[med-svn] [Git][med-team/mosdepth][master] 12 commits: Repack to remove binary files

Nilesh Patra gitlab at salsa.debian.org
Tue Nov 3 11:26:22 GMT 2020



Nilesh Patra pushed to branch master at Debian Med / mosdepth


Commits:
4f3ebae9 by Nilesh Patra at 2020-11-03T16:55:50+05:30
Repack to remove binary files

- - - - -
81fa4545 by Nilesh Patra at 2020-11-03T16:55:50+05:30
New upstream version 0.3.1+ds
- - - - -
98f8c404 by Nilesh Patra at 2020-11-03T16:55:50+05:30
Add missing sources for sourceless binaries

- - - - -
76ead057 by Nilesh Patra at 2020-11-03T16:55:50+05:30
Regenerate repacked binaries during build

- - - - -
b4877f95 by Nilesh Patra at 2020-11-03T16:55:50+05:30
Fix help2man command

- - - - -
62a3dc54 by Nilesh Patra at 2020-11-03T16:55:50+05:30
Add samtools to build-deps for generating binaries

- - - - -
9c0b932c by Nilesh Patra at 2020-11-03T16:55:50+05:30
Enhance metadata

- - - - -
d33c904f by Nilesh Patra at 2020-11-03T16:55:50+05:30
add --nimcache: for addressing problems in sbuild/cowbuilder

- - - - -
0dcfea2f by Nilesh Patra at 2020-11-03T16:55:50+05:30
Remove compat, switch to debhelper-compat 13

- - - - -
c06cc58c by Nilesh Patra at 2020-11-03T16:55:50+05:30
Binary split to install testing data

- - - - -
fc20ecea by Nilesh Patra at 2020-11-03T16:55:50+05:30
Fix copyright

- - - - -
7180f278 by Nilesh Patra at 2020-11-03T16:55:50+05:30
Add autopkgtest

- - - - -


26 changed files:

- + debian/README.source
- debian/changelog
- − debian/compat
- debian/control
- debian/copyright
- + debian/missing-sources/big.sam
- + debian/missing-sources/empty-tids.sam
- + debian/missing-sources/nanopore.sam
- + debian/missing-sources/overlapping-pairs.sam
- + debian/missing-sources/ovl.sam
- + debian/mosdepth-examples.install
- debian/rules
- debian/tests/control
- debian/tests/run-unit-test
- debian/upstream/metadata
- debian/watch
- − tests/big.bam
- − tests/big.bam.csi
- − tests/empty-tids.bam
- − tests/empty-tids.bam.bai
- − tests/nanopore.bam
- − tests/nanopore.bam.bai
- − tests/overlapping-pairs.bam
- − tests/overlapping-pairs.bam.bai
- − tests/ovl.bam
- − tests/ovl.bam.bai


Changes:

=====================================
debian/README.source
=====================================
@@ -0,0 +1,27 @@
+
+Upstream provides binary files without sources for:
+
+* tests/big.bam.csi
+* tests/empty-tids.bam.bai
+* tests/ovl.bam.bai
+* tests/nanopore.bam
+* tests/nanopore.bam.bai
+* tests/ovl.bam
+* tests/overlapping-pairs.bam.bai
+* tests/overlapping-pairs.bam
+* tests/big.bam
+* tests/empty-tids.bam
+
+These have been converted to corresponding text (.sam) files with command:
+* samtools view -h -o <out>.sam <in>.bam 
+
+And the corresponding *.sam files are added to: debian/missing-sources
+
+They can be generated back with the following commands:
+*	cat debian/<sam-file> | samtools view -Sb - > tests/<corresponding-bam>
+*	samtools index <bam-files>
+
+
+These commands are also being run in debian/rules since these binaries are needed for autopkgtests.
+
+ -- Nilesh Patra <npatra974 at gmail.com>  Sun, 03 Nov 2020 14:38:35 +0530


=====================================
debian/changelog
=====================================
@@ -1,4 +1,4 @@
-mosdepth (0.3.1-1) UNRELEASED; urgency=medium
+mosdepth (0.3.1+ds-1) UNRELEASED; urgency=medium
 
