<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN" "http://www.w3.org/TR/REC-html40/loose.dtd">
<html lang="en" style='--code-editor-font: var(--default-mono-font, "GitLab Mono"), JetBrains Mono, Menlo, DejaVu Sans Mono, Liberation Mono, Consolas, Ubuntu Mono, Courier New, andale mono, lucida console, monospace;'>
<head>
<meta content="text/html; charset=utf-8" http-equiv="Content-Type">
<title>
GitLab
</title>

<style data-premailer="ignore" type="text/css">
a { color: #1068bf; }
</style>


<style>img {
max-width: 100%; height: auto;
}
body {
font-size: .875rem;
}
body {
-webkit-text-shadow: rgba(255,255,255,.01) 0 0 1px;
}
body {
font-family: "GitLab Sans",-apple-system,BlinkMacSystemFont,"Segoe UI",Roboto,"Noto Sans",Ubuntu,Cantarell,"Helvetica Neue",sans-serif,"Apple Color Emoji","Segoe UI Emoji","Segoe UI Symbol","Noto Color Emoji"; font-size: inherit;
}
</style>
</head>
<body style='font-size: inherit; -webkit-text-shadow: rgba(255,255,255,.01) 0 0 1px; font-family: "GitLab Sans",-apple-system,BlinkMacSystemFont,"Segoe UI",Roboto,"Noto Sans",Ubuntu,Cantarell,"Helvetica Neue",sans-serif,"Apple Color Emoji","Segoe UI Emoji","Segoe UI Symbol","Noto Color Emoji";'>
<div class="content">

<h3 style="margin-top: 20px; margin-bottom: 10px;">
Andreas Tille pushed to branch master at <a href="https://salsa.debian.org/med-team/megadepth">Debian Med / megadepth</a>
</h3>
<h4 style="margin-top: 10px; margin-bottom: 10px;">
Commits:
</h4>
<ul>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/megadepth/-/commit/5b07eff05187b7436074d89d4456300344b07795">5b07eff0</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2025-10-19T08:27:13+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono", "JetBrains Mono", "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; font-variant-ligatures: none; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>New upstream version 1.04</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/megadepth/-/commit/765e455baced8ae2e2621a498ac09fc9221e81d0">765e455b</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2025-10-19T08:27:13+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono", "JetBrains Mono", "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; font-variant-ligatures: none; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>New upstream version
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/megadepth/-/commit/3d49fa5f15d44b60056237918dfa9712c65405a8">3d49fa5f</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2025-10-19T08:27:13+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono", "JetBrains Mono", "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; font-variant-ligatures: none; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Update upstream source from tag 'upstream/1.04'

Update to upstream version '1.04'
with Debian dir 3b32e239be5869282573165966f75dbe6002b485</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/megadepth/-/commit/669c393abdd9b85272091f911d63c2d93e2a6e44">669c393a</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2025-10-19T08:27:13+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono", "JetBrains Mono", "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; font-variant-ligatures: none; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Standards-Version: 4.7.2 (routine-update)
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/megadepth/-/commit/6068be6eb3e07cd019c8543bb08dcd8d33414c28">6068be6e</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2025-10-19T08:34:47+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono", "JetBrains Mono", "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; font-variant-ligatures: none; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Remove trailing whitespace in debian/changelog (routine-update)
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/megadepth/-/commit/1e60838ed398c5fa60c389acc5197124f50d1cf5">1e60838e</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2025-10-19T08:53:08+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono", "JetBrains Mono", "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; font-variant-ligatures: none; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>New upstream now provides CMakeLists.txt
</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/megadepth/-/commit/db5fbdc60505f07a9a5acd6f44bacc666e284781">db5fbdc6</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2025-10-19T08:56:49+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono", "JetBrains Mono", "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; font-variant-ligatures: none; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Drop useless override of dh_installman
</pre>
</li>
</ul>
<h4 style="margin-top: 10px; margin-bottom: 10px;">
73 changed files:
</h4>
<ul>
<li class="file-stats">
<a href="#fe77d5d1439f26e353a42bbd38dece2467ff6558">
.github/workflows/build.yml
</a>
</li>
<li class="file-stats">
<a href="#a5cc2925ca8258af241be7e5b0381edf30266302">
.gitignore
</a>
</li>
<li class="file-stats">
<a href="#7445606fbf8f3683cd42bdc54b05d7a0bc2dfc44">
<span class="deleted-file">

