<!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: hsla(0,0%,100%,.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: hsla(0,0%,100%,.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 upstream at <a href="https://salsa.debian.org/med-team/sortmerna">Debian Med / sortmerna</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/sortmerna/-/commit/dd6a730d3de721b2c0430563429a75d7fb8f9d2d">dd6a730d</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2026-09-17T08:15:40+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 7.0.0</pre>
</li>
<li>
<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/sortmerna/-/commit/5f68260340054634d63601355c3bcd370c15f33a">5f682603</a></strong>
<div>
<span> by Andreas Tille </span> <i> at 2026-10-19T14:40:31+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 7.1.0</pre>
</li>
</ul>
<h4 style="margin-top: 10px; margin-bottom: 10px;">
258 changed files:
</h4>
<ul>
<li class="file-stats">
<a href="#add24da63784daf4acbf844c22fc7a2a36b80459">
.github/workflows/build_linux.yml
</a>
</li>
<li class="file-stats">
<a href="#121e7eec6593be5c5f305bcc43e4fe441404806d">
<span class="new-file">
+
.github/workflows/build_linux_arm64.yml
</span>
</a>
</li>
<li class="file-stats">
<a href="#fa81809ff864bef64d9685b419727db01828d69f">
.github/workflows/build_multi_platform.yml
</a>
</li>
<li class="file-stats">
<a href="#f0d7db178c1e62b9b5f7cb8999ff270e00c6f6e5">
.github/workflows/build_osx.yml
</a>
</li>
<li class="file-stats">
<a href="#d399ec3b5e0f008cc57b0efa7a0880b487fa4abc">
<span class="deleted-file">
−
.github/workflows/build_windows.yml
</span>
</a>
</li>
<li class="file-stats">
<a href="#16911b9809e0d05b7b124ba8453fa5303d74924c">
<span class="new-file">
+
.github/workflows/release.yml
</span>
</a>
</li>
<li class="file-stats">
<a href="#a5cc2925ca8258af241be7e5b0381edf30266302">
.gitignore
</a>
</li>
<li class="file-stats">
<a href="#0fef6c45e48f5bbbf478ab9c5dc2c0c3fc29c8fd">
3rdparty.jinja
</a>
</li>
<li class="file-stats">
<a href="#0a47600d43022ce06918a7df733713df5e62808d">
3rdparty/alp/CMakeLists.txt
</a>
</li>
<li class="file-stats">
<a href="#5ffb845f90d6ed89c7aa2ffecacb4bf0d2657d2d">
<span class="deleted-file">
−
3rdparty/cmph/CMakeLists.txt
</span>
</a>
</li>
<li class="file-stats">
<a href="#fc8d98cf3097a96b3072ea12e9109648574f6da7">
<span class="deleted-file">
−
3rdparty/cmph/bdz.c
</span>
</a>
</li>
<li class="file-stats">
<a href="#d16f3f2ca4e558023cb1df8b97afa8036c0617b9">
<span class="deleted-file">
−
3rdparty/cmph/bdz.h
</span>
</a>
</li>
<li class="file-stats">
<a href="#81d2e198f86b70827e92fa4ea979bede7a045d66">
<span class="deleted-file">
−
3rdparty/cmph/bdz_ph.c
</span>
</a>
</li>
<li class="file-stats">
<a href="#d59c858c1af184bb49806e7f392adc5ee693a9ec">
<span class="deleted-file">
−
3rdparty/cmph/bdz_ph.h
</span>
</a>
</li>
<li class="file-stats">
<a href="#69b53bb16d9b45485560d7eb4b4ff8be4fd439ff">
<span class="deleted-file">
