[med-svn] [Git][med-team/tiddit][master] 7 commits: New upstream version 2.12.0+dfsg

Andreas Tille gitlab at salsa.debian.org
Tue Jun 16 21:11:11 BST 2020



Andreas Tille pushed to branch master at Debian Med / tiddit


Commits:
5573c455 by Andreas Tille at 2020-06-16T22:08:50+02:00
New upstream version 2.12.0+dfsg
- - - - -
896a7e4a by Andreas Tille at 2020-06-16T22:08:50+02:00
routine-update: New upstream version

- - - - -
046921cc by Andreas Tille at 2020-06-16T22:08:50+02:00
Update upstream source from tag 'upstream/2.12.0+dfsg'

Update to upstream version '2.12.0+dfsg'
with Debian dir 7233100093e735edf5ac12edfbf1a0a5dcdcb67e
- - - - -
0ceaa361 by Andreas Tille at 2020-06-16T22:08:51+02:00
routine-update: debhelper-compat 13

- - - - -
1dcbe52e by Andreas Tille at 2020-06-16T22:08:54+02:00
routine-update: Rules-Requires-Root: no

- - - - -
9882d404 by Andreas Tille at 2020-06-16T22:08:57+02:00
Set upstream metadata fields: Bug-Database, Bug-Submit, Repository, Repository-Browse.

Fixes: lintian: upstream-metadata-missing-bug-tracking
See-also: https://lintian.debian.org/tags/upstream-metadata-missing-bug-tracking.html


Fixes: lintian: upstream-metadata-missing-repository
See-also: https://lintian.debian.org/tags/upstream-metadata-missing-repository.html

- - - - -
8418e325 by Andreas Tille at 2020-06-16T22:10:03+02:00
routine-update: Ready to upload to unstable

- - - - -


8 changed files:

- TIDDIT.py
- debian/changelog
- debian/control
- debian/upstream/metadata
- src/TIDDIT.cpp
- src/TIDDIT_calling.py
- src/TIDDIT_coverage.py
- + versioned_singularity/TIDDIT.2.12.0


Changes:

=====================================
TIDDIT.py
=====================================
@@ -8,7 +8,7 @@ wd=os.path.dirname(os.path.realpath(__file__))
 sys.path.insert(0, '{}/src/'.format(wd))
 import TIDDIT_calling
 
-version = "2.11.0"
+version = "2.12.0"
 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")


=====================================
debian/changelog
=====================================
@@ -1,3 +1,13 @@
+tiddit (2.12.0+dfsg-1) unstable; urgency=medium
+
+  * New upstream version
+  * debhelper-compat 13 (routine-update)
+  * Rules-Requires-Root: no (routine-update)
+  * Set upstream metadata fields: Bug-Database, Bug-Submit, Repository,
+    Repository-Browse.
+
+ -- Andreas Tille <tille at debian.org>  Tue, 16 Jun 2020 22:08:57 +0200
+
 tiddit (2.11.0+dfsg-1) unstable; urgency=medium
 
   * Initial release (Closes: #961659)


=====================================
debian/control
=====================================
@@ -3,7 +3,7 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.
 Uploaders: Andreas Tille <tille at debian.org>
 Section: science
 Priority: optional
-Build-Depends: debhelper-compat (= 12),
+Build-Depends: debhelper-compat (= 13),
                cmake,
                dh-python,
                cython3,
@@ -14,6 +14,7 @@ Standards-Version: 4.5.0
 Vcs-Browser: https://salsa.debian.org/med-team/tiddit
 Vcs-Git: https://salsa.debian.org/med-team/tiddit.git
 Homepage: https://github.com/SciLifeLab/TIDDIT
+Rules-Requires-Root: no
 
 Package: tiddit
 Architecture: any


=====================================
debian/upstream/metadata
=====================================
@@ -1,3 +1,7 @@
+Bug-Database: https://github.com/SciLifeLab/TIDDIT/issues
+Bug-Submit: https://github.com/SciLifeLab/TIDDIT/issues/new
 Registry:
  - Name: conda:bioconda
    Entry: tiddit
+Repository: https://github.com/SciLifeLab/TIDDIT.git
+Repository-Browse: https://github.com/SciLifeLab/TIDDIT


