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mindthegap_2.2.0-1_amd64.changes (click to toggle)
Format:1.8
Date:Tue, 02 Jul 2019 13:41:39 +0100
Source:mindthegap
Binary:mindthegap mindthegap-examples
Architecture:source amd64 all
Version:2.2.0-1
Distribution:unstable
Urgency:medium
Maintainer:Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By:Shayan Doust <hello@shayandoust.me>
Description:
mindthegap - performs detection and assembly of DNA insertion variants in NGS
mindthegap-examples - optional scripts and example resources for mindthegap
Closes:931826
Changes:
mindthegap (2.2.0-1) unstable; urgency=medium

  * Initial release (Closes: #931826)
Files:
bc6bb3d34f82eed13c848ebacf7998ea 2116 science optional mindthegap_2.2.0-1.dsc
5ac92d834ee4d634f5aad27727863bd0 722722 science optional mindthegap_2.2.0.orig.tar.gz
fac7ea200da5e023f85fdafb10cda216 17044 science optional mindthegap_2.2.0-1.debian.tar.xz
c65a92cb0b5a3e47262cc71f912ee522 3177270 debug optional mindthegap-dbgsym_2.2.0-1_amd64.deb
174d21623174e0e4790869281cba5ad7 617944 science optional mindthegap-examples_2.2.0-1_all.deb
f0f44bb04d641fa7d9b53a1720d1d586 7699 science optional mindthegap_2.2.0-1_amd64.buildinfo
eef5e86136920476aa2e05192aceed6b 222138 science optional mindthegap_2.2.0-1_amd64.deb
mindthegap_2.2.0-1.dsc (click to toggle)
Format:3.0 (quilt)
Source:mindthegap
Binary:mindthegap, mindthegap-examples
Architecture:any all
Version:2.2.0-1
Maintainer:Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders:Shayan Doust <hello@shayandoust.me>
Homepage:http://github.com/GATB/MindTheGap
Standards-Version:4.3.0
Vcs-Browser:https://salsa.debian.org/med-team/mindthegap
Vcs-Git:https://salsa.debian.org/med-team/mindthegap.git
Testsuite:autopkgtest
Build-Depends:debhelper (>=12~), cmake, libgatbcore-dev, libboost-dev, zlib1g-dev, libhdf5-dev
Package-List:mindthegap deb science optional arch=any mindthegap-examples deb science optional arch=all
Files:
5ac92d834ee4d634f5aad27727863bd0 722722 mindthegap_2.2.0.orig.tar.gz
fac7ea200da5e023f85fdafb10cda216 17044 mindthegap_2.2.0-1.debian.tar.xz
lintian 2.15.0~bpo9+1 check for mindthegap_2.2.0-1.dsc (click to toggle)
README.source for mindthegap_2.2.0-1.dsc (click to toggle)
No README.source in this package
control file for mindthegap_2.2.0-1_amd64.deb (click to toggle)
Package:mindthegap
Version:2.2.0-1
Architecture:amd64
Maintainer:Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size:963
Depends:libc6 (>=2.14), libgatbcore2 (>=1.4.1+git20181225.44d5a44), libgcc1 (>=1:3.0), libhdf5-103, libstdc++6 (>=5.2)
Section:science
Priority:optional
Homepage:http://github.com/GATB/MindTheGap
Description:
performs detection and assembly of DNA insertion variants in NGS read datasets
 Designed to call insertions of any size, whether they are novel or
 duplicated, homozygous or heterozygous in the donor genome. It takes as
 input a set of reads and a reference genome. It outputs two sets of
 FASTA sequences: one is the set of breakpoints of detection insertion
 sites, the other is the set of assembled insertions for each
 breakpoint. MindTheGap can also be used as a genome assembly finishing
 tool. It can fill the gaps between a set of input contigs without any a
 priori on their relative order and orientation. It outputs the results
 in gfa file.