   * Initial release (Closes: #973658)
 


=====================================
debian/compat deleted
=====================================
@@ -1 +0,0 @@
-12


=====================================
debian/control
=====================================
@@ -3,12 +3,14 @@ Section: science
 Priority: optional
 Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
 Uploaders: Steffen Moeller <moeller at debian.org>
-Build-Depends: debhelper (>= 12~),
+Build-Depends: debhelper-compat (= 13),
                nim,
                nim-docopt-dev,
                nim-regex-dev,
                nim-hts-dev,
-               help2man
+               help2man,
+               samtools,
+               libhts-dev
 Standards-Version: 4.5.0
 Vcs-Browser: https://salsa.debian.org/med-team/mosdepth
 Vcs-Git: https://salsa.debian.org/med-team/mosdepth.git
@@ -40,3 +42,32 @@ Description: BAM/CRAM depth calculation biological sequencing
      covered at the given thresholds.
  when appropriate, the output files are bgzipped and indexed for ease
  of use.
+
+Package: mosdepth-examples
+Architecture: all
+Depends: ${misc:Depends}
+Description: Test data for mosdepth
+ Many small reads are produced by high-throughput "next generation"
+ sequencing technologies. The final sequence is derived from how
+ these reads are overlapping towards a consensus.
+ The more reads are covering/confirming parts of a nucleotide seq,
+ the higher the confidence is. Too many reads would be indicative
+ of e.g. repeats in the genome.
+ .
+ mosdepth can output:
+  *  per-base depth about 2x as fast samtools depth--about 25 minutes
+     of CPU time for a 30X genome.
+  *  mean per-window depth given a window size--as would be used for
+     CNV calling.
+  *  the mean per-region given a BED file of regions.
+  *  a distribution of proportion of bases covered at or above a given
+     threshhold for each chromosome and genome-wide.
+  *  quantized output that merges adjacent bases as long as they fall
+     in the same coverage bins e.g. (10-20)
+  *  threshold output to indicate how many bases in each region are
+     covered at the given thresholds.
+ when appropriate, the output files are bgzipped and indexed for ease
+ of use.
+ .
+ This package contains a test data set as well as sample scripts
+ running some test suite provided by Debian also as autopkgtest.


=====================================
debian/copyright
=====================================
@@ -1,12 +1,13 @@
 Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
 Upstream-Name: mosdepth
 Source: https://github.com/brentp/mosdepth
+Files-Excluded: tests/*.bam*
 
 Files: *
 Copyright: 2017-2020 Brent Pedersen
 License: Expat
 
-Files: intToStr.nim
+Files: int2str.nim
 Copyright: 2014 Milo Yip
  adpated from: https://github.com/miloyip/itoa-benchmark countlut method..
  https://github.com/miloyip/itoa-benchmark/blob/master/license.txt


=====================================
debian/missing-sources/big.sam
=====================================
@@ -0,0 +1,3 @@
+ at SQ	SN:ref	LN:600000045
+ at PG	ID:samtools	PN:samtools	VN:1.10	CL:samtools view -h -o missing-sources/big.sam tests/big.bam
+r001	163	ref	600000007	30	8M4I4M1D3M	=	37	39	TTAGATAAAGAGGATACTG	*	XX:B:S,12561,2,20,112


=====================================
debian/missing-sources/empty-tids.sam
=====================================
The diff for this file was not included because it is too large.

=====================================
debian/missing-sources/nanopore.sam
=====================================
The diff for this file was not included because it is too large.

