268 KB
ariba version 2.14.5+ds-2~jan+unchanged1 (unchanged) vs.
ariba version 2.14.5+git20200607.58b996f-1~jan+nus1 (fresh-snapshots)
1.54 KB
ariba-dbgsym_2.14.5+ds-2~jan+unchanged1_amd64.deb vs.
ariba-dbgsym_2.14.5+git20200607.58b996f-1~jan+nus1_amd64.deb
370 B
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1 -rw-r--r--···0········0········0········4·2020-06-30·10:37:54.000000·debian-binary1 -rw-r--r--···0········0········0········4·2020-06-30·10:37:54.000000·debian-binary
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control.tar.xz
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control.tar
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1 drwxr-xr-x···0·root·········(0)·root·········(0)········0·2020-06-30·10:37:54.000000·./1 drwxr-xr-x···0·root·········(0)·root·········(0)········0·2020-06-30·10:37:54.000000·./
2 -rw-r--r--···0·root·········(0)·root·········(0)······482·2020-06-30·10:37:54.000000·./control2 -rw-r--r--···0·root·········(0)·root·········(0)······504·2020-06-30·10:37:54.000000·./control
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./control
    
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1 Package:·ariba-dbgsym1 Package:·ariba-dbgsym
2 Source:·ariba2 Source:·ariba
3 Version:·2.14.5+ds-2~jan+unchanged13 Version:·2.14.5+git20200607.58b996f-1~jan+nus1
4 Auto-Built-Package:·debug-symbols4 Auto-Built-Package:·debug-symbols
5 Architecture:·amd645 Architecture:·amd64
6 Maintainer:·Debian·Med·Packaging·Team·<debian-med-packaging@lists.alioth.debian.org>6 Maintainer:·Debian·Med·Packaging·Team·<debian-med-packaging@lists.alioth.debian.org>
7 Installed-Size:·4337 Installed-Size:·433
8 Depends:·ariba·(=·2.14.5+ds-2~jan+unchanged1)8 Depends:·ariba·(=·2.14.5+git20200607.58b996f-1~jan+nus1)
9 Section:·debug9 Section:·debug
10 Priority:·optional10 Priority:·optional
11 Description:·debug·symbols·for·ariba11 Description:·debug·symbols·for·ariba
12 Build-Ids:·263aa1f54d92d37f926de7f829af90e37004519e·391f390fe16b5119c25996f0c7f5df844294e0bf·3d2110b09c20df289a3f92ba9e3d35aa5f2f3e0712 Build-Ids:·263aa1f54d92d37f926de7f829af90e37004519e·391f390fe16b5119c25996f0c7f5df844294e0bf·3d2110b09c20df289a3f92ba9e3d35aa5f2f3e07
267 KB
ariba_2.14.5+ds-2~jan+unchanged1_amd64.deb vs.
ariba_2.14.5+git20200607.58b996f-1~jan+nus1_amd64.deb
452 B
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1 -rw-r--r--···0········0········0········4·2020-06-30·10:37:54.000000·debian-binary1 -rw-r--r--···0········0········0········4·2020-06-30·10:37:54.000000·debian-binary
2 -rw-r--r--···0········0········0····17884·2020-06-30·10:37:54.000000·control.tar.xz2 -rw-r--r--···0········0········0····17888·2020-06-30·10:37:54.000000·control.tar.xz
3 -rw-r--r--···0········0········0··1936312·2020-06-30·10:37:54.000000·data.tar.xz3 -rw-r--r--···0········0········0··1935500·2020-06-30·10:37:54.000000·data.tar.xz
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control.tar.xz
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control.tar
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1 drwxr-xr-x···0·root·········(0)·root·········(0)········0·2020-06-30·10:37:54.000000·./1 drwxr-xr-x···0·root·········(0)·root·········(0)········0·2020-06-30·10:37:54.000000·./
2 -rw-r--r--···0·root·········(0)·root·········(0)·····1079·2020-06-30·10:37:54.000000·./control2 -rw-r--r--···0·root·········(0)·root·········(0)·····1090·2020-06-30·10:37:54.000000·./control
3 -rw-r--r--···0·root·········(0)·root·········(0)····91201·2020-06-30·10:37:54.000000·./md5sums3 -rw-r--r--···0·root·········(0)·root·········(0)····91201·2020-06-30·10:37:54.000000·./md5sums
4 -rwxr-xr-x···0·root·········(0)·root·········(0)······235·2020-06-30·10:37:54.000000·./postinst4 -rwxr-xr-x···0·root·········(0)·root·········(0)······235·2020-06-30·10:37:54.000000·./postinst