lintian 2.15.0~bpo9+1 check for mindthegap_2.2.0-1_amd64.deb (click to toggle)
contents of mindthegap_2.2.0-1_amd64.deb (click to toggle)
drwxr-xr-x root/root         0 2019-07-02 12:41 ./
drwxr-xr-x root/root         0 2019-07-02 12:41 ./usr/
drwxr-xr-x root/root         0 2019-07-02 12:41 ./usr/bin/
-rwxr-xr-x root/root    928088 2019-07-02 12:41 ./usr/bin/MindTheGap
drwxr-xr-x root/root         0 2019-07-02 12:41 ./usr/share/
drwxr-xr-x root/root         0 2019-07-02 12:41 ./usr/share/doc/
drwxr-xr-x root/root         0 2019-07-02 12:41 ./usr/share/doc/mindthegap/
-rw-r--r-- root/root      8128 2018-07-06 10:40 ./usr/share/doc/mindthegap/README.md.gz
-rw-r--r-- root/root       158 2019-07-02 12:41 ./usr/share/doc/mindthegap/changelog.Debian.gz
-rw-r--r-- root/root      1432 2018-07-06 10:40 ./usr/share/doc/mindthegap/changelog.gz
-rw-r--r-- root/root     35093 2019-07-02 12:41 ./usr/share/doc/mindthegap/copyright
drwxr-xr-x root/root         0 2019-07-02 12:41 ./usr/share/man/
drwxr-xr-x root/root         0 2019-07-02 12:41 ./usr/share/man/man1/
-rw-r--r-- root/root       629 2019-07-02 12:41 ./usr/share/man/man1/MindTheGap.1.gz
control file for mindthegap-dbgsym_2.2.0-1_amd64.deb (click to toggle)
Package:mindthegap-dbgsym
Source:mindthegap
Version:2.2.0-1
Architecture:amd64
Maintainer:Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size:3378
Depends:mindthegap (=2.2.0-1)
Section:debug
Priority:optional
Description:
debug symbols for mindthegap
Auto-Built-Package:debug-symbols
Build-Ids:bf0279d78a4522bfd05a8bf1089c83920b6fcfe9
lintian 2.15.0~bpo9+1 check for mindthegap-dbgsym_2.2.0-1_amd64.deb (click to toggle)
contents of mindthegap-dbgsym_2.2.0-1_amd64.deb (click to toggle)
drwxr-xr-x root/root         0 2019-07-02 12:41 ./
drwxr-xr-x root/root         0 2019-07-02 12:41 ./usr/
drwxr-xr-x root/root         0 2019-07-02 12:41 ./usr/lib/
drwxr-xr-x root/root         0 2019-07-02 12:41 ./usr/lib/debug/
drwxr-xr-x root/root         0 2019-07-02 12:41 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root         0 2019-07-02 12:41 ./usr/lib/debug/.build-id/bf/
-rw-r--r-- root/root   3448200 2019-07-02 12:41 ./usr/lib/debug/.build-id/bf/0279d78a4522bfd05a8bf1089c83920b6fcfe9.debug
drwxr-xr-x root/root         0 2019-07-02 12:41 ./usr/share/
drwxr-xr-x root/root         0 2019-07-02 12:41 ./usr/share/doc/
lrwxrwxrwx root/root         0 2019-07-02 12:41 ./usr/share/doc/mindthegap-dbgsym -> mindthegap
control file for mindthegap-examples_2.2.0-1_all.deb (click to toggle)
Package:mindthegap-examples
Source:mindthegap
Version:2.2.0-1
Architecture:all
Maintainer:Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size:707
Depends:python3
Recommends:mindthegap
Section:science
Priority:optional
Homepage:http://github.com/GATB/MindTheGap
Description:
optional scripts and example resources for mindthegap
 Designed to call insertions of any size, whether they are novel or
 duplicated, homozygous or heterozygous in the donor genome. it takes
 as input a set of reads and a reference genome. It outputs two sets
 of FASTA sequences: one is the set of breakpoints of detection
 insertion sites, the other is the set of assembled insertions for
 each breakpoint. MindTheGap can also be used as a genome assembly
 finishing tool. It can fill the gap between a set of input contigs
 without any a priori on their relative order and orientation. It
 outputs the results in gfa file. Please note that this package is
 meant to accommodate the mindthegap package and only acts as example
 to how this package can be utilised.
