return original if assertion error

nextgenusfs · Nov 4, 2023 · 14ccbcd · 14ccbcd
1 parent 1059dee
commit 14ccbcd
Showing 1 changed file with 4 additions and 20 deletions.
diff --git a/gapmm2/align.py b/gapmm2/align.py
@@ -149,10 +149,7 @@ def left_update_paf_plus(paf, align, slide, offset):
         try:
             assert intron_len > 0, "Introns cannot be less than zero"
         except AssertionError as e:
-            print(f"Assertion failed: {str(e)}")
-            print(paf)
-            print(align)
-            raise SystemExit(1)
+            return paf
         new_cs = "cs:Z::{}~gt{}ag{}".format(
             align["cigar"].strip("="), intron_len, new_cs_str
         )
@@ -199,10 +196,7 @@ def left_update_paf_minus(paf, align, slide, offset):
         try:
             assert intron_len > 0, "Introns cannot be less than zero"
         except AssertionError as e:
-            print(f"Assertion failed: {str(e)}")
-            print(paf)
-            print(align)
-            raise SystemExit(1)
+            return paf
         new_cs = "cs:Z:{}~ct{}ac:{}".format(
             new_cs_str, intron_len, align["cigar"].strip("=")
         )
@@ -251,10 +245,7 @@ def right_update_paf_plus(paf, align, slide, offset):
         try:
             assert intron_len > 0, "Introns cannot be less than zero"
         except AssertionError as e:
-            print(f"Assertion failed: {str(e)}")
-            print(paf)
-            print(align)
-            raise SystemExit(1)
+            return paf
         new_cs = "cs:Z:{}~gt{}ag:{}".format(
             old_cs, intron_len, align["cigar"].strip("=")
         )
@@ -301,14 +292,7 @@ def right_update_paf_minus(paf, align, slide, offset):
         try:
             assert intron_len > 0, "Introns cannot be less than zero"
         except AssertionError as e:
-            print(f"Assertion failed: {str(e)}")
-            print(f"function=right_update_paf_minus")
-            print(f"paf={paf}")
-            print(f"align={align}")
-            print(f"slide={slide}")
-            print(f"offset={offset}")
-            print(f"old_cs_tup={old_cs_tup}")
-            raise SystemExit(1)
+            return paf
         new_cs = "cs:Z::{}~ct{}ac{}".format(
             align["cigar"].strip("="), intron_len, new_cs_str
         )