5 -rwxr-xr-x···0·root·········(0)·root·········(0)······384·2020-06-30·10:37:54.000000·./prerm5 -rwxr-xr-x···0·root·········(0)·root·········(0)······384·2020-06-30·10:37:54.000000·./prerm
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./control
    
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1 Package:·ariba1 Package:·ariba
2 Version:·2.14.5+ds-2~jan+unchanged12 Version:·2.14.5+git20200607.58b996f-1~jan+nus1
3 Architecture:·amd643 Architecture:·amd64
4 Maintainer:·Debian·Med·Packaging·Team·<debian-med-packaging@lists.alioth.debian.org>4 Maintainer:·Debian·Med·Packaging·Team·<debian-med-packaging@lists.alioth.debian.org>
5 Installed-Size:·204635 Installed-Size:·20463
6 Depends:·fastaq·(>=·3.12.0),·python3·(<<·3.9),·python3·(>=·3.8~),·python3-biopython,·python3-bs4,·python3-dendropy,·python3-matplotlib,·python3-pymummer·(>=·0.10.2),·python3-pysam·(>=·0.9.1),·python3:any,·libc6·(>=·2.14),·libfml0·(>=·0.1-4~),·libgcc-s1·(>=·3.0),·libminimap0·(>=·0.2),·libstdc++6·(>=·5.2),·zlib1g·(>=·1:1.1.4),·bowtie2·(>=·2.1.0),·cd-hit,·mash,·mummer,·python3-tk6 Depends:·fastaq·(>=·3.12.0),·python3·(<<·3.9),·python3·(>=·3.8~),·python3-biopython,·python3-bs4,·python3-dendropy,·python3-matplotlib,·python3-pymummer·(>=·0.10.2),·python3-pysam·(>=·0.9.1),·python3:any,·libc6·(>=·2.14),·libfml0·(>=·0.1-4~),·libgcc-s1·(>=·3.0),·libminimap0·(>=·0.2),·libstdc++6·(>=·5.2),·zlib1g·(>=·1:1.1.4),·bowtie2·(>=·2.1.0),·cd-hit,·mash,·mummer,·python3-tk
7 Suggests:·spades7 Suggests:·spades
8 Section:·science8 Section:·science
9 Priority:·optional9 Priority:·optional
48.0 B
./md5sums
30.0 B
./md5sums
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265 KB
data.tar.xz
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data.tar
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2 drwxr-xr-x···0·root·········(0)·root·········(0)········0·2020-06-30·10:37:54.000000·./usr/2 drwxr-xr-x···0·root·········(0)·root·········(0)········0·2020-06-30·10:37:54.000000·./usr/
3 drwxr-xr-x···0·root·········(0)·root·········(0)········0·2020-06-30·10:37:54.000000·./usr/bin/3 drwxr-xr-x···0·root·········(0)·root·········(0)········0·2020-06-30·10:37:54.000000·./usr/bin/
4 -rwxr-xr-x···0·root·········(0)·root·········(0)····26193·2020-06-30·10:37:54.000000·./usr/bin/ariba4 -rwxr-xr-x···0·root·········(0)·root·········(0)····26193·2020-06-30·10:37:54.000000·./usr/bin/ariba
5 drwxr-xr-x···0·root·········(0)·root·········(0)········0·2020-06-30·10:37:54.000000·./usr/lib/5 drwxr-xr-x···0·root·········(0)·root·········(0)········0·2020-06-30·10:37:54.000000·./usr/lib/
6 drwxr-xr-x···0·root·········(0)·root·········(0)········0·2020-06-30·10:37:54.000000·./usr/lib/python3/6 drwxr-xr-x···0·root·········(0)·root·········(0)········0·2020-06-30·10:37:54.000000·./usr/lib/python3/
7 drwxr-xr-x···0·root·········(0)·root·········(0)········0·2020-06-30·10:37:54.000000·./usr/lib/python3/dist-packages/7 drwxr-xr-x···0·root·········(0)·root·········(0)········0·2020-06-30·10:37:54.000000·./usr/lib/python3/dist-packages/
8 drwxr-xr-x···0·root·········(0)·root·········(0)········0·2020-06-30·10:37:54.000000·./usr/lib/python3/dist-packages/ariba/8 drwxr-xr-x···0·root·········(0)·root·········(0)········0·2020-06-30·10:37:54.000000·./usr/lib/python3/dist-packages/ariba/
9 -rw-r--r--···0·root·········(0)·root·········(0)·····1063·2018-11-21·15:29:30.000000·./usr/lib/python3/dist-packages/ariba/__init__.py9 -rw-r--r--···0·root·········(0)·root·········(0)·····1063·2020-06-07·14:34:35.000000·./usr/lib/python3/dist-packages/ariba/__init__.py
10 -rw-r--r--···0·root·········(0)·root·········(0)····10940·2016-08-18·20:31:52.000000·./usr/lib/python3/dist-packages/ariba/aln_to_metadata.py10 -rw-r--r--···0·root·········(0)·root·········(0)····10940·2020-06-07·14:34:35.000000·./usr/lib/python3/dist-packages/ariba/aln_to_metadata.py