=====================================
src/TIDDIT.cpp
=====================================
@@ -46,7 +46,7 @@ int main(int argc, char **argv) {
 	int min_variant_size= 100;
 	int sample = 100000000;
 	string outputFileHeader ="output";
-	string version = "2.11.0";
+	string version = "2.12.0";
 	
 	//collect all options as a vector
 	vector<string> arguments(argv, argv + argc);


=====================================
src/TIDDIT_calling.py
=====================================
@@ -234,9 +234,21 @@ def cluster(args):
 	for chrA in chromosomes:
 		calls[chrA] =[]
 		print ("{}".format(chrA))
+		signals_chrA={}
+		signals=[ [hit[0],hit[1],hit[2],hit[3],hit[4],hit[5],hit[6],hit[7],hit[8]] for hit in args.c.execute('SELECT chrB,posA,posB,forwardA,qualA,forwardB,qualB,resolution,name FROM TIDDITcall WHERE chrA == \'{}\''.format(chrA)).fetchall()]
+
 		for chrB in chromosomes:
-			signal_data=numpy.array([ [hit[0],hit[1],hit[2],hit[3],hit[4],hit[5],hit[6],hit[7]] for hit in args.c.execute('SELECT posA,posB,forwardA,qualA,forwardB,qualB,resolution,name FROM TIDDITcall WHERE chrA == \'{}\' AND chrB == \'{}\''.format(chrA,chrB)).fetchall()])
+			if not chrB in signals_chrA:
+				signals_chrA[chrB] = []
+
+		for signal in signals:
+			signals_chrA[signal[0]].append(signal[1:])
 
+		for chrB in signals_chrA:
+			signals_chrA[chrB]=numpy.array(signals_chrA[chrB])
+		
+		for chrB in chromosomes:
+			signal_data=signals_chrA[chrB]
 			if not len(signal_data):
 				continue
 


=====================================
src/TIDDIT_coverage.py
=====================================
@@ -88,7 +88,7 @@ def determine_ploidy(args,chromosomes,coverage_data,Ncontent,library_stats):
 			print ("make sure that the contigs of the bam file and the reference match")
 			quit()
 
-	if len(cov):
+	if cov.size:
 		coverage_norm=numpy.median(cov)
 	else:
 		coverage_norm=1
@@ -107,7 +107,11 @@ def determine_ploidy(args,chromosomes,coverage_data,Ncontent,library_stats):
 		else:
 			cov=coverage_data[chromosome][numpy.where( (coverage_data[chromosome][:,1] > args.Q) | (coverage_data[chromosome][:,1] == 0) ),0]
 
-		chromosomal_average=numpy.median(cov)
+		if cov.size:
+			chromosomal_average=numpy.median(cov)
+		else:
+			chromosomal_average=0
+
 		if not args.force_ploidy:
 			try:
 				ploidies[chromosome]=int(round((chromosomal_average)/coverage_norm*args.n))


=====================================
versioned_singularity/TIDDIT.2.12.0
=====================================
@@ -0,0 +1,23 @@
+BootStrap: debootstrap
+OSVersion: trusty
+MirrorURL: http://us.archive.ubuntu.com/ubuntu/
+
+
+%runscript
+    echo "This is what happens when you run the container..."
+
+
+%post
+    echo "Hello from inside the container"
+    sed -i 's/$/ universe/' /etc/apt/sources.list
+    apt-get update
+    apt-get -y --force-yes install build-essential cmake make zlib1g-dev python python-dev python-setuptools git wget libbz2-dev unzip
+    easy_install pip
+    pip install numpy cython
+
+    wget https://github.com/SciLifeLab/TIDDIT/archive/TIDDIT-2.12.0.zip
+    unzip TIDDIT-2.12.0.zip
+
+    mv TIDDIT-TIDDIT-2.12.0/* /bin/
+    cd /bin/ && ./INSTALL.sh
+    chmod +x /bin/TIDDIT.py



View it on GitLab: https://salsa.debian.org/med-team/tiddit/-/compare/5c956ccf3bc42619eba486b8db871781570e0601...8418e3259546b3928f4153b9849ac62a3b5518c1

-- 
View it on GitLab: https://salsa.debian.org/med-team/tiddit/-/compare/5c956ccf3bc42619eba486b8db871781570e0601...8418e3259546b3928f4153b9849ac62a3b5518c1
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