.gitmodules
</span>
</a>
</li>
<li class="file-stats">
<a href="#9a2aa4db38d3115ed60da621e012c0efc0172aae">
<span class="new-file">
+
CMakeLists.txt
</span>
</a>
</li>
<li class="file-stats">
<a href="#f2eb13930933f078921013aab0553fe342d1f047">
<span class="deleted-file">

CMakeLists.txt.ci
</span>
</a>
</li>
<li class="file-stats">
<a href="#0e7bdb49d8c4fd570401b11f8769c58991cf413c">
CMakeLists.txt.static
</a>
</li>
<li class="file-stats">
<a href="#2773c1d991c3d1d4932c2b6d3a79bf7a516dbe97">
CMakeLists.txt.statlib
</a>
</li>
<li class="file-stats">
<a href="#009110bbae815b9e2d9c8cad5299a815f38999ba">
<span class="deleted-file">

CMakeLists.txt.windows
</span>
</a>
</li>
<li class="file-stats">
<a href="#79b82ce9b64a924266619555502f890dd80c83b9">
LICENSE.txt
</a>
</li>
<li class="file-stats">
<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
README.md
</a>
</li>
<li class="file-stats">
<a href="#b33892fbddeffc3368077b4904ad0b3d562a7312">
VERSION
</a>
</li>
<li class="file-stats">
<a href="#59f81c123b3abbcb97274545796dd18706c3e106">
docker_build.sh

build.sh
</a>
</li>
<li class="file-stats">
<a href="#7f776ab0959e3b526323e30da4f66c8066687f81">
build_megadepth.sh

build_no_container.sh
</a>
</li>
<li class="file-stats">
<a href="#08a4cb43618177f48d01c3921d158c74365b6f9c">
build_no_container_hbb.sh
</a>
</li>
<li class="file-stats">
<a href="#12bbbb27f633b352c6f30e69588989fc4257b0ec">
build_no_container_windows.sh
</a>
</li>
<li class="file-stats">
<a href="#839cfced5b2a0eba2a961e87fb1a8202c471e478">
build_no_container_macos.sh

build_no_container_xcross.sh
</a>
</li>
<li class="file-stats">
<a href="#4c880cda68795fafd082483979df43a92a59633f">
<span class="deleted-file">

conda/megadepth/CMakeLists.txt
</span>
</a>
</li>
<li class="file-stats">
<a href="#61beca805f85409dd7a4698d5bf97bfb765b665c">
<span class="deleted-file">

conda/megadepth/LICENSE.txt
</span>
</a>
</li>
<li class="file-stats">
<a href="#6c1cd3c335470ca7197d72a6f459d1385a117512">
<span class="deleted-file">

conda/megadepth/build.sh
</span>
</a>
</li>
<li class="file-stats">
<a href="#ebda47c4bf7647b225f4db14c305e91d8d29daa1">
<span class="deleted-file">

conda/megadepth/cross-linux.cmake
</span>
</a>
</li>
<li class="file-stats">
<a href="#e49794e2673032a256710ad61ba3ee8ee41fca9e">
<span class="deleted-file">

conda/megadepth/meta.yaml
</span>
</a>
</li>
<li class="file-stats">
<a href="#dd06a2275115934552379e95310fbcbc086cc36d">
<span class="deleted-file">

countdecimaldigit.h
</span>
</a>
</li>
<li class="file-stats">
<a href="#30b4e3878374287d245bfb9d705b83322932918f">
<span class="deleted-file">

countlut.hpp
</span>
</a>
</li>
<li class="file-stats">
<a href="#3f9753535064fdd2b26ae1475f5d74cd1e110ef3">
<span class="deleted-file">

create_docker_to_run_megadepth.sh
</span>
</a>
</li>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
</li>
<li class="file-stats">
<a href="#c1ae4f7a5189b908cda85747a19ed7a4f1c69dcc">
debian/patches/addCurlLibrary.patch
</a>
</li>
<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
</a>
</li>
<li class="file-stats">
<a href="#f80d10ec131c8982ce71b9312bac781087cd04f7">
<span class="deleted-file">

digitslut.h
</span>
</a>
</li>
<li class="file-stats">
<a href="#f490e89ec5432707f9557e44a0532b750277b2a2">
get_htslib.sh
</a>
</li>
<li class="file-stats">
<a href="#ffcb624998488564441f8f8d0274be32122828b1">
get_libBigWig.sh
</a>
</li>
<li class="file-stats">
<a href="#1423ce8124966f220bea14860b422efb8d245c28">
get_libdeflate.sh
</a>
</li>
<li class="file-stats">
<a href="#4580dc0ae1af5df6ab8200042680876487b6ba1b">
get_zlib.sh
</a>
</li>
<li class="file-stats">
<a href="#6515ce6d3b4af1127aa6893b69e16d02d8e158c6">
<span class="deleted-file">