11 -rw-r--r--···0·root·········(0)·root·········(0)····15088·2020-06-30·10:37:54.000000·./usr/lib/python3/dist-packages/ariba/assembly.py11 -rw-r--r--···0·root·········(0)·root·········(0)····15088·2020-06-30·10:37:54.000000·./usr/lib/python3/dist-packages/ariba/assembly.py
12 -rw-r--r--···0·root·········(0)·root·········(0)····16416·2017-04-04·11:45:15.000000·./usr/lib/python3/dist-packages/ariba/assembly_compare.py12 -rw-r--r--···0·root·········(0)·root·········(0)····16416·2020-06-07·14:34:35.000000·./usr/lib/python3/dist-packages/ariba/assembly_compare.py
13 -rw-r--r--···0·root·········(0)·root·········(0)····15177·2017-04-04·11:45:15.000000·./usr/lib/python3/dist-packages/ariba/assembly_variants.py13 -rw-r--r--···0·root·········(0)·root·········(0)····15177·2020-06-07·14:34:35.000000·./usr/lib/python3/dist-packages/ariba/assembly_variants.py
14 -rw-r--r--···0·root·········(0)·root·········(0)·····3586·2015-12-05·07:43:06.000000·./usr/lib/python3/dist-packages/ariba/bam_parse.py14 -rw-r--r--···0·root·········(0)·root·········(0)·····3586·2020-06-07·14:34:35.000000·./usr/lib/python3/dist-packages/ariba/bam_parse.py
15 -rw-r--r--···0·root·········(0)·root·········(0)·····3328·2017-05-29·14:58:08.000000·./usr/lib/python3/dist-packages/ariba/card_record.py15 -rw-r--r--···0·root·········(0)·root·········(0)·····3328·2020-06-07·14:34:35.000000·./usr/lib/python3/dist-packages/ariba/card_record.py
16 -rw-r--r--···0·root·········(0)·root·········(0)·····6274·2019-07-08·16:07:58.000000·./usr/lib/python3/dist-packages/ariba/cdhit.py16 -rw-r--r--···0·root·········(0)·root·········(0)·····6274·2020-06-07·14:34:35.000000·./usr/lib/python3/dist-packages/ariba/cdhit.py
17 -rw-r--r--···0·root·········(0)·root·········(0)····19456·2018-11-21·15:29:30.000000·./usr/lib/python3/dist-packages/ariba/cluster.py17 -rw-r--r--···0·root·········(0)·root·········(0)····19456·2020-06-07·14:34:35.000000·./usr/lib/python3/dist-packages/ariba/cluster.py
18 -rw-r--r--···0·root·········(0)·root·········(0)····28393·2019-07-08·16:07:58.000000·./usr/lib/python3/dist-packages/ariba/clusters.py18 -rw-r--r--···0·root·········(0)·root·········(0)····28393·2020-06-07·14:34:35.000000·./usr/lib/python3/dist-packages/ariba/clusters.py
19 -rw-r--r--···0·root·········(0)·root·········(0)·····2380·2018-11-21·15:29:30.000000·./usr/lib/python3/dist-packages/ariba/common.py19 -rw-r--r--···0·root·········(0)·root·········(0)·····2380·2020-06-07·14:34:35.000000·./usr/lib/python3/dist-packages/ariba/common.py
20 -rw-r--r--···0·root·········(0)·root·········(0)·····5279·2019-07-08·16:07:58.000000·./usr/lib/python3/dist-packages/ariba/external_progs.py20 -rw-r--r--···0·root·········(0)·root·········(0)·····5279·2020-06-07·14:34:35.000000·./usr/lib/python3/dist-packages/ariba/external_progs.py
21 -rw-r--r--···0·root·········(0)·root·········(0)······324·2016-08-31·13:24:23.000000·./usr/lib/python3/dist-packages/ariba/faidx.py21 -rw-r--r--···0·root·········(0)·root·········(0)······324·2020-06-07·14:34:35.000000·./usr/lib/python3/dist-packages/ariba/faidx.py
22 -rw-r--r--···0·root·········(0)·root·········(0)·····1430·2017-06-28·17:04:37.000000·./usr/lib/python3/dist-packages/ariba/flag.py22 -rw-r--r--···0·root·········(0)·root·········(0)·····1430·2020-06-07·14:34:35.000000·./usr/lib/python3/dist-packages/ariba/flag.py
23 -rw-r--r--···0·root·········(0)·root·········(0)·····1339·2016-07-31·16:56:52.000000·./usr/lib/python3/dist-packages/ariba/histogram.py23 -rw-r--r--···0·root·········(0)·root·········(0)·····1339·2020-06-07·14:34:35.000000·./usr/lib/python3/dist-packages/ariba/histogram.py
24 -rw-r--r--···0·root·········(0)·root·········(0)·····3981·2015-12-05·07:43:06.000000·./usr/lib/python3/dist-packages/ariba/link.py24 -rw-r--r--···0·root·········(0)·root·········(0)·····3981·2020-06-07·14:34:35.000000·./usr/lib/python3/dist-packages/ariba/link.py
