[med-svn] [Git][med-team/megadepth][master] 7 commits: New upstream version 1.04

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Med / megadepth


Commits:
5b07eff0 by Andreas Tille at 2025-10-19T08:27:13+02:00
New upstream version 1.04
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765e455b by Andreas Tille at 2025-10-19T08:27:13+02:00
New upstream version

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3d49fa5f by Andreas Tille at 2025-10-19T08:27:13+02:00
Update upstream source from tag 'upstream/1.04'

Update to upstream version '1.04'
with Debian dir 3b32e239be5869282573165966f75dbe6002b485
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669c393a by Andreas Tille at 2025-10-19T08:27:13+02:00
Standards-Version: 4.7.2 (routine-update)

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6068be6e by Andreas Tille at 2025-10-19T08:34:47+02:00
Remove trailing whitespace in debian/changelog (routine-update)

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1e60838e by Andreas Tille at 2025-10-19T08:53:08+02:00
New upstream now provides CMakeLists.txt

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db5fbdc6 by Andreas Tille at 2025-10-19T08:56:49+02:00
Drop useless override of dh_installman

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73 changed files:

- .github/workflows/build.yml
- .gitignore
- − .gitmodules
- + CMakeLists.txt
- − CMakeLists.txt.ci
- CMakeLists.txt.static
- CMakeLists.txt.statlib
- − CMakeLists.txt.windows
- LICENSE.txt
- README.md
- VERSION
- docker_build.sh → build.sh
- build_megadepth.sh → build_no_container.sh
- build_no_container_hbb.sh
- build_no_container_windows.sh
- build_no_container_macos.sh → build_no_container_xcross.sh
- − conda/megadepth/CMakeLists.txt
- − conda/megadepth/LICENSE.txt
- − conda/megadepth/build.sh
- − conda/megadepth/cross-linux.cmake
- − conda/megadepth/meta.yaml
- − countdecimaldigit.h
- − countlut.hpp
- − create_docker_to_run_megadepth.sh
- debian/changelog
- debian/control
- debian/patches/addCurlLibrary.patch
- debian/rules
- − digitslut.h
- get_htslib.sh
- get_libBigWig.sh
- get_libdeflate.sh
- get_zlib.sh
- − junctions/process_jx_output.sh
- megadepth → md_runner
- megadepthd → mdd_runner
- megadepth.cpp
- − megadepth_detailed.png
- − megadepth_logo.png
- release.sh
- run_hbb_build_container.sh
- − run_macos_build_container.sh
- − run_windows_build_container.sh
- tests/TCGA_BLCA_A13J.vcf.gz_cg_cov5.bw.bg.gz.chr1.60379.62229.bw → sample_aggregation/.Snakefile.paste.swp
- − tests/TCGA_BLCA_A13J_vs_chr1.61863.62160.annotation.tsv
- − tests/bw.all_overlap_types.test_input.bw
- − tests/bw.all_overlap_types.test_output.bed
- − tests/check_overlaps.pl
- − tests/chr1.61863.62160.bad_chrm_order.bed
- − tests/chr1.61863.62160.bed
- − tests/gh_bug_9.bed
- tests/long_reads.bam.jxs.tsv
- tests/test.bam
- tests/test.bam.bai
- − tests/test.bam.names.alts.tsv
- tests/test.bam.orig.alts.tsv
- − tests/test.cram
- − tests/test.cram.coverage.tsv
- − tests/test.cram.crai
- − tests/test.cram.window.summed.tsv
- tests/test.sh
- − tests/test1.bam
- − tests/test1.bam.bai
- − tests/test2.bam.all_jxs.tsv
- tests/test2.bam.jxs.tsv
- tests/test3.out.tsv
- − tests/test_noprefix.bam
- − tests/test_noprefix.bam.bai
- tests/testbw1.bed.out.tsv
- tests/testbw2.bed.max
- tests/testbw2.bed.mean
- tests/testbw2.bed.min
- tests/testbw2.bed.out.tsv


The diff was not included because it is too large.


View it on GitLab: https://salsa.debian.org/med-team/megadepth/-/compare/aa371401ed6f213287aca0e5a7b868db05e6a93b...db5fbdc60505f07a9a5acd6f44bacc666e284781

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View it on GitLab: https://salsa.debian.org/med-team/megadepth/-/compare/aa371401ed6f213287aca0e5a7b868db05e6a93b...db5fbdc60505f07a9a5acd6f44bacc666e284781
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