−
3rdparty/cmph/bdz_structs.h
</span>
</a>
</li>
<li class="file-stats">
<a href="#a89f3381a7717ec433f3496cc39e21abee6eaada">
<span class="deleted-file">
−
3rdparty/cmph/bdz_structs_ph.h
</span>
</a>
</li>
<li class="file-stats">
<a href="#aeb14729a7f06c1fac2b9e5793c1d10901e3e767">
<span class="deleted-file">
−
3rdparty/cmph/bitbool.h
</span>
</a>
</li>
<li class="file-stats">
<a href="#49de2b7072f2e8180201b48122cc6825c20c61cf">
<span class="deleted-file">
−
3rdparty/cmph/bmz.c
</span>
</a>
</li>
<li class="file-stats">
<a href="#9afcd4bb77eee64abbcb5021d0a765b92ac7dd21">
<span class="deleted-file">
−
3rdparty/cmph/bmz.h
</span>
</a>
</li>
<li class="file-stats">
<a href="#fd5889d9bb776bbf9e067e2e2ebdab539256788d">
<span class="deleted-file">
−
3rdparty/cmph/bmz8.c
</span>
</a>
</li>
<li class="file-stats">
<a href="#4233986e95f81881b3076941cbe917c501a836e6">
<span class="deleted-file">
−
3rdparty/cmph/bmz8.h
</span>
</a>
</li>
<li class="file-stats">
<a href="#5983124549f8fb5cc5270a8873d0cf8a993c4788">
<span class="deleted-file">
−
3rdparty/cmph/bmz8_structs.h
</span>
</a>
</li>
<li class="file-stats">
<a href="#f9bd2549238b6c7622ff79759779de98f111d7bd">
<span class="deleted-file">
−
3rdparty/cmph/bmz_structs.h
</span>
</a>
</li>
<li class="file-stats">
<a href="#33590dc49843553169e7a8218dbe35571fec9945">
<span class="deleted-file">
−
3rdparty/cmph/brz.c
</span>
</a>
</li>
<li class="file-stats">
<a href="#6babe8bcc19f974e066dcf20566f614123296c62">
<span class="deleted-file">
−
3rdparty/cmph/brz.h
</span>
</a>
</li>
<li class="file-stats">
<a href="#f1add404cedf9b26a434fe64918421992e2e080c">
<span class="deleted-file">
−
3rdparty/cmph/brz_structs.h
</span>
</a>
</li>
<li class="file-stats">
<a href="#b52ca71420d9a1069fac3c836bacf236a265157d">
<span class="deleted-file">
−
3rdparty/cmph/buffer_entry.c
</span>
</a>
</li>
<li class="file-stats">
<a href="#72aa82d7111ba0809848c78ecff0e9d0f662e46b">
<span class="deleted-file">
−
3rdparty/cmph/buffer_entry.h
</span>
</a>
</li>
<li class="file-stats">
<a href="#02a3c80630849369f7cc41c588a1c7f1f02e00e1">
<span class="deleted-file">
−
3rdparty/cmph/buffer_manager.c
</span>
</a>
</li>
<li class="file-stats">
<a href="#b58d93491590ea706105d7175a993db79fd1de50">
<span class="deleted-file">
−
3rdparty/cmph/buffer_manager.h
</span>
</a>
</li>
<li class="file-stats">
<a href="#4c243360a660ce7c390f1bc4b772b6857e2ce65b">
<span class="deleted-file">
−
3rdparty/cmph/chd.c
</span>
</a>
</li>
<li class="file-stats">
<a href="#2cacbead374da140f50135efd33a2a1c2e7d75d3">
<span class="deleted-file">
−
3rdparty/cmph/chd.h
</span>
</a>
</li>
<li class="file-stats">
<a href="#1981a0a2f094ce686c3c8100ccde26c332f10f57">
<span class="deleted-file">
−
3rdparty/cmph/chd_ph.c
</span>
</a>
</li>
<li class="file-stats">
<a href="#afa519c090b982bdc69bba597458c584d799e74f">
<span class="deleted-file">
−
3rdparty/cmph/chd_ph.h
</span>
</a>
</li>
<li class="file-stats">