=====================================
debian/missing-sources/overlapping-pairs.sam
=====================================
@@ -0,0 +1,7 @@
+ at HD	VN:1.3	SO:coordinate
+ at SQ	SN:1	LN:249250621
+ at PG	ID:bwa	PN:bwa	VN:0.7.15-r1142-dirty	CL:./tools/bwa mem -M -t 4 /data/resources/human/GRCh37/index/bwa/GRCh37.fa /data/analysis/40626039-599f-4679-8fa5-8d3eebec6276/input_files/9d7d1b21-a694-416f-8d65-84d0fb943040_1.fastq.gz /data/analysis/40626039-599f-4679-8fa5-8d3eebec6276/input_files/9d7d1b21-a694-416f-8d65-84d0fb943040_2.fastq.gz
+ at PG	ID:samtools	PN:samtools	PP:bwa	VN:1.10	CL:samtools view -h -o missing-sources/overlapping-pairs.sam tests/overlapping-pairs.bam
+ at RG	ID:9d7d1b21-a694-416f-8d65-84d0fb943040	SM:9d7d1b21-a694-416f-8d65-84d0fb943040	PL:protocol	LB:lib1	PU:unit
+M00551:66:000000000-B6BF6:1:2103:9642:22936	99	1	565174	0	80M	=	565174	80	CCACAGAAGCTGCCATCAAGTATTTCCTCACGCAAGCAACCGCATCCATAATCCTTCTAATAGCTATCCTCTTCAACAAT	CCCCCGGFFGFEFGGGGFFFGGGGGDGGGGGFGGGGGFGGGEGCGFGGGFFGGGGGGGGGGCFGGFGGGFADEFGGG,FF	NM:i:0	MD:Z:80	AS:i:80	XS:i:80	XA:Z:M,+4624,80M,0;	RG:Z:9d7d1b21-a694-416f-8d65-84d0fb943040
+M00551:66:000000000-B6BF6:1:2103:9642:22936	147	1	565174	0	80M	=	565174	-80	CCACAGAAGCTGCCATCAAGTATTTCCTCACGCAAGCAACCGCATCCATAATCCTTCTAATAGCTATCCTCTCCAACAAT	CFCF<E<<@B at GEGFCGFAFGFECEC:GGGGFCE,F:C6GECCFFCFGF<68FC-GDGFEGGFC;C8 at EFC--FFC8--C	NM:i:1	MD:Z:72T7	AS:i:75	XS:i:75	XA:Z:M,-4624,80M,1;	RG:Z:9d7d1b21-a694-416f-8d65-84d0fb943040