junctions/process_jx_output.sh
</span>
</a>
</li>
<li class="file-stats">
<a href="#1b5f1d9d377c2831a681da55380495184962f298">
megadepth

md_runner
</a>
</li>
<li class="file-stats">
<a href="#8ea55db38cb6868020186eef865468f87108a154">
megadepthd

mdd_runner
</a>
</li>
<li class="file-stats">
<a href="#6ae744995ee5aa8f996da5b6101af5d112b12e7b">
megadepth.cpp
</a>
</li>
<li class="file-stats">
<a href="#721f52a51b72be24c88d090709bc7936d529cede">
<span class="deleted-file">

megadepth_detailed.png
</span>
</a>
</li>
<li class="file-stats">
<a href="#abd53881cfa988444c890e9c74bf4d4b4caaa717">
<span class="deleted-file">

megadepth_logo.png
</span>
</a>
</li>
<li class="file-stats">
<a href="#dee5c4430f3aa3a43132ee80817c8d207bada8d9">
release.sh
</a>
</li>
<li class="file-stats">
<a href="#75abf9c4aac2f7c4ce9270d495cf534c5a05a096">
run_hbb_build_container.sh
</a>
</li>
<li class="file-stats">
<a href="#467837ebd82abf1d80253ab2b0d3e4760b539450">
<span class="deleted-file">

run_macos_build_container.sh
</span>
</a>
</li>
<li class="file-stats">
<a href="#fa9239b125bd282c3f1e13f673bb7152e83ae344">
<span class="deleted-file">

run_windows_build_container.sh
</span>
</a>
</li>
<li class="file-stats">
<a href="#96fd2c5304db7bef3e057241e519b13b98461c00">
tests/TCGA_BLCA_A13J.vcf.gz_cg_cov5.bw.bg.gz.chr1.60379.62229.bw

sample_aggregation/.Snakefile.paste.swp
</a>
</li>
<li class="file-stats">
<a href="#89c6a3c5991a0917ea332c32be9ee999195fb554">
<span class="deleted-file">

tests/TCGA_BLCA_A13J_vs_chr1.61863.62160.annotation.tsv
</span>
</a>
</li>
<li class="file-stats">
<a href="#af9d1ea7aac025978be424fb12d41ab3e980773f">
<span class="deleted-file">

tests/bw.all_overlap_types.test_input.bw
</span>
</a>
</li>
<li class="file-stats">
<a href="#84cdfa74250d240dd8f2f1e1632bf2a4cf0ac9dd">
<span class="deleted-file">

tests/bw.all_overlap_types.test_output.bed
</span>
</a>
</li>
<li class="file-stats">
<a href="#2ced2d16de0dbbb82e3c6001289271a00e3ac316">
<span class="deleted-file">

tests/check_overlaps.pl
</span>
</a>
</li>
<li class="file-stats">
<a href="#5da7cbc242c14e78264e4037205595375ac0152b">
<span class="deleted-file">

tests/chr1.61863.62160.bad_chrm_order.bed
</span>
</a>
</li>
<li class="file-stats">
<a href="#888e25837e161582e5c007323efe4a8fe778beef">
<span class="deleted-file">

tests/chr1.61863.62160.bed
</span>
</a>
</li>
<li class="file-stats">
<a href="#7265a80b3bcc6cb8a990aa72377c4662b206f2b9">
<span class="deleted-file">

tests/gh_bug_9.bed
</span>
</a>
</li>
<li class="file-stats">
<a href="#963f2c23bc9f8a0477bc924de73c4bfc4c098524">
tests/long_reads.bam.jxs.tsv
</a>
</li>
<li class="file-stats">
<a href="#fc22c0280c3aa06109ab77e7aa32bf140e2260f4">
tests/test.bam
</a>
</li>
<li class="file-stats">
<a href="#7705e592a008c7abf602fb71ec6c51d3624b6d20">
tests/test.bam.bai
</a>
</li>
<li class="file-stats">
<a href="#6471b3178ea8e6f5cdbb10bc299e9f89b29c5e69">
<span class="deleted-file">

tests/test.bam.names.alts.tsv
</span>
</a>
</li>
<li class="file-stats">
<a href="#f25b63c769b1e25334fed67680a083efeee186fa">
tests/test.bam.orig.alts.tsv
</a>
</li>
<li class="file-stats">
<a href="#6a4dfc5de1975bfaa0b86d9b4b32d20df7adb425">
<span class="deleted-file">