25 -rw-r--r--···0·root·········(0)·root·········(0)·····5037·2019-07-08·16:07:58.000000·./usr/lib/python3/dist-packages/ariba/mapping.py25 -rw-r--r--···0·root·········(0)·root·········(0)·····5037·2020-06-07·14:34:35.000000·./usr/lib/python3/dist-packages/ariba/mapping.py
26 -rw-r--r--···0·root·········(0)·root·········(0)·····2078·2017-01-17·11:47:35.000000·./usr/lib/python3/dist-packages/ariba/megares_data_finder.py26 -rw-r--r--···0·root·········(0)·root·········(0)·····2078·2020-06-07·14:34:35.000000·./usr/lib/python3/dist-packages/ariba/megares_data_finder.py
27 -rw-r--r--···0·root·········(0)·root·········(0)·····6045·2020-05-21·17:18:17.000000·./usr/lib/python3/dist-packages/ariba/megares_zip_parser.py27 -rw-r--r--···0·root·········(0)·root·········(0)·····6045·2020-06-07·14:34:35.000000·./usr/lib/python3/dist-packages/ariba/megares_zip_parser.py
28 -rw-r--r--···0·root·········(0)·root·········(0)····25422·2018-11-21·15:29:30.000000·./usr/lib/python3/dist-packages/ariba/mic_plotter.py28 -rw-r--r--···0·root·········(0)·root·········(0)····25422·2020-06-07·14:34:35.000000·./usr/lib/python3/dist-packages/ariba/mic_plotter.py
29 -rw-r--r--···0·root·········(0)·root·········(0)·····2216·2016-12-21·19:13:28.000000·./usr/lib/python3/dist-packages/ariba/mlst_profile.py29 -rw-r--r--···0·root·········(0)·root·········(0)·····2216·2020-06-07·14:34:35.000000·./usr/lib/python3/dist-packages/ariba/mlst_profile.py
30 -rw-r--r--···0·root·········(0)·root·········(0)·····3975·2018-11-21·15:29:30.000000·./usr/lib/python3/dist-packages/ariba/mlst_reporter.py30 -rw-r--r--···0·root·········(0)·root·········(0)·····3975·2020-06-07·14:34:35.000000·./usr/lib/python3/dist-packages/ariba/mlst_reporter.py
31 -rw-r--r--···0·root·········(0)·root·········(0)·····4042·2018-11-21·15:29:30.000000·./usr/lib/python3/dist-packages/ariba/pubmlst_getter.py31 -rw-r--r--···0·root·········(0)·root·········(0)·····4042·2020-06-07·14:34:35.000000·./usr/lib/python3/dist-packages/ariba/pubmlst_getter.py
32 -rw-r--r--···0·root·········(0)·root·········(0)·····3850·2016-12-21·10:38:42.000000·./usr/lib/python3/dist-packages/ariba/pubmlst_ref_preparer.py32 -rw-r--r--···0·root·········(0)·root·········(0)·····3850·2020-06-07·14:34:35.000000·./usr/lib/python3/dist-packages/ariba/pubmlst_ref_preparer.py
33 -rw-r--r--···0·root·········(0)·root·········(0)·····2508·2018-11-21·15:29:30.000000·./usr/lib/python3/dist-packages/ariba/read_filter.py33 -rw-r--r--···0·root·········(0)·root·········(0)·····2508·2020-06-07·14:34:35.000000·./usr/lib/python3/dist-packages/ariba/read_filter.py
34 -rw-r--r--···0·root·········(0)·root·········(0)·····2968·2016-07-31·16:56:52.000000·./usr/lib/python3/dist-packages/ariba/read_store.py34 -rw-r--r--···0·root·········(0)·root·········(0)·····2968·2020-06-07·14:34:35.000000·./usr/lib/python3/dist-packages/ariba/read_store.py
35 -rw-r--r--···0·root·········(0)·root·········(0)····30530·2019-09-26·08:24:34.000000·./usr/lib/python3/dist-packages/ariba/ref_genes_getter.py35 -rw-r--r--···0·root·········(0)·root·········(0)····30574·2020-06-07·14:34:35.000000·./usr/lib/python3/dist-packages/ariba/ref_genes_getter.py
36 -rw-r--r--···0·root·········(0)·root·········(0)·····8690·2019-09-09·19:05:20.000000·./usr/lib/python3/dist-packages/ariba/ref_preparer.py36 -rw-r--r--···0·root·········(0)·root·········(0)·····8690·2020-06-07·14:34:35.000000·./usr/lib/python3/dist-packages/ariba/ref_preparer.py
37 -rw-r--r--···0·root·········(0)·root·········(0)·····8370·2018-11-21·15:29:30.000000·./usr/lib/python3/dist-packages/ariba/ref_seq_chooser.py37 -rw-r--r--···0·root·········(0)·root·········(0)·····8370·2020-06-07·14:34:35.000000·./usr/lib/python3/dist-packages/ariba/ref_seq_chooser.py
38 -rw-r--r--···0·root·········(0)·root·········(0)·····3165·2016-07-31·16:56:52.000000·./usr/lib/python3/dist-packages/ariba/refdata_query.py38 -rw-r--r--···0·root·········(0)·root·········(0)·····3165·2020-06-07·14:34:35.000000·./usr/lib/python3/dist-packages/ariba/refdata_query.py