lintian 2.15.0~bpo9+1 check for mindthegap-examples_2.2.0-1_all.deb (click to toggle)
contents of mindthegap-examples_2.2.0-1_all.deb (click to toggle)
drwxr-xr-x root/root         0 2019-07-02 12:41 ./
drwxr-xr-x root/root         0 2019-07-02 12:41 ./usr/
drwxr-xr-x root/root         0 2019-07-02 12:41 ./usr/share/
drwxr-xr-x root/root         0 2019-07-02 12:41 ./usr/share/doc/
drwxr-xr-x root/root         0 2019-07-02 12:41 ./usr/share/doc/mindthegap/
drwxr-xr-x root/root         0 2019-07-02 12:41 ./usr/share/doc/mindthegap/examples/
drwxr-xr-x root/root         0 2019-07-02 12:41 ./usr/share/doc/mindthegap/examples/data/
-rw-r--r-- root/root    198678 2019-07-02 12:41 ./usr/share/doc/mindthegap/examples/data/contig-reads.fasta.gz
-rw-r--r-- root/root      1720 2018-07-06 10:40 ./usr/share/doc/mindthegap/examples/data/contigs.fasta.gz
-rw-r--r-- root/root     25637 2018-07-06 10:40 ./usr/share/doc/mindthegap/examples/data/reads_r1.fastq.gz
-rw-r--r-- root/root     25619 2018-07-06 10:40 ./usr/share/doc/mindthegap/examples/data/reads_r2.fastq.gz
-rw-r--r-- root/root      1701 2018-07-06 10:40 ./usr/share/doc/mindthegap/examples/data/reference.fasta.gz
drwxr-xr-x root/root         0 2019-07-02 12:41 ./usr/share/doc/mindthegap/examples/test/
-rwxr-xr-x root/root       399 2018-07-06 10:40 ./usr/share/doc/mindthegap/examples/test/compare_vcf.sh
drwxr-xr-x root/root         0 2019-07-02 12:41 ./usr/share/doc/mindthegap/examples/test/contig_test/
-rw-r--r-- root/root      1872 2018-07-06 10:40 ./usr/share/doc/mindthegap/examples/test/contig_test/README
-rw-r--r-- root/root      2385 2018-07-06 10:40 ./usr/share/doc/mindthegap/examples/test/contig_test/genome-variant.fasta.gz
-rw-r--r-- root/root      3223 2018-07-06 10:40 ./usr/share/doc/mindthegap/examples/test/contig_test/genome.fasta.gz
-rw-r--r-- root/root      5824 2018-07-06 10:40 ./usr/share/doc/mindthegap/examples/test/contig_test/gold.gfa.gz
-rw-r--r-- root/root       395 2018-07-06 10:40 ./usr/share/doc/mindthegap/examples/test/contig_test/gold.info.txt
-rw-r--r-- root/root      4003 2018-07-06 10:40 ./usr/share/doc/mindthegap/examples/test/contig_test/gold.insertions.fasta.gz
-rw-r--r-- root/root      1606 2018-07-06 10:40 ./usr/share/doc/mindthegap/examples/test/contig_test/gold.log
-rw-r--r-- root/root       767 2018-07-06 10:40 ./usr/share/doc/mindthegap/examples/test/contig_test/gold_seed_dictionary.fasta
-rw-r--r-- root/root      4148 2018-07-06 10:40 ./usr/share/doc/mindthegap/examples/test/eval.cpp.gz
drwxr-xr-x root/root         0 2019-07-02 12:41 ./usr/share/doc/mindthegap/examples/test/full_test/
-rw-r--r-- root/root      3153 2018-07-06 10:40 ./usr/share/doc/mindthegap/examples/test/full_test/README.gz
-rw-r--r-- root/root      1787 2018-07-06 10:40 ./usr/share/doc/mindthegap/examples/test/full_test/allele1.fasta.gz
-rw-r--r-- root/root      1914 2018-07-06 10:40 ./usr/share/doc/mindthegap/examples/test/full_test/allele2.fasta.gz
-rw-r--r-- root/root      1069 2018-07-06 10:40 ./usr/share/doc/mindthegap/examples/test/full_test/gold.breakpoints
-rw-r--r-- root/root      1382 2018-07-06 10:40 ./usr/share/doc/mindthegap/examples/test/full_test/gold.insertions.fasta
-rw-r--r-- root/root      2362 2018-07-06 10:40 ./usr/share/doc/mindthegap/examples/test/full_test/gold.insertions.vcf
-rw-r--r-- root/root      1727 2018-07-06 10:40 ./usr/share/doc/mindthegap/examples/test/full_test/gold.othervariants.vcf
-rw-r--r-- root/root      1338 2018-07-06 10:40 ./usr/share/doc/mindthegap/examples/test/full_test/gold_fill.output
-rw-r--r-- root/root      2094 2018-07-06 10:40 ./usr/share/doc/mindthegap/examples/test/full_test/gold_find.output
-rw-r--r-- root/root      1701 2018-07-06 10:40 ./usr/share/doc/mindthegap/examples/test/full_test/reference.fasta.gz
-rw-r--r-- root/root       669 2018-07-06 10:40 ./usr/share/doc/mindthegap/examples/test/full_test/variants.txt
drwxr-xr-x root/root         0 2019-07-02 12:41 ./usr/share/doc/mindthegap/examples/test/reads/
-rw-r--r-- root/root      1802 2018-07-06 10:40 ./usr/share/doc/mindthegap/examples/test/reads/beginfuzzySNP.fasta.gz
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-rwxr-xr-x root/root      2778 2019-07-02 12:41 ./usr/share/doc/mindthegap/examples/test/scripts/generate_read.py
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-rw-r--r-- root/root       492 2019-07-02 12:41 ./usr/share/doc/mindthegap-examples/run-unit-test

Timestamp: 12.07.2019 / 09:01:29 (UTC)