=====================================
debian/missing-sources/ovl.sam
=====================================
@@ -0,0 +1,95 @@
+ at HD	VN:1.5	GO:none	SO:coordinate
+ at SQ	SN:1	LN:249250621
+ at SQ	SN:2	LN:243199373
+ at SQ	SN:3	LN:198022430
+ at SQ	SN:4	LN:191154276
+ at SQ	SN:5	LN:180915260
+ at SQ	SN:6	LN:171115067
+ at SQ	SN:7	LN:159138663
+ at SQ	SN:8	LN:146364022
+ at SQ	SN:9	LN:141213431
+ at SQ	SN:10	LN:135534747
+ at SQ	SN:11	LN:135006516
+ at SQ	SN:12	LN:133851895
+ at SQ	SN:13	LN:115169878
+ at SQ	SN:14	LN:107349540
+ at SQ	SN:15	LN:102531392
+ at SQ	SN:16	LN:90354753
+ at SQ	SN:17	LN:81195210
+ at SQ	SN:18	LN:78077248
+ at SQ	SN:19	LN:59128983
+ at SQ	SN:20	LN:63025520
+ at SQ	SN:21	LN:48129895
+ at SQ	SN:22	LN:51304566
+ at SQ	SN:X	LN:155270560
+ at SQ	SN:Y	LN:59373566
+ at SQ	SN:MT	LN:16569
+ at SQ	SN:GL000207.1	LN:4262
+ at SQ	SN:GL000226.1	LN:15008
+ at SQ	SN:GL000229.1	LN:19913
+ at SQ	SN:GL000231.1	LN:27386
+ at SQ	SN:GL000210.1	LN:27682
+ at SQ	SN:GL000239.1	LN:33824
+ at SQ	SN:GL000235.1	LN:34474
+ at SQ	SN:GL000201.1	LN:36148
+ at SQ	SN:GL000247.1	LN:36422
+ at SQ	SN:GL000245.1	LN:36651
+ at SQ	SN:GL000197.1	LN:37175
+ at SQ	SN:GL000203.1	LN:37498
+ at SQ	SN:GL000246.1	LN:38154
+ at SQ	SN:GL000249.1	LN:38502
+ at SQ	SN:GL000196.1	LN:38914
+ at SQ	SN:GL000248.1	LN:39786
+ at SQ	SN:GL000244.1	LN:39929
+ at SQ	SN:GL000238.1	LN:39939
+ at SQ	SN:GL000202.1	LN:40103
+ at SQ	SN:GL000234.1	LN:40531
+ at SQ	SN:GL000232.1	LN:40652
+ at SQ	SN:GL000206.1	LN:41001
+ at SQ	SN:GL000240.1	LN:41933
+ at SQ	SN:GL000236.1	LN:41934
+ at SQ	SN:GL000241.1	LN:42152
+ at SQ	SN:GL000243.1	LN:43341
+ at SQ	SN:GL000242.1	LN:43523
+ at SQ	SN:GL000230.1	LN:43691
+ at SQ	SN:GL000237.1	LN:45867
+ at SQ	SN:GL000233.1	LN:45941
+ at SQ	SN:GL000204.1	LN:81310
+ at SQ	SN:GL000198.1	LN:90085
+ at SQ	SN:GL000208.1	LN:92689
+ at SQ	SN:GL000191.1	LN:106433
+ at SQ	SN:GL000227.1	LN:128374
+ at SQ	SN:GL000228.1	LN:129120
+ at SQ	SN:GL000214.1	LN:137718
+ at SQ	SN:GL000221.1	LN:155397
+ at SQ	SN:GL000209.1	LN:159169
+ at SQ	SN:GL000218.1	LN:161147
+ at SQ	SN:GL000220.1	LN:161802
+ at SQ	SN:GL000213.1	LN:164239
+ at SQ	SN:GL000211.1	LN:166566
+ at SQ	SN:GL000199.1	LN:169874
+ at SQ	SN:GL000217.1	LN:172149
+ at SQ	SN:GL000216.1	LN:172294
+ at SQ	SN:GL000215.1	LN:172545
+ at SQ	SN:GL000205.1	LN:174588
+ at SQ	SN:GL000219.1	LN:179198
+ at SQ	SN:GL000224.1	LN:179693
+ at SQ	SN:GL000223.1	LN:180455
+ at SQ	SN:GL000195.1	LN:182896
+ at SQ	SN:GL000212.1	LN:186858
+ at SQ	SN:GL000222.1	LN:186861
+ at SQ	SN:GL000200.1	LN:187035
+ at SQ	SN:GL000193.1	LN:189789
+ at SQ	SN:GL000194.1	LN:191469
+ at SQ	SN:GL000225.1	LN:211173
+ at SQ	SN:GL000192.1	LN:547496
+ at SQ	SN:NC_007605	LN:171823
+ at SQ	SN:hs37d5	LN:35477943
+ at SQ	SN:phix	LN:5386
+ at RG	ID:GT04008021_119	LB:GT04008021	PL:ILLUMINA	PU:ILLUMINA_119	SM:GT04008021
+ at PG	ID:SAMBLASTER	CL:samblaster -i stdin -o stdout --addMateTags	VN:0.1.22
+ at PG	ID:bwa	PN:bwa	CL:/scratch/ucgd/lustre/ugpuser/apps/kingspeak.peaks/bwa/0.7.12/bwa mem -R @RG\tID:GT04008021_119\tSM:GT04008021\tPL:ILLUMINA\tLB:GT04008021\tPU:ILLUMINA_119 -t 48 -v 1 /scratch/ucgd/lustre/ugpuser/ucgd_data/references/human_g1k_v37_decoy.fasta < tail -c +1760660595 /scratch/ucgd/lustre/other-transfer/Process_Data/16-12-27_PCGC-Tristani-CHD2/processing_tmp/GT04008021_002_002_1_sequence.txt.fastq | head -c 1690234286 < tail -c +1760660595 /scratch/ucgd/lustre/other-transfer/Process_Data/16-12-27_PCGC-Tristani-CHD2/processing_tmp/GT04008021_002_002_2_sequence.txt.fastq | head -c 1690234286	VN:0.7.12-r1039
+ at PG	ID:GATK IndelRealigner	VN:3.5-0-g36282e4	CL:knownAlleles=[(RodBinding name=knownAlleles source=/scratch/ucgd/lustre/ugpuser/ucgd_data/GATK_Bundle/Mills_and_1000G_gold_standard.indels.b37.vcf), (RodBinding name=knownAlleles2 source=/scratch/ucgd/lustre/ugpuser/ucgd_data/GATK_Bundle/1000G_phase1.indels.b37.vcf)] targetIntervals=/scratch/local/ugp_K3jrtq/0.realign.intervals LODThresholdForCleaning=5.0 consensusDeterminationModel=USE_READS entropyThreshold=0.15 maxReadsInMemory=150000 maxIsizeForMovement=3000 maxPositionalMoveAllowed=200 maxConsensuses=30 maxReadsForConsensuses=120 maxReadsForRealignment=5000 noOriginalAlignmentTags=false nWayOut=null generate_nWayOut_md5s=false check_early=false noPGTag=false keepPGTags=false indelsFileForDebugging=null statisticsFileForDebugging=null SNPsFileForDebugging=null
+ at PG	ID:samtools	PN:samtools	PP:GATK IndelRealigner	VN:1.10	CL:samtools view -h -o missing-sources/ovl.sam tests/ovl.bam
+D8WCT8Q1_0255:5:1116:4474:27171#CGATGTCGATGT	163	MT	1	21	32S42M	=	7	80	CACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCT	@=BDDDDHHHH3CFGHHIHIIIIGHIGHIECGGHGGG at FEGHIEGEIIFDBBFHF@F at GIGGEHIIHEBDCEEE	XA:Z:17,+22020695,74M,4;	MC:Z:74M	MD:Z:42	RG:Z:GT04008021_119	NM:i:0	MQ:i:60	AS:i:42	XS:i:54
+D8WCT8Q1_0255:5:1116:4474:27171#CGATGTCGATGT	83	MT	7	60	74M	=	1	-80	AGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGCATGCACGC	CCCDDCCB?ABDCDECEDCA?;B?EAFHIIHCF at JIIGFF=@IJIJIHGEIIJJJJIGHIGEFHHHHDFDFFCC	MC:Z:32S42M	MD:Z:65T8	RG:Z:GT04008021_119	NM:i:1	MQ:i:21	AS:i:69	XS:i:39