39 -rw-r--r--···0·root·········(0)·root·········(0)····19480·2019-09-09·19:05:20.000000·./usr/lib/python3/dist-packages/ariba/reference_data.py39 -rw-r--r--···0·root·········(0)·root·········(0)····19480·2020-06-07·14:34:35.000000·./usr/lib/python3/dist-packages/ariba/reference_data.py
40 -rw-r--r--···0·root·········(0)·root·········(0)····18629·2016-12-21·10:38:42.000000·./usr/lib/python3/dist-packages/ariba/report.py40 -rw-r--r--···0·root·········(0)·root·········(0)····18629·2020-06-07·14:34:35.000000·./usr/lib/python3/dist-packages/ariba/report.py
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94 -rw-r--r--···0·root·········(0)·root·········(0)····15487·2018-11-21·15:29:30.000000·./usr/lib/python3/dist-packages/ariba/tests/clusters_test.py94 -rw-r--r--···0·root·········(0)·root·········(0)····15487·2020-06-07·14:34:35.000000·./usr/lib/python3/dist-packages/ariba/tests/clusters_test.py
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97 -rw-r--r--···0·root·········(0)·root·········(0)·······26·2016-05-27·11:01:28.000000·./usr/lib/python3/dist-packages/ariba/tests/data/aln_to_metadata_load_aln_file.in.fa97 -rw-r--r--···0·root·········(0)·root·········(0)·······26·2020-06-07·14:34:35.000000·./usr/lib/python3/dist-packages/ariba/tests/data/aln_to_metadata_load_aln_file.in.fa
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99 -rw-r--r--···0·root·········(0)·root·········(0)·······64·2016-05-27·11:01:28.000000·./usr/lib/python3/dist-packages/ariba/tests/data/aln_to_metadata_load_vars_file_bad.2.tsv99 -rw-r--r--···0·root·········(0)·root·········(0)·······64·2020-06-07·14:34:35.000000·./usr/lib/python3/dist-packages/ariba/tests/data/aln_to_metadata_load_vars_file_bad.2.tsv
100 -rw-r--r--···0·root·········(0)·root·········(0)·······85·2016-05-27·11:01:28.000000·./usr/lib/python3/dist-packages/ariba/tests/data/aln_to_metadata_load_vars_file_good.tsv100 -rw-r--r--···0·root·········(0)·root·········(0)·······85·2020-06-07·14:34:35.000000·./usr/lib/python3/dist-packages/ariba/tests/data/aln_to_metadata_load_vars_file_good.tsv
101 -rw-r--r--···0·root·········(0)·root·········(0)·······15·2016-07-31·16:56:52.000000·./usr/lib/python3/dist-packages/ariba/tests/data/aln_to_metadata_make_cluster_file.out101 -rw-r--r--···0·root·········(0)·root·········(0)·······15·2020-06-07·14:34:35.000000·./usr/lib/python3/dist-packages/ariba/tests/data/aln_to_metadata_make_cluster_file.out
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104 -rw-r--r--···0·root·········(0)·root·········(0)·······25·2016-07-31·16:56:52.000000·./usr/lib/python3/dist-packages/ariba/tests/data/aln_to_metadata_run_coding.out.cluster104 -rw-r--r--···0·root·········(0)·root·········(0)·······25·2020-06-07·14:34:35.000000·./usr/lib/python3/dist-packages/ariba/tests/data/aln_to_metadata_run_coding.out.cluster
105 -rw-r--r--···0·root·········(0)·root·········(0)······101·2016-05-27·11:01:28.000000·./usr/lib/python3/dist-packages/ariba/tests/data/aln_to_metadata_run_coding.out.fa105 -rw-r--r--···0·root·········(0)·root·········(0)······101·2020-06-07·14:34:35.000000·./usr/lib/python3/dist-packages/ariba/tests/data/aln_to_metadata_run_coding.out.fa
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107 -rw-r--r--···0·root·········(0)·root·········(0)······110·2016-05-27·11:01:28.000000·./usr/lib/python3/dist-packages/ariba/tests/data/aln_to_metadata_run_noncoding.in.fa107 -rw-r--r--···0·root·········(0)·root·········(0)······110·2020-06-07·14:34:35.000000·./usr/lib/python3/dist-packages/ariba/tests/data/aln_to_metadata_run_noncoding.in.fa
108 -rw-r--r--···0·root·········(0)·root·········(0)·······54·2016-05-27·11:01:28.000000·./usr/lib/python3/dist-packages/ariba/tests/data/aln_to_metadata_run_noncoding.in.tsv108 -rw-r--r--···0·root·········(0)·root·········(0)·······54·2020-06-07·14:34:35.000000·./usr/lib/python3/dist-packages/ariba/tests/data/aln_to_metadata_run_noncoding.in.tsv
