corner image corner image corner image corner image Debian NEW package overview for svim
svim_1.4.1+ds-1_amd64.changes (click to toggle)
Format:1.8
Date:Mon, 07 Sep 2020 22:19:40 +0530
Source:svim
Binary:svim
Architecture:source all
Version:1.4.1+ds-1
Distribution:unstable
Urgency:medium
Maintainer:Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By:Nilesh Patra <npatra974@gmail.com>
Description:
svim       - Structural variant caller for long sequencing reads
Closes:969743
Changes:
svim (1.4.1+ds-1) unstable; urgency=medium

  * Initial release (Closes: #969743)
Files:
0b3977e728c63de87411a4ac93c9c6d8 2008 science optional svim_1.4.1+ds-1.dsc
8dc4dce103e84d7287c97322c5726278 213456 science optional svim_1.4.1+ds.orig.tar.xz
558766f5229aa2a2d4b23ecfca3e179f 8960 science optional svim_1.4.1+ds-1.debian.tar.xz
c7aa9a44532a95edd61a7bb79a5389f6 30772 science optional svim_1.4.1+ds-1_all.deb
1f73593e29e9be4bb01373aa8c87daba 8133 science optional svim_1.4.1+ds-1_amd64.buildinfo
svim_1.4.1+ds-1.dsc (click to toggle)
Format:3.0 (quilt)
Source:svim
Binary:svim
Architecture:all
Version:1.4.1+ds-1
Maintainer:Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders:Nilesh Patra <npatra974@gmail.com>
Homepage:https://github.com/eldariont/svim
Standards-Version:4.5.0
Vcs-Browser:https://salsa.debian.org/med-team/svim
Vcs-Git:https://salsa.debian.org/med-team/svim.git
Build-Depends:debhelper-compat (=13), dh-python, python3-all, python3-setuptools, python3-numpy, python3-pysam, python3-matplotlib, python3-scipy, samtools
Package-List:svim deb science optional arch=all
Files:
8dc4dce103e84d7287c97322c5726278 213456 svim_1.4.1+ds.orig.tar.xz
558766f5229aa2a2d4b23ecfca3e179f 8960 svim_1.4.1+ds-1.debian.tar.xz
lintian 2.90.0~bpo10+1 check for svim_1.4.1+ds-1.dsc (click to toggle)
README.source for svim_1.4.1+ds-1.dsc (click to toggle)
Upstream provides binary files without sources for:

* src/tests/chimeric_read_errors.sam 

These have been converted to corresponding text (.sam) files with the commands:
* samtools view -h -o chimeric_read.sam chimeric_read.bam

And the corresponding *.sam files are added to: debian/missing-sources

They can be generated back with the following commands:
*	cat debian/missing-sources/chimeric_read.sam| samtools view -Sb - > src/tests/chimeric_read.bam
*	samtools index src/tests/chimeric_read.bam src/tests/chimeric_read.bam.bai
*	cat src/tests/chimeric_read_errors.sam| samtools view -Sb - > src/tests/chimeric_read_errors.bam
*	samtools index src/tests/chimeric_read_errors.bam src/tests/chimeric_read_errors.bam.bai

The corresponding ".bam.bai" file is also being generated from the source(s) which is required during tests but not provided by upstream.
These commands are also being run in debian/rules since these binaries are needed for testing.