=====================================
debian/mosdepth-examples.install
=====================================
@@ -0,0 +1,5 @@
+tests/*.bam*		usr/share/doc/mosdepth-examples
+tests/*.cfg		usr/share/doc/mosdepth-examples
+tests/*.nim		usr/share/doc/mosdepth-examples
+tests/*.bed		usr/share/doc/mosdepth-examples
+scripts/*.py		usr/share/doc/mosdepth-examples


=====================================
debian/rules
=====================================
@@ -4,14 +4,28 @@ DH_VERBOSE := 1
 export LC_ALL=C.UTF-8
 export HOME=/tmp
 
+export DEB_BUILD_MAINT_OPTIONS = hardening=+all
 include /usr/share/dpkg/default.mk
 
 %:
 	dh $@
 
 override_dh_auto_build:
-	nim c -p:/usr/share/nimble/unicodeplus  -p:/usr/share/nimble/unicodedb  -p:/usr/share/nimble/regex  -p:/usr/share/nimble/docopt -p:/usr/share/nimble/hts  mosdepth.nim
-	help2man mosdepth > debian/mosdepth.1
+	nim c -p:/usr/share/nimble/unicodeplus  -p:/usr/share/nimble/unicodedb  -p:/usr/share/nimble/regex  -p:/usr/share/nimble/docopt -p:/usr/share/nimble/hts --nimcache:$(CURDIR)/tests/nimcache mosdepth.nim
+	help2man --no-info --no-discard-stderr --help-option="-h" ./mosdepth > debian/mosdepth.1
+
+override_dh_auto_test:
+	rm -f tests/missing.bed
+	for f in debian/missing-sources/*; do \
+		outp=tests/`echo $$f | sed -e 's/sam/bam/' -e 's/debian\/missing\-sources\///'` ; \
+		cat $$f | samtools view -Sb - > $$outp ; \
+		if [ "$$outp" = "tests/big.bam" ] ; then \
+			samtools index $$outp -c ; \
+			continue ; \
+		fi ; \
+		samtools index $$outp ; \
+	done
+	dh_auto_test
 