109 -rw-r--r--···0·root·········(0)·root·········(0)·······25·2016-07-31·16:56:52.000000·./usr/lib/python3/dist-packages/ariba/tests/data/aln_to_metadata_run_noncoding.out.cluster109 -rw-r--r--···0·root·········(0)·root·········(0)·······25·2020-06-07·14:34:35.000000·./usr/lib/python3/dist-packages/ariba/tests/data/aln_to_metadata_run_noncoding.out.cluster
110 -rw-r--r--···0·root·········(0)·root·········(0)······101·2016-05-27·11:01:28.000000·./usr/lib/python3/dist-packages/ariba/tests/data/aln_to_metadata_run_noncoding.out.fa110 -rw-r--r--···0·root·········(0)·root·········(0)······101·2020-06-07·14:34:35.000000·./usr/lib/python3/dist-packages/ariba/tests/data/aln_to_metadata_run_noncoding.out.fa
111 -rw-r--r--···0·root·········(0)·root·········(0)······217·2016-07-31·16:56:52.000000·./usr/lib/python3/dist-packages/ariba/tests/data/aln_to_metadata_run_noncoding.out.tsv111 -rw-r--r--···0·root·········(0)·root·········(0)······217·2020-06-07·14:34:35.000000·./usr/lib/python3/dist-packages/ariba/tests/data/aln_to_metadata_run_noncoding.out.tsv
112 -rw-r--r--···0·root·········(0)·root·········(0)·····2805·2016-11-18·19:54:31.000000·./usr/lib/python3/dist-packages/ariba/tests/data/assembly_assemble_with_fermilite.expected.fa112 -rw-r--r--···0·root·········(0)·root·········(0)·····2805·2020-06-07·14:34:35.000000·./usr/lib/python3/dist-packages/ariba/tests/data/assembly_assemble_with_fermilite.expected.fa
113 -rw-r--r--···0·root·········(0)·root·········(0)······180·2016-11-18·19:54:31.000000·./usr/lib/python3/dist-packages/ariba/tests/data/assembly_assemble_with_fermilite.expected.log113 -rw-r--r--···0·root·········(0)·root·········(0)······180·2020-06-07·14:34:35.000000·./usr/lib/python3/dist-packages/ariba/tests/data/assembly_assemble_with_fermilite.expected.log
114 -rw-r--r--···0·root·········(0)·root·········(0)····10083·2016-07-31·16:56:52.000000·./usr/lib/python3/dist-packages/ariba/tests/data/assembly_assemble_with_fermilite.reads_1.fq114 -rw-r--r--···0·root·········(0)·root·········(0)····10083·2020-06-07·14:34:35.000000·./usr/lib/python3/dist-packages/ariba/tests/data/assembly_assemble_with_fermilite.reads_1.fq
115 -rw-r--r--···0·root·········(0)·root·········(0)····10083·2016-07-31·16:56:52.000000·./usr/lib/python3/dist-packages/ariba/tests/data/assembly_assemble_with_fermilite.reads_2.fq115 -rw-r--r--···0·root·········(0)·root·········(0)····10083·2020-06-07·14:34:35.000000·./usr/lib/python3/dist-packages/ariba/tests/data/assembly_assemble_with_fermilite.reads_2.fq
116 -rw-r--r--···0·root·········(0)·root·········(0)······156·2016-11-18·19:54:31.000000·./usr/lib/python3/dist-packages/ariba/tests/data/assembly_assemble_with_fermilite_fails.expected.log116 -rw-r--r--···0·root·········(0)·root·········(0)······156·2020-06-07·14:34:35.000000·./usr/lib/python3/dist-packages/ariba/tests/data/assembly_assemble_with_fermilite_fails.expected.log
117 -rw-r--r--···0·root·········(0)·root·········(0)······103·2016-07-31·16:56:52.000000·./usr/lib/python3/dist-packages/ariba/tests/data/assembly_assemble_with_fermilite_fails.reads_1.fq117 -rw-r--r--···0·root·········(0)·root·········(0)······103·2020-06-07·14:34:35.000000·./usr/lib/python3/dist-packages/ariba/tests/data/assembly_assemble_with_fermilite_fails.reads_1.fq
118 -rw-r--r--···0·root·········(0)·root·········(0)·······79·2016-07-31·16:56:52.000000·./usr/lib/python3/dist-packages/ariba/tests/data/assembly_assemble_with_fermilite_fails.reads_2.fq118 -rw-r--r--···0·root·········(0)·root·········(0)·······79·2020-06-07·14:34:35.000000·./usr/lib/python3/dist-packages/ariba/tests/data/assembly_assemble_with_fermilite_fails.reads_2.fq
