTC
-+++ scripts/simple_phaser.py
-@@ -108,7 +108,7 @@ class SimplePhaser:
-         return informativeHets, informativeCoords, informativeIndexes
-     
-     def getRefPairedAllele(self, anchorIndex, pairedIndex):
--#         print "\t".join([str(anchorIndex), str(pairedIndex - anchorIndex  - 1), str(len(self.ldMap.dVals)),str(len(self.ldMap.dVals[anchorIndex]))]) # prints intermarker counts
-+#         print("\t".join([str(anchorIndex), str(pairedIndex - anchorIndex  - 1), str(len(self.ldMap.dVals)),str(len(self.ldMap.dVals[anchorIndex]))]) # prints intermarker counts)
-         if (pairedIndex - anchorIndex - 1) >= len(self.ldMap.dVals[anchorIndex]):
-             pRef = random.uniform(0,1)
-             if pRef > 0.5:
-@@ -166,8 +166,8 @@ class SimplePhaser:
-                 altHap = temp 
-             
-             if pairedAllele not in [ref,alt]:
--                print "pairedAllele not ref or alt " + ref + " " + alt
--                print pairedAllele               
-+                print("pairedAllele not ref or alt " + ref + " " + alt)
-+                print(pairedAllele)
-          
-         return phasedAlleles, informativeCoords
-             
-@@ -182,7 +182,7 @@ class SimplePhaser:
-             elif candidateHap[i].upper() == phasedHaps[1][i].upper():
-                 currentMatch = 1
-             else:
--                print "ERROR: " + candidateHap[i] + " does not match " + phasedHaps[0][i] + " or " + phasedHaps[1][i] + "\t" + self.ldMap.coords[i] + "\t" + self.ldMap.refs[i] + "\t" + self.ldMap.alts[i]
-+                print("ERROR: " + candidateHap[i] + " does not match " + phasedHaps[0][i] + " or " + phasedHaps[1][i] + "\t" + self.ldMap.coords[i] + "\t" + self.ldMap.refs[i] + "\t" + self.ldMap.alts[i])
- #                 # randomly assign match
- #                 p0 = random.uniform(0,1)
- #                 if p0 > 0.5: