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lumpy-sv_0.3.0+dfsg-1_amd64.changes (click to toggle)
Format:1.8
Date:Wed, 03 Jun 2020 08:49:09 +0200
Source:lumpy-sv
Binary:lumpy-sv lumpy-sv-dbgsym lumpy-sv-examples
Architecture:source amd64 all
Version:0.3.0+dfsg-1
Distribution:unstable
Urgency:medium
Maintainer:Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By:Andreas Tille <tille@debian.org>
Description:
lumpy-sv   - general probabilistic framework for structural variant discovery
lumpy-sv-examples - general probabilistic framework for structural variant discovery
Closes:961998
Changes:
lumpy-sv (0.3.0+dfsg-1) unstable; urgency=medium

  * Initial release (Closes: #961998)
Files:
47fec24782b683df7082805af07dd9c5 2220 science optional lumpy-sv_0.3.0+dfsg-1.dsc
989f72083c83f2914b9325f38ca17fbc 54717628 science optional lumpy-sv_0.3.0+dfsg.orig.tar.xz
62f1d8a85e1259b2b5b7f221cd7d9c50 8020 science optional lumpy-sv_0.3.0+dfsg-1.debian.tar.xz
d66f41a078a3535772677b0bba358342 2045748 debug optional lumpy-sv-dbgsym_0.3.0+dfsg-1_amd64.deb
bfbf2675b3c1fced4783c86db5920ddc 54647432 science optional lumpy-sv-examples_0.3.0+dfsg-1_all.deb
fb5128e9fa47451363859a744c543ef5 7561 science optional lumpy-sv_0.3.0+dfsg-1_amd64.buildinfo
d857eb933be89e010a6028803c106ab9 186744 science optional lumpy-sv_0.3.0+dfsg-1_amd64.deb
lumpy-sv_0.3.0+dfsg-1.dsc (click to toggle)
Format:3.0 (quilt)
Source:lumpy-sv
Binary:lumpy-sv, lumpy-sv-examples
Architecture:any all
Version:0.3.0+dfsg-1
Maintainer:Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders:Andreas Tille <tille@debian.org>
Homepage:https://github.com/arq5x/lumpy-sv
Standards-Version:4.5.0
Vcs-Browser:https://salsa.debian.org/med-team/lumpy-sv
Vcs-Git:https://salsa.debian.org/med-team/lumpy-sv.git
Testsuite:autopkgtest
Build-Depends:debhelper-compat (=12), dh-python, python3, libbamtools-dev, libfastahack-dev, libgzstream-dev, libsqlite3-dev, libhts-dev, libssl-dev, libcurl4-openssl-dev | libcurl4-dev
Package-List:lumpy-sv deb science optional arch=any lumpy-sv-examples deb science optional arch=all
Files:
989f72083c83f2914b9325f38ca17fbc 54717628 lumpy-sv_0.3.0+dfsg.orig.tar.xz
62f1d8a85e1259b2b5b7f221cd7d9c50 8020 lumpy-sv_0.3.0+dfsg-1.debian.tar.xz
lintian 2.77.1~bpo10+1 check for lumpy-sv_0.3.0+dfsg-1.dsc (click to toggle)
README.source for lumpy-sv_0.3.0+dfsg-1.dsc (click to toggle)
No README.source in this package
control file for lumpy-sv_0.3.0+dfsg-1_amd64.deb (click to toggle)
Package:lumpy-sv
Version:0.3.0+dfsg-1
Architecture:amd64
Maintainer:Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size:627
Depends:libbamtools2.5.1 (>=2.5.1+dfsg), libc6 (>=2.29), libgcc-s1 (>=3.0), libgzstream0 (>=1.5+dfsg), libhts3 (>=1.10), libstdc++6 (>=5.2), python3:any, samblaster, samtools, python3, python3-pysam, python3-numpy, bamkit
Recommends:sambamba
Section:science
Priority:optional
Homepage:https://github.com/arq5x/lumpy-sv
Description:
general probabilistic framework for structural variant discovery
 LUMPY, a novel SV discovery framework that naturally integrates multiple
 SV signals jointly across multiple samples.  LUMPY yields improved
 sensitivity, especially when SV signal is reduced owing to either low
 coverage data or low intra-sample variant allele frequency.
lintian 2.77.1~bpo10+1 check for lumpy-sv_0.3.0+dfsg-1_amd64.deb (click to toggle)
contents of lumpy-sv_0.3.0+dfsg-1_amd64.deb (click to toggle)
drwxr-xr-x root/root         0 2020-06-03 06:49 ./
drwxr-xr-x root/root         0 2020-06-03 06:49 ./etc/
drwxr-xr-x root/root         0 2020-06-03 06:49 ./etc/lumpy-sv/
-rw-r--r-- root/root       380 2020-06-03 06:49 ./etc/lumpy-sv/lumpyexpress.config
drwxr-xr-x root/root         0 2020-06-03 06:49 ./usr/
drwxr-xr-x root/root         0 2020-06-03 06:49 ./usr/bin/
-rwxr-xr-x root/root    460984 2020-06-03 06:49 ./usr/bin/lumpy
-rwxr-xr-x root/root     18736 2020-06-03 06:49 ./usr/bin/lumpy_filter
-rwxr-xr-x root/root     17464 2020-06-03 06:49 ./usr/bin/lumpyexpress
drwxr-xr-x root/root         0 2020-06-03 06:49 ./usr/share/
drwxr-xr-x root/root         0 2020-06-03 06:49 ./usr/share/doc/
drwxr-xr-x root/root         0 2020-06-03 06:49 ./usr/share/doc/lumpy-sv/
-rw-r--r-- root/root      4503 2019-02-13 04:30 ./usr/share/doc/lumpy-sv/README.md.gz
-rw-r--r-- root/root       159 2020-06-03 06:49 ./usr/share/doc/lumpy-sv/changelog.Debian.gz
-rw-r--r-- root/root      2701 2020-06-03 06:49 ./usr/share/doc/lumpy-sv/copyright
drwxr-xr-x root/root         0 2020-06-03 06:49 ./usr/share/lumpy-sv/
drwxr-xr-x root/root         0 2020-06-03 06:49 ./usr/share/lumpy-sv/scripts/
-rwxr-xr-x root/root       931 2020-06-03 06:49 ./usr/share/lumpy-sv/scripts/bedpe_sort.py
-rwxr-xr-x root/root      1764 2020-06-03 06:49 ./usr/share/lumpy-sv/scripts/check_sorting.py
-rwxr-xr-x root/root      2612 2020-06-03 06:49 ./usr/share/lumpy-sv/scripts/cnvanator_to_bedpes.py
-rw-r--r-- root/root       739 2019-02-13 04:30 ./usr/share/lumpy-sv/scripts/extract-sites.py
-rwxr-xr-x root/root      6216 2020-06-03 06:49 ./usr/share/lumpy-sv/scripts/extractSplitReads_BwaMem
-rwxr-xr-x root/root      1819 2020-06-03 06:49 ./usr/share/lumpy-sv/scripts/get_coverages.py
-rwxr-xr-x root/root       766 2020-06-03 06:49 ./usr/share/lumpy-sv/scripts/get_exclude_regions.py
-rw-r--r-- root/root     10926 2019-02-13 04:30 ./usr/share/lumpy-sv/scripts/l_bp.py
-rwxr-xr-x root/root     22140 2020-06-03 06:49 ./usr/share/lumpy-sv/scripts/l_merge.py
-rwxr-xr-x root/root      1984 2020-06-03 06:49 ./usr/share/lumpy-sv/scripts/l_sort.py
-rwxr-xr-x root/root      7592 2019-02-13 04:30 ./usr/share/lumpy-sv/scripts/lumpy_smooth
-rwxr-xr-x root/root     17464 2020-06-03 06:49 ./usr/share/lumpy-sv/scripts/lumpyexpress
-rwxr-xr-x root/root      3510 2020-06-03 06:49 ./usr/share/lumpy-sv/scripts/pairend_distro.py
-rw-r--r-- root/root      2116 2019-02-13 04:30 ./usr/share/lumpy-sv/scripts/par-svtyper.sh
-rwxr-xr-x root/root      1313 2020-06-03 06:49 ./usr/share/lumpy-sv/scripts/prob_bedpe_to_bedgraph.py
-rwxr-xr-x root/root       745 2019-02-13 04:30 ./usr/share/lumpy-sv/scripts/run_histo.sh
-rwxr-xr-x root/root      1521 2019-02-13 04:30 ./usr/share/lumpy-sv/scripts/split_unmapped_to_fasta.pl
-rwxr-xr-x root/root     16316 2020-06-03 06:49 ./usr/share/lumpy-sv/scripts/vcfToBedpe
drwxr-xr-x root/root         0 2020-06-03 06:49 ./usr/share/man/
drwxr-xr-x root/root         0 2020-06-03 06:49 ./usr/share/man/man1/
-rw-r--r-- root/root       882 2020-06-03 06:49 ./usr/share/man/man1/lumpy.1.gz
-rw-r--r-- root/root       328 2020-06-03 06:49 ./usr/share/man/man1/lumpy_filter.1.gz
-rw-r--r-- root/root       728 2020-06-03 06:49 ./usr/share/man/man1/lumpyexpress.1.gz
drwxr-xr-x root/root         0 2020-06-03 06:49 ./usr/share/python3/
drwxr-xr-x root/root         0 2020-06-03 06:49 ./usr/share/python3/runtime.d/
-rwxr-xr-x root/root       137 2020-06-03 06:49 ./usr/share/python3/runtime.d/lumpy-sv.rtupdate
lrwxrwxrwx root/root         0 2020-06-03 06:49 ./usr/share/lumpy-sv/scripts/lumpyexpress.config -> /etc/lumpy-sv/lumpyexpress.config
control file for lumpy-sv-dbgsym_0.3.0+dfsg-1_amd64.deb (click to toggle)
Package:lumpy-sv-dbgsym
Source:lumpy-sv
Version:0.3.0+dfsg-1
Auto-Built-Package:debug-symbols
Architecture:amd64
Maintainer:Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size:2107
Depends:lumpy-sv (=0.3.0+dfsg-1)
Section:debug
Priority:optional
Description:
debug symbols for lumpy-sv
Build-Ids:32f3d955b7f234c92ba3b52b1d718618ea665c79 73ab2c6b0f01cc35aed33f3a8e7d88b782ecec70
lintian 2.77.1~bpo10+1 check for lumpy-sv-dbgsym_0.3.0+dfsg-1_amd64.deb (click to toggle)
W: lumpy-sv-dbgsym: debug-file-with-no-debug-symbols usr/lib/debug/.build-id/73/ab2c6b0f01cc35aed33f3a8e7d88b782ecec70.debug
contents of lumpy-sv-dbgsym_0.3.0+dfsg-1_amd64.deb (click to toggle)
drwxr-xr-x root/root         0 2020-06-03 06:49 ./
drwxr-xr-x root/root         0 2020-06-03 06:49 ./usr/
drwxr-xr-x root/root         0 2020-06-03 06:49 ./usr/lib/
drwxr-xr-x root/root         0 2020-06-03 06:49 ./usr/lib/debug/
drwxr-xr-x root/root         0 2020-06-03 06:49 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root         0 2020-06-03 06:49 ./usr/lib/debug/.build-id/32/
-rw-r--r-- root/root   2138552 2020-06-03 06:49 ./usr/lib/debug/.build-id/32/f3d955b7f234c92ba3b52b1d718618ea665c79.debug
drwxr-xr-x root/root         0 2020-06-03 06:49 ./usr/lib/debug/.build-id/73/
-rw-r--r-- root/root      6616 2020-06-03 06:49 ./usr/lib/debug/.build-id/73/ab2c6b0f01cc35aed33f3a8e7d88b782ecec70.debug
drwxr-xr-x root/root         0 2020-06-03 06:49 ./usr/share/
drwxr-xr-x root/root         0 2020-06-03 06:49 ./usr/share/doc/
lrwxrwxrwx root/root         0 2020-06-03 06:49 ./usr/share/doc/lumpy-sv-dbgsym -> lumpy-sv
control file for lumpy-sv-examples_0.3.0+dfsg-1_all.deb (click to toggle)
Package:lumpy-sv-examples
Source:lumpy-sv
Version:0.3.0+dfsg-1
Architecture:all
Maintainer:Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size:53406
Enhances:lumpy-sv
Section:science
Priority:optional
Homepage:https://github.com/arq5x/lumpy-sv
Description:
general probabilistic framework for structural variant discovery (data)
 LUMPY, a novel SV discovery framework that naturally integrates multiple
 SV signals jointly across multiple samples.  LUMPY yields improved
 sensitivity, especially when SV signal is reduced owing to either low
 coverage data or low intra-sample variant allele frequency.
 .
 This package contains some example data and scripts to test lumpy-sv.
lintian 2.77.1~bpo10+1 check for lumpy-sv-examples_0.3.0+dfsg-1_all.deb (click to toggle)
contents of lumpy-sv-examples_0.3.0+dfsg-1_all.deb (click to toggle)
drwxr-xr-x root/root         0 2020-06-03 06:49 ./
drwxr-xr-x root/root         0 2020-06-03 06:49 ./usr/
drwxr-xr-x root/root         0 2020-06-03 06:49 ./usr/share/
drwxr-xr-x root/root         0 2020-06-03 06:49 ./usr/share/doc/
drwxr-xr-x root/root         0 2020-06-03 06:49 ./usr/share/doc/lumpy-sv/
drwxr-xr-x root/root         0 2020-06-03 06:49 ./usr/share/doc/lumpy-sv/examples/
drwxr-xr-x root/root         0 2020-06-03 06:49 ./usr/share/doc/lumpy-sv/examples/data/
-rw-r--r-- root/root      1397 2019-02-13 04:30 ./usr/share/doc/lumpy-sv/examples/data/example.cns.gz
-rw-r--r-- root/root  54178575 2019-02-13 04:30 ./usr/share/doc/lumpy-sv/examples/data/pe.pos_sorted.bam.gz
-rw-r--r-- root/root      2014 2019-02-13 04:30 ./usr/share/doc/lumpy-sv/examples/data/pe.pos_sorted.histo.gz
-rw-r--r-- root/root      2988 2019-02-13 04:30 ./usr/share/doc/lumpy-sv/examples/data/pe.pos_sorted.pe.bedpe
-rw-r--r-- root/root      5598 2019-02-13 04:30 ./usr/share/doc/lumpy-sv/examples/data/pe.pos_sorted.pesr.bedpe.gz
-rw-r--r-- root/root     20500 2019-02-13 04:30 ./usr/share/doc/lumpy-sv/examples/data/sim.bedpe.gz
-rw-r--r-- root/root    427019 2019-02-13 04:30 ./usr/share/doc/lumpy-sv/examples/data/sr.pos_sorted.bam.gz
-rw-r--r-- root/root      2476 2019-02-13 04:30 ./usr/share/doc/lumpy-sv/examples/data/sr.pos_sorted.sr.bedpe
drwxr-xr-x root/root         0 2020-06-03 06:49 ./usr/share/doc/lumpy-sv/examples/lumpy_tests/