 override_dh_auto_clean:
 	rm -f debian/mosdepth.1


=====================================
debian/tests/control
=====================================
@@ -1,3 +1,3 @@
 Tests: run-unit-test
-Depends: @
+Depends: @, python3, libhts-dev
 Restrictions: allow-stderr


=====================================
debian/tests/run-unit-test
=====================================
@@ -1,7 +1,7 @@
 #!/bin/bash
 set -e
 
-pkg=#PACKAGENAME#
+pkg=mosdepth
 
 if [ "${AUTOPKGTEST_TMP}" = "" ] ; then
   AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
@@ -11,8 +11,31 @@ if [ "${AUTOPKGTEST_TMP}" = "" ] ; then
   trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM
 fi
 
-cp -a /usr/share/doc/${pkg}/examples/* "${AUTOPKGTEST_TMP}"
+cp -a /usr/share/doc/${pkg}-examples/* "${AUTOPKGTEST_TMP}"
 
 cd "${AUTOPKGTEST_TMP}"
+gunzip -r *.gz
 
-#do_stuff_to_test_package#
+echo "Test 1"
+mosdepth --by empty-tids.bed --thresholds 1,10,20,30 test1 empty-tids.bam
+for f in test1*
+do
+	[ -s $f ] || exit 1
+done
+cat test1.*.txt | tail -20
+rm test1*
+echo "PASS"
+
+echo "Test 2"
+mosdepth --by empty-tids.bed --quantize 0:1:4:100:200 test2 empty-tids.bam
+for f in test2*
+do
+	[ -s $f ] || exit 1
+done
+cat test2.*.txt | tail -20
+echo "PASS"
+
+echo "Tet 3"
+python3 plot-dist.py test2.mosdepth.global.dist.txt
+[ -s dist.html ]
+echo "PASS"


=====================================
debian/upstream/metadata
=====================================
@@ -1,3 +1,10 @@
+---
+Archive: GitHub
+Bug-Database: https://github.com/brentp/mosdepth/issues
+Bug-Submit: https://github.com/brentp/mosdepth/issues/new
+Changelog: https://github.com/brentp/mosdepth/tags
+Repository: https://github.com/brentp/mosdepth.git
+Repository-Browse: https://github.com/brentp/mosdepth
 Reference:
  - Author: Brent S Pedersen and Aaron R. Quinlan
    Title: >


=====================================
debian/watch
=====================================
@@ -1,4 +1,3 @@
 version=4
-#https://github.com/brentp/mospdepth/releases/latest .*/archive/#PREFIX#@ANY_VERSION@@ARCHIVE_EXT@
-https://github.com/brentp/mosdepth/tags .*/v([\d.])+\.tar\.gz
-
+opts="filenamemangle=s%(?:.*?)?v?(\d[\d.]*)\.tar\.gz%@PACKAGE at -$1.tar.gz%,repacksuffix=+ds,dversionmangle=auto" \
+https://github.com/brentp/mosdepth/releases .*/archive/v?@ANY_VERSION@\.tar\.gz


=====================================
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=====================================
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=====================================
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=====================================
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=====================================
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=====================================
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=====================================
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=====================================
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=====================================
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=====================================
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=====================================
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=====================================
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=====================================
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=====================================
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=====================================
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=====================================
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=====================================
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View it on GitLab: https://salsa.debian.org/med-team/mosdepth/-/compare/4973ef6c6b225a8a3f692936c5295feab98861af...7180f278a1c980168c46579282d19a8e9cb547f0

-- 
View it on GitLab: https://salsa.debian.org/med-team/mosdepth/-/compare/4973ef6c6b225a8a3f692936c5295feab98861af...7180f278a1c980168c46579282d19a8e9cb547f0
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