tests/test.cram
</span>
</a>
</li>
<li class="file-stats">
<a href="#8385944e0f723d80677c326cbb37804dd5dbc1dd">
<span class="deleted-file">

tests/test.cram.coverage.tsv
</span>
</a>
</li>
<li class="file-stats">
<a href="#42cc7c91e92b0a116d0e208977ebe1aad1b41789">
<span class="deleted-file">

tests/test.cram.crai
</span>
</a>
</li>
<li class="file-stats">
<a href="#fdc9d783d0ea7d387b7208c2b11e44046045f78a">
<span class="deleted-file">

tests/test.cram.window.summed.tsv
</span>
</a>
</li>
<li class="file-stats">
<a href="#08f4007a2dcdd77b75167cfe678d33d187bd0572">
tests/test.sh
</a>
</li>
<li class="file-stats">
<a href="#4913a4ecccd2aa3c04c9fc5f5b0e3f835467c6a4">
<span class="deleted-file">

tests/test1.bam
</span>
</a>
</li>
<li class="file-stats">
<a href="#4087cf80c875a7fe082620bfae7a0fea329848d1">
<span class="deleted-file">

tests/test1.bam.bai
</span>
</a>
</li>
<li class="file-stats">
<a href="#275aa1cbb298009b8b5eb23578cbe2acde9c218b">
<span class="deleted-file">

tests/test2.bam.all_jxs.tsv
</span>
</a>
</li>
<li class="file-stats">
<a href="#1a6e0ca746827693eefcd3219fc89f2d552f96d9">
tests/test2.bam.jxs.tsv
</a>
</li>
<li class="file-stats">
<a href="#f11a20a5bfe208eac9dbf1281d5e7ace7798fba7">
tests/test3.out.tsv
</a>
</li>
<li class="file-stats">
<a href="#38112538ca65ac406f1485732845b76d43544ab7">
<span class="deleted-file">

tests/test_noprefix.bam
</span>
</a>
</li>
<li class="file-stats">
<a href="#e957589b9ffeb6e9119fbb5bc67c0e8d9c038287">
<span class="deleted-file">

tests/test_noprefix.bam.bai
</span>
</a>
</li>
<li class="file-stats">
<a href="#91a3115ee04c17ea52c0aecc3d4390254ca61207">
tests/testbw1.bed.out.tsv
</a>
</li>
<li class="file-stats">
<a href="#275e49ed5790d28bb5c98c1e24e721790771c2c6">
tests/testbw2.bed.max
</a>
</li>
<li class="file-stats">
<a href="#248ea1b4225273e8315ce22a98d339adcdd2040e">
tests/testbw2.bed.mean
</a>
</li>
<li class="file-stats">
<a href="#ec3d485ecbd319c1764899871439eda31553bf1b">
tests/testbw2.bed.min
</a>
</li>
<li class="file-stats">
<a href="#c33e1179ce1ed885028a931c4e16b57821fa67c9">
tests/testbw2.bed.out.tsv
</a>
</li>
</ul>
<h5 style="margin-top: 10px; margin-bottom: 10px; font-size: .875rem;">
The diff was not included because it is too large.
</h5>

</div>
<div class="footer" style="margin-top: 10px;">
<p style="font-size: small; color: #626168;">

<br>
<a href="https://salsa.debian.org/med-team/megadepth/-/compare/aa371401ed6f213287aca0e5a7b868db05e6a93b...db5fbdc60505f07a9a5acd6f44bacc666e284781">View it on GitLab</a>.
<br>
You're receiving this email because of your account on <a target="_blank" rel="noopener noreferrer" href="https://salsa.debian.org">salsa.debian.org</a>. <a href="https://salsa.debian.org/-/profile/notifications" target="_blank" rel="noopener noreferrer" class="mng-notif-link">Manage all notifications</a> · <a href="https://salsa.debian.org/help" target="_blank" rel="noopener noreferrer" class="help-link">Help</a>
<span style="color: transparent; font-size: 0; display: none; overflow: hidden; opacity: 0; width: 0; height: 0; max-width: 0; max-height: 0;">
Notification message regarding https://salsa.debian.org/med-team/megadepth/-/compare/aa371401ed6f213287aca0e5a7b868db05e6a93b...db5fbdc60505f07a9a5acd6f44bacc666e284781 at 1760857033
</span>



</p>
</div>
</body>
</html>