119 -rw-r--r--···0·root·········(0)·root·········(0)······268·2016-05-27·11:01:28.000000·./usr/lib/python3/dist-packages/ariba/tests/data/assembly_compare_parse_nucmer_coords_file.coords119 -rw-r--r--···0·root·········(0)·root·········(0)······268·2020-06-07·14:34:35.000000·./usr/lib/python3/dist-packages/ariba/tests/data/assembly_compare_parse_nucmer_coords_file.coords
120 -rw-r--r--···0·root·········(0)·root·········(0)·····2823·2016-11-18·19:54:31.000000·./usr/lib/python3/dist-packages/ariba/tests/data/assembly_run_fermilite.expected.fa120 -rw-r--r--···0·root·········(0)·root·········(0)·····2823·2020-06-07·14:34:35.000000·./usr/lib/python3/dist-packages/ariba/tests/data/assembly_run_fermilite.expected.fa
121 -rw-r--r--···0·root·········(0)·root·········(0)······169·2016-11-18·19:54:31.000000·./usr/lib/python3/dist-packages/ariba/tests/data/assembly_run_fermilite.expected.log121 -rw-r--r--···0·root·········(0)·root·········(0)······169·2020-06-07·14:34:35.000000·./usr/lib/python3/dist-packages/ariba/tests/data/assembly_run_fermilite.expected.log
122 -rw-r--r--···0·root·········(0)·root·········(0)····20166·2016-07-31·16:56:52.000000·./usr/lib/python3/dist-packages/ariba/tests/data/assembly_run_fermilite.reads.fq122 -rw-r--r--···0·root·········(0)·root·········(0)····20166·2020-06-07·14:34:35.000000·./usr/lib/python3/dist-packages/ariba/tests/data/assembly_run_fermilite.reads.fq
123 -rw-r--r--···0·root·········(0)·root·········(0)·······51·2016-07-31·16:56:52.000000·./usr/lib/python3/dist-packages/ariba/tests/data/assembly_run_fermilite_fail.reads.fq123 -rw-r--r--···0·root·········(0)·root·········(0)·······51·2020-06-07·14:34:35.000000·./usr/lib/python3/dist-packages/ariba/tests/data/assembly_run_fermilite_fail.reads.fq
124 -rw-r--r--···0·root·········(0)·root·········(0)······145·2016-11-18·19:54:31.000000·./usr/lib/python3/dist-packages/ariba/tests/data/assembly_run_fermilite_fails.expected.log124 -rw-r--r--···0·root·········(0)·root·········(0)······145·2020-06-07·14:34:35.000000·./usr/lib/python3/dist-packages/ariba/tests/data/assembly_run_fermilite_fails.expected.log
125 -rw-r--r--···0·root·········(0)·root·········(0)······147·2018-03-04·23:27:53.000000·./usr/lib/python3/dist-packages/ariba/tests/data/assembly_test_assemble_with_spades_fails_reads_1.fq125 -rw-r--r--···0·root·········(0)·root·········(0)······147·2020-06-07·14:34:35.000000·./usr/lib/python3/dist-packages/ariba/tests/data/assembly_test_assemble_with_spades_fails_reads_1.fq
126 -rw-r--r--···0·root·········(0)·root·········(0)······148·2018-03-04·23:27:53.000000·./usr/lib/python3/dist-packages/ariba/tests/data/assembly_test_assemble_with_spades_fails_reads_2.fq126 -rw-r--r--···0·root·········(0)·root·········(0)······148·2020-06-07·14:34:35.000000·./usr/lib/python3/dist-packages/ariba/tests/data/assembly_test_assemble_with_spades_fails_reads_2.fq
127 -rw-r--r--···0·root·········(0)·root·········(0)····10083·2018-03-04·23:27:53.000000·./usr/lib/python3/dist-packages/ariba/tests/data/assembly_test_assemble_with_spades_reads_1.fq127 -rw-r--r--···0·root·········(0)·root·········(0)····10083·2020-06-07·14:34:35.000000·./usr/lib/python3/dist-packages/ariba/tests/data/assembly_test_assemble_with_spades_reads_1.fq
128 -rw-r--r--···0·root·········(0)·root·········(0)····10083·2018-03-04·23:27:53.000000·./usr/lib/python3/dist-packages/ariba/tests/data/assembly_test_assemble_with_spades_reads_2.fq128 -rw-r--r--···0·root·········(0)·root·········(0)····10083·2020-06-07·14:34:35.000000·./usr/lib/python3/dist-packages/ariba/tests/data/assembly_test_assemble_with_spades_reads_2.fq
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1.84 KB
./usr/lib/python3/dist-packages/ariba/ref_genes_getter.py
    
Offset 179, 15 lines modifiedOffset 179, 15 lines modified
179 ············common.rmtree(tmpdir)179 ············common.rmtree(tmpdir)
  
180 ········print('Extracted·data·and·written·ARIBA·input·files\n')180 ········print('Extracted·data·and·written·ARIBA·input·files\n')
