[med-svn] [Git][med-team/tiddit][upstream] New upstream version 3.5.2+dfsg

[Lance Lin (@linqigang)]

Lance Lin pushed to branch upstream at Debian Med / tiddit


Commits:
d579434e by Lance Lin at 2023-02-13T20:38:29+07:00
New upstream version 3.5.2+dfsg
- - - - -


3 changed files:

- setup.py
- tiddit/__main__.py
- tiddit/tiddit_contig_analysis.pyx


Changes:

=====================================
setup.py
=====================================
@@ -20,7 +20,7 @@ else:
 
 setup(
     name = 'tiddit',
-    version = '3.5.1',
+    version = '3.5.2',
 
     url = "https://github.com/SciLifeLab/TIDDIT",
     author = "Jesper Eisfeldt",


=====================================
tiddit/__main__.py
=====================================
@@ -17,7 +17,7 @@ import tiddit.tiddit_variant as tiddit_variant
 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")


=====================================
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)



View it on GitLab: https://salsa.debian.org/med-team/tiddit/-/commit/d579434e2cc58b4d1e8e1fc25338c22778e2aa1e

-- 
View it on GitLab: https://salsa.debian.org/med-team/tiddit/-/commit/d579434e2cc58b4d1e8e1fc25338c22778e2aa1e
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