[med-svn] [Git][med-team/tiddit][master] 6 commits: routine-update: New upstream version

[Lance Lin (@linqigang)]

Lance Lin pushed to branch master at Debian Med / tiddit


Commits:
021eea35 by Lance Lin at 2023-02-13T20:38:13+07:00
routine-update: New upstream version

- - - - -
d579434e by Lance Lin at 2023-02-13T20:38:29+07:00
New upstream version 3.5.2+dfsg
- - - - -
8f6f4dfb by Lance Lin at 2023-02-13T20:38:29+07:00
Update upstream source from tag 'upstream/3.5.2+dfsg'

Update to upstream version '3.5.2+dfsg'
with Debian dir 0325ccb91c7bb404586c4cc885a52d4091f69265
- - - - -
af115602 by Lance Lin at 2023-02-13T20:39:25+07:00
routine-update: Ready to upload to unstable

- - - - -
c4c358bd by Lance Lin at 2023-02-13T22:47:30+07:00
update copyright year

- - - - -
f42e6cd6 by Lance Lin at 2023-02-13T22:48:22+07:00
upload new upstream

- - - - -


5 changed files:

- debian/changelog
- debian/copyright
- setup.py
- tiddit/__main__.py
- tiddit/tiddit_contig_analysis.pyx


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,11 @@
+tiddit (3.5.2+dfsg-1) UNRELEASED; urgency=medium
+
+  * Team upload.
+  * New upstream version 3.5.2+dfsg
+  * d/copyright: Update year to 2023
+
+ -- Lance Lin <lq27267 at gmail.com>  Mon, 13 Feb 2023 20:39:25 +0700
+
 tiddit (3.5.1+dfsg-1) unstable; urgency=medium
 
   * Team Upload.


=====================================
debian/copyright
=====================================
@@ -13,7 +13,7 @@ Copyright: 2016-2020 Francesco Vezzi <francesco.vezzi at scilifelab.se>,
 License: GPL-3
 
 Files: debian/*
-Copyright: 2020-2022 Andreas Tille <tille at debian.org>
+Copyright: 2020-2023 Andreas Tille <tille at debian.org>
 License: GPL-3
 
 License: GPL-3


=====================================
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/-/compare/c284581f3bc8fe877654e1be7eca6266d1ce2f90...f42e6cd649e9b443532af71d9db478595121759c

-- 
View it on GitLab: https://salsa.debian.org/med-team/tiddit/-/compare/c284581f3bc8fe877654e1be7eca6266d1ce2f90...f42e6cd649e9b443532af71d9db478595121759c
You're receiving this email because of your account on salsa.debian.org.


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20230213/60690010/attachment-0001.htm>