181 ········print('Finished.·Final·files·are:',·final_fasta,·final_tsv,·sep='\n\t',·end='\n\n')181 ········print('Finished.·Final·files·are:',·final_fasta,·final_tsv,·sep='\n\t',·end='\n\n')
182 ········print('You·can·use·them·with·ARIBA·like·this:')182 ········print('You·can·use·them·with·ARIBA·like·this:')
183 ········print('ariba·prepareref·-f',·final_fasta,·'-m',·final_tsv,·'output_directory\n')183 ········print('ariba·prepareref·-f',·final_fasta,·'-m',·final_tsv,·'output_directory\n')
184 ········print('If·you·use·this·downloaded·data,·please·cite:')184 ········print('If·you·use·this·downloaded·data,·please·cite:')
185 ········print('"The·Comprehensive·Antibiotic·Resistance·Database",·McArthur·et·al·2013,·PMID:·23650175')185 ········print('"CARD·2020:·antibiotic·resistome·surveillance·with·the·comprehensive·antibiotic·resistance·database",·Alcock·et·al·2020,·PMID:·31665441')
186 ········print('and·in·your·methods·say·that·version',·self.version,·'of·the·database·was·used')186 ········print('and·in·your·methods·say·that·version',·self.version,·'of·the·database·was·used')
  
  
187 ····@classmethod187 ····@classmethod
188 ····def·_get_genetic_epi_database_from_bitbucket(cls,·db_name,·outdir,·git_commit=None):188 ····def·_get_genetic_epi_database_from_bitbucket(cls,·db_name,·outdir,·git_commit=None):
189 ········assert·db_name·in·{'plasmidfinder',·'resfinder',·'virulencefinder'}189 ········assert·db_name·in·{'plasmidfinder',·'resfinder',·'virulencefinder'}
190 ········cmd·=·'git·clone·'·+·'https://bitbucket.org/genomicepidemiology/'·+·db_name·+·'_db.git·'·+·outdir190 ········cmd·=·'git·clone·'·+·'https://bitbucket.org/genomicepidemiology/'·+·db_name·+·'_db.git·'·+·outdir
Offset 655, 10 lines modifiedOffset 655, 10 lines modified
655 ························f_out_tsv.write(f"{id[0]}.{accession}\t1\t0\t.\t.\t{gb_feature.qualifiers['product'][0]}\n")655 ························f_out_tsv.write(f"{id[0]}.{accession}\t1\t0\t.\t.\t{gb_feature.qualifiers['product'][0]}\n")
656 ····················if·idx·==·len(acc_list)-1:656 ····················if·idx·==·len(acc_list)-1:
657 ························print('Finished.·Final·files·are:',·final_fasta,·final_tsv,·sep='\n\t',·end='\n\n')657 ························print('Finished.·Final·files·are:',·final_fasta,·final_tsv,·sep='\n\t',·end='\n\n')
658 ························print('You·can·use·them·with·ARIBA·like·this:')658 ························print('You·can·use·them·with·ARIBA·like·this:')
659 ························print('ariba·prepareref·-f',·final_fasta,·'-m',·final_tsv,·'output_directory\n')659 ························print('ariba·prepareref·-f',·final_fasta,·'-m',·final_tsv,·'output_directory\n')
  
660 ········else:660 ········else:
661 ············print(f"Nothing·to·do.·Exiting.")····661 ············print(f"Nothing·to·do.·Exiting.")
662 ····def·run(self,·outprefix):662 ····def·run(self,·outprefix):
663 ········exec('self._get_from_'·+·self.ref_db·+·'(outprefix)')663 ········exec('self._get_from_'·+·self.ref_db·+·'(outprefix)')
630 B
./usr/share/doc/ariba/changelog.Debian.gz
548 B
changelog.Debian
    
Offset 1, 12 lines modifiedOffset 1, 13 lines modified
1 ariba·(2.14.5+ds-2~jan+unchanged1)·unchanged;·urgency=medium1 ariba·(2.14.5+git20200607.58b996f-1~jan+nus1)·fresh-snapshots;·urgency=medium
  
 2 ··*·New·upstream·snapshot.
2 ··*·Build·for·debian-janitor·apt·repository.3 ··*·Build·for·debian-janitor·apt·repository.
  
3 ·--·Debian·Janitor·<janitor@jelmer.uk>··Thu,·02·Jul·2020·18:39:04·+01004 ·--·Debian·Janitor·<janitor@jelmer.uk>··Thu,·02·Jul·2020·18:34:11·+0100
  
4 ariba·(2.14.5+ds-2)·unstable;·urgency=medium5 ariba·(2.14.5+ds-2)·unstable;·urgency=medium
  
5 ··[·Andreas·Tille·]6 ··[·Andreas·Tille·]
6 ··*·Build-Depends:·spades·<!nocheck>7 ··*·Build-Depends:·spades·<!nocheck>
7 ··*·Suggests:·spades8 ··*·Suggests:·spades