Merge pull request #104 from kristinebilgrav/master

Fix XA - splitting
SciLifeLab · Feb 7, 2023 · f5218d1 · f5218d1
2 parents f75f7cd + 502ee52
commit f5218d1
Show file tree

Hide file tree

Showing 3 changed files with 5 additions and 5 deletions.
diff --git a/setup.py b/setup.py
@@ -20,7 +20,7 @@
 
 setup(
     name = 'tiddit',
-    version = '3.5.1',
+    version = '3.5.2',
 
     url = "https://github.com/SciLifeLab/TIDDIT",
     author = "Jesper Eisfeldt",

diff --git a/tiddit/__main__.py b/tiddit/__main__.py
@@ -17,7 +17,7 @@
 import tiddit.tiddit_contig_analysis as tiddit_contig_analysis
 
 def main():
-	version="3.5.1"
+	version="3.5.2"
 	parser = argparse.ArgumentParser("""tiddit-{}""".format(version),add_help=False)
 	parser.add_argument("--sv"	 , help="call structural variation", required=False, action="store_true")
 	parser.add_argument("--cov"        , help="generate a coverage bed file", required=False, action="store_true")

diff --git a/tiddit/tiddit_contig_analysis.pyx b/tiddit/tiddit_contig_analysis.pyx
@@ -39,13 +39,13 @@ def read_contigs(aligned_contigs,prefix,sample_id,min_size):
 		elif read.has_tag("XA") and not (read.is_supplementary or read.is_secondary):
 			XA=read.get_tag("XA")
 			if XA.count(";") == 1:
-				if "-" in XA:
-					XA=XA.replace("-","")
+				if ",-" in XA:
+					XA=XA.replace(",-",",")
 					xa_list=XA.split(",")
 					xa_list.insert(2,"-")
 					XA=",".join(xa_list)
 				else:
-					XA=XA.replace("+","")
+					XA=XA.replace(",+",",")
 					xa_list=XA.split(",")
 					xa_list.insert(2,"+")
 					XA=",".join(xa_list)