[med-svn] [Git][med-team/tiddit][master] 5 commits: New upstream version 3.6.1+dfsg

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Med / tiddit


Commits:
de66d7f7 by Andreas Tille at 2023-11-08T21:28:41+01:00
New upstream version 3.6.1+dfsg
- - - - -
3f3391f0 by Andreas Tille at 2023-11-08T21:28:41+01:00
routine-update: New upstream version

- - - - -
3a7a37f6 by Andreas Tille at 2023-11-08T21:28:41+01:00
Update upstream source from tag 'upstream/3.6.1+dfsg'

Update to upstream version '3.6.1+dfsg'
with Debian dir 2740c57fba4cdd6d85d7f4442d4bbf9bc8cc675e
- - - - -
3b509fcf by Andreas Tille at 2023-11-08T21:28:45+01:00
routine-update: Build-Depends: s/dh-python/dh-sequence-python3/

- - - - -
a220e413 by Andreas Tille at 2023-11-08T21:31:53+01:00
routine-update: Ready to upload to unstable

- - - - -


6 changed files:

- debian/changelog
- debian/control
- debian/rules
- setup.py
- tiddit/__main__.py
- tiddit/tiddit_variant.pyx


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,10 @@
+tiddit (3.6.1+dfsg-1) unstable; urgency=medium
+
+  * New upstream version
+  * Build-Depends: s/dh-python/dh-sequence-python3/ (routine-update)
+
+ -- Andreas Tille <tille at debian.org>  Wed, 08 Nov 2023 21:29:47 +0100
+
 tiddit (3.6.0+dfsg-1) unstable; urgency=medium
 
   * Team Upload.


=====================================
debian/control
=====================================
@@ -4,7 +4,7 @@ Uploaders: Andreas Tille <tille at debian.org>
 Section: science
 Priority: optional
 Build-Depends: debhelper-compat (= 13),
-               dh-python,
+               dh-sequence-python3,
                cython3,
                python3-all-dev,
                python3-setuptools,


=====================================
debian/rules
=====================================
@@ -8,7 +8,7 @@ export DEB_BUILD_MAINT_OPTIONS=hardening=+all
 export PYBUILD_NAME=tiddit
 
 %:
-	dh $@ --with python3 --buildsystem=pybuild
+	dh $@ --buildsystem=pybuild
 
 override_dh_clean:
 	dh_clean


=====================================
setup.py
=====================================
@@ -20,7 +20,7 @@ else:
 
 setup(
     name = 'tiddit',
-    version = '3.6.0',
+    version = '3.6.1',
 
 
     url = "https://github.com/SciLifeLab/TIDDIT",


=====================================
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="3.6.0"
+	version="3.6.1"
 	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_variant.pyx
=====================================
@@ -7,6 +7,22 @@ from joblib import Parallel, delayed
 from pysam import AlignmentFile, AlignedSegment
 
 
+
+def percentile(a, q):
+	size = len(a)
+	percentiles=[]
+
+	sorted_a=sorted(a)
+
+	for v in q:
+		if not size:
+			percentiles.append(0)
+		else:
+			percentiles.append( sorted_a[ int(math.ceil((size * v) / 100.0)) - 1 ] )
+
+	return(percentiles)
+
+
 def scoring(scoring_dict,percentiles):
 	score=[0]
 	if scoring_dict["n_contigs"]:
@@ -543,7 +559,8 @@ def main(str bam_file_name,dict sv_clusters,args,dict library,int min_mapq,sampl
 
 
 	p=[1,5,10,20,30,40,50,60,70,75,80,85,90,95,97.5,99]
-	percentiles={"FA":numpy.percentile(ratios["fragments_A"],p),"FB":numpy.percentile(ratios["fragments_B"],p),"RA":numpy.percentile(ratios["reads_A"],p),"RB":numpy.percentile(ratios["reads_B"],p)}
+
+	percentiles={"FA":percentile(ratios["fragments_A"],p),"FB":percentile(ratios["fragments_B"],p),"RA":percentile(ratios["reads_A"],p),"RB":percentile(ratios["reads_B"],p)}
 
 	for v in variants_list:
 		for variant in v:	



View it on GitLab: https://salsa.debian.org/med-team/tiddit/-/compare/0b98ccd9aac5ff68314b987b0d93b667c737619b...a220e413a05bb5c61cc5177ecd94391a0035b501

-- 
View it on GitLab: https://salsa.debian.org/med-team/tiddit/-/compare/0b98ccd9aac5ff68314b987b0d93b667c737619b...a220e413a05bb5c61cc5177ecd94391a0035b501
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