drwxr-xr-x root/root         0 2019-02-13 04:30 ./usr/share/doc/lumpy-sv/examples/lumpy_tests/NA12878/
-rw-r--r-- root/root       764 2019-02-13 04:30 ./usr/share/doc/lumpy-sv/examples/lumpy_tests/NA12878/README.md
drwxr-xr-x root/root         0 2019-02-13 04:30 ./usr/share/doc/lumpy-sv/examples/lumpy_tests/honeybee/
-rw-r--r-- root/root       302 2019-02-13 04:30 ./usr/share/doc/lumpy-sv/examples/lumpy_tests/honeybee/run_pe.sh
-rw-r--r-- root/root       392 2019-02-13 04:30 ./usr/share/doc/lumpy-sv/examples/lumpy_tests/honeybee/run_pesr.sh
-rw-r--r-- root/root       147 2019-02-13 04:30 ./usr/share/doc/lumpy-sv/examples/lumpy_tests/honeybee/run_sr.sh
drwxr-xr-x root/root         0 2020-06-03 06:49 ./usr/share/doc/lumpy-sv/examples/lumpy_tests/orig/
-rwxr-xr-x root/root       871 2019-02-13 04:30 ./usr/share/doc/lumpy-sv/examples/lumpy_tests/orig/bp_pe.sh
-rwxr-xr-x root/root       873 2020-06-03 06:49 ./usr/share/doc/lumpy-sv/examples/lumpy_tests/orig/bp_pesr.sh
-rwxr-xr-x root/root       364 2020-06-03 06:49 ./usr/share/doc/lumpy-sv/examples/lumpy_tests/orig/bp_sr.sh
drwxr-xr-x root/root         0 2019-02-13 04:30 ./usr/share/doc/lumpy-sv/examples/lumpy_tests/rice/
-rwxr-xr-x root/root       347 2019-02-13 04:30 ./usr/share/doc/lumpy-sv/examples/lumpy_tests/rice/run.sh
-rw-r--r-- root/root      1112 2019-02-13 04:30 ./usr/share/doc/lumpy-sv/examples/lumpy_tests/test.sh.gz
drwxr-xr-x root/root         0 2020-06-03 06:49 ./usr/share/doc/lumpy-sv/examples/test/
-rwxr-xr-x root/root      1341 2020-06-03 06:49 ./usr/share/doc/lumpy-sv/examples/test/bp_pe.sh
-rwxr-xr-x root/root      1333 2020-06-03 06:49 ./usr/share/doc/lumpy-sv/examples/test/bp_pe_pl.sh
-rwxr-xr-x root/root      1465 2020-06-03 06:49 ./usr/share/doc/lumpy-sv/examples/test/bp_pesr.sh
-rwxr-xr-x root/root      1457 2020-06-03 06:49 ./usr/share/doc/lumpy-sv/examples/test/bp_pesr_pl.sh
-rwxr-xr-x root/root       924 2020-06-03 06:49 ./usr/share/doc/lumpy-sv/examples/test/bp_sr.sh
-rwxr-xr-x root/root      1808 2019-02-13 04:30 ./usr/share/doc/lumpy-sv/examples/test/functional-test.sh
-rwxr-xr-x root/root       531 2019-02-13 04:30 ./usr/share/doc/lumpy-sv/examples/test/test.sh
-rwxr-xr-x root/root       551 2019-02-13 04:30 ./usr/share/doc/lumpy-sv/examples/test/test_pl.sh
drwxr-xr-x root/root         0 2020-06-03 06:49 ./usr/share/doc/lumpy-sv-examples/
-rw-r--r-- root/root       159 2020-06-03 06:49 ./usr/share/doc/lumpy-sv-examples/changelog.Debian.gz
-rw-r--r-- root/root      2701 2020-06-03 06:49 ./usr/share/doc/lumpy-sv-examples/copyright

Timestamp: 03.06.2020 / 11:02:21 (UTC)