 -- Nilesh Patra <npatra974@gmail.com>

control file for svim_1.4.1+ds-1_all.deb (click to toggle)
Package:svim
Version:1.4.1+ds-1
Architecture:all
Maintainer:Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size:236
Depends:python3-matplotlib, python3-numpy, python3-pysam, python3-scipy, python3:any
Section:science
Priority:optional
Homepage:https://github.com/eldariont/svim
Description:
Structural variant caller for long sequencing reads
 SVIM is a structural variant caller for long sequencing reads.
 It is able to detect, classify and genotype five different
 classes of structural variants. Unlike existing methods, SVIM
 integrates information from across the genome to precisely
 distinguish similar events, such as tandem and interspersed
 duplications and simple insertions.
lintian 2.90.0~bpo10+1 check for svim_1.4.1+ds-1_all.deb (click to toggle)
contents of svim_1.4.1+ds-1_all.deb (click to toggle)
drwxr-xr-x root/root         0 2020-09-07 16:49 ./
drwxr-xr-x root/root         0 2020-09-07 16:49 ./usr/
drwxr-xr-x root/root         0 2020-09-07 16:49 ./usr/bin/
-rwxr-xr-x root/root     12014 2020-09-07 16:49 ./usr/bin/svim
drwxr-xr-x root/root         0 2020-09-07 16:49 ./usr/lib/
drwxr-xr-x root/root         0 2020-09-07 16:49 ./usr/lib/python3/
drwxr-xr-x root/root         0 2020-09-07 16:49 ./usr/lib/python3/dist-packages/
drwxr-xr-x root/root         0 2020-09-07 16:49 ./usr/lib/python3/dist-packages/svim/
-rw-r--r-- root/root     37054 2020-09-07 16:49 ./usr/lib/python3/dist-packages/svim/SVCandidate.py
-rw-r--r-- root/root      6634 2020-09-07 16:49 ./usr/lib/python3/dist-packages/svim/SVIM_CLUSTER.py
-rw-r--r-- root/root      6922 2020-09-07 16:49 ./usr/lib/python3/dist-packages/svim/SVIM_COLLECT.py
-rw-r--r-- root/root     21092 2020-09-07 16:49 ./usr/lib/python3/dist-packages/svim/SVIM_COMBINE.py
-rw-r--r-- root/root      3322 2020-09-07 16:49 ./usr/lib/python3/dist-packages/svim/SVIM_alignment.py
-rw-r--r-- root/root     17073 2020-09-07 16:49 ./usr/lib/python3/dist-packages/svim/SVIM_clustering.py
-rw-r--r-- root/root      4791 2020-09-07 16:49 ./usr/lib/python3/dist-packages/svim/SVIM_genotyping.py
-rw-r--r-- root/root     39442 2020-09-07 16:49 ./usr/lib/python3/dist-packages/svim/SVIM_input_parsing.py
-rw-r--r-- root/root     22650 2020-09-07 16:49 ./usr/lib/python3/dist-packages/svim/SVIM_inter.py
-rw-r--r-- root/root      2341 2020-09-07 16:49 ./usr/lib/python3/dist-packages/svim/SVIM_intra.py
-rw-r--r-- root/root     10661 2020-09-07 16:49 ./usr/lib/python3/dist-packages/svim/SVIM_merging.py
-rw-r--r-- root/root      6497 2020-09-07 16:49 ./usr/lib/python3/dist-packages/svim/SVIM_plot.py
-rw-r--r-- root/root     13160 2020-09-07 16:49 ./usr/lib/python3/dist-packages/svim/SVSignature.py
-rw-r--r-- root/root         0 2020-09-07 16:49 ./usr/lib/python3/dist-packages/svim/__init__.py
drwxr-xr-x root/root         0 2020-09-07 16:49 ./usr/lib/python3/dist-packages/svim-1.4.1.egg-info/
-rw-r--r-- root/root      7516 2020-09-07 16:49 ./usr/lib/python3/dist-packages/svim-1.4.1.egg-info/PKG-INFO
-rw-r--r-- root/root         1 2020-09-07 16:49 ./usr/lib/python3/dist-packages/svim-1.4.1.egg-info/dependency_links.txt
-rw-r--r-- root/root         1 2020-09-07 16:49 ./usr/lib/python3/dist-packages/svim-1.4.1.egg-info/not-zip-safe
-rw-r--r-- root/root         0 2020-09-07 16:49 ./usr/lib/python3/dist-packages/svim-1.4.1.egg-info/requires.txt
-rw-r--r-- root/root        11 2020-09-07 16:49 ./usr/lib/python3/dist-packages/svim-1.4.1.egg-info/top_level.txt
drwxr-xr-x root/root         0 2020-09-07 16:49 ./usr/share/
drwxr-xr-x root/root         0 2020-09-07 16:49 ./usr/share/doc/
drwxr-xr-x root/root         0 2020-09-07 16:49 ./usr/share/doc/svim/
-rw-r--r-- root/root       160 2020-09-07 16:49 ./usr/share/doc/svim/changelog.Debian.gz
-rw-r--r-- root/root       904 2020-09-07 16:49 ./usr/share/doc/svim/copyright
drwxr-xr-x root/root         0 2020-09-07 16:49 ./usr/share/man/
drwxr-xr-x root/root         0 2020-09-07 16:49 ./usr/share/man/man1/
-rw-r--r-- root/root       898 2020-09-07 16:49 ./usr/share/man/man1/svim.1.gz

Timestamp: 07.09.2020 / 20:11:54 (UTC)