<a href="#ec4cf8ac8a32690b9e3245781fa26c65b8f8d4b7">
<span class="deleted-file">
−
3rdparty/cmph/chd_structs.h
</span>
</a>
</li>
<li class="file-stats">
<a href="#4354b7d9cd24b15ce5021b97ba1f0e4762c73321">
<span class="deleted-file">
−
3rdparty/cmph/chd_structs_ph.h
</span>
</a>
</li>
<li class="file-stats">
<a href="#bdcf0f03fbdae0c21c44d8d216acb6d6da0d9176">
<span class="deleted-file">
−
3rdparty/cmph/chm.c
</span>
</a>
</li>
<li class="file-stats">
<a href="#294206870ee3d580b91fdc51601a8c6a14b5b5df">
<span class="deleted-file">
−
3rdparty/cmph/chm.h
</span>
</a>
</li>
<li class="file-stats">
<a href="#5eca40f39aceeffeb08ee07c725e3b8990ba5a39">
<span class="deleted-file">
−
3rdparty/cmph/chm_structs.h
</span>
</a>
</li>
<li class="file-stats">
<a href="#56d96f7f3bccf9bb68f51257ffed4ca5f199c743">
<span class="deleted-file">
−
3rdparty/cmph/cmph.c
</span>
</a>
</li>
<li class="file-stats">
<a href="#23c21de2ecabae9c5e8ba245ef69316b5b7f379f">
<span class="deleted-file">
−
3rdparty/cmph/cmph.h
</span>
</a>
</li>
<li class="file-stats">
<a href="#0ec5154ccf827dd3c9b2323122d73ba7cc33077a">
<span class="deleted-file">
−
3rdparty/cmph/cmph_structs.c
</span>
</a>
</li>
<li class="file-stats">
<a href="#04c62ad72bff8a1b8f4e820ec4f9ea4b2d85da79">
<span class="deleted-file">
−
3rdparty/cmph/cmph_structs.h
</span>
</a>
</li>
<li class="file-stats">
<a href="#afda719c48972d77d7a7515e12c3fb808aeda7b6">
<span class="deleted-file">
−
3rdparty/cmph/cmph_time.h
</span>
</a>
</li>
<li class="file-stats">
<a href="#98ad543e4195293f2ac7bdd4a82b831815affd46">
<span class="deleted-file">
−
3rdparty/cmph/cmph_types.h
</span>
</a>
</li>
<li class="file-stats">
<a href="#f49b261235efedaebfb8a6b45fabfe2985ac10ef">
<span class="deleted-file">
−
3rdparty/cmph/compressed_rank.c
</span>
</a>
</li>
<li class="file-stats">
<a href="#dcc52f1ec0370b45d360295594335815cc88557b">
<span class="deleted-file">
−
3rdparty/cmph/compressed_rank.h
</span>
</a>
</li>
<li class="file-stats">
<a href="#cd1223cca52fe9f1d021aaebcb7e65144b62e9c8">
<span class="deleted-file">
−
3rdparty/cmph/compressed_seq.c
</span>
</a>
</li>
<li class="file-stats">
<a href="#7a75251b4d9aca8209487b3fc124832170585f86">
<span class="deleted-file">
−
3rdparty/cmph/compressed_seq.h
</span>
</a>
</li>
<li class="file-stats">
<a href="#2231b32edf3fc64143282fc273083a480f5a2dd6">
<span class="deleted-file">
−
3rdparty/cmph/debug.h
</span>
</a>
</li>
<li class="file-stats">
<a href="#660600b30a1846be5a4eda5d7e5de046518a2fd4">
<span class="deleted-file">
−
3rdparty/cmph/fch.c
</span>
</a>
</li>
<li class="file-stats">
<a href="#650d7be262673f62b41f0084d15875ada91a6a52">
<span class="deleted-file">
−
3rdparty/cmph/fch.h
</span>
</a>
</li>
<li class="file-stats">
<a href="#f718d43c2dd72ac5ea083b315c37d8bce64c703d">
<span class="deleted-file">
−
3rdparty/cmph/fch_buckets.c
</span>
</a>
</li>
<li class="file-stats">
<a href="#f5a60c613fea72e3377987f2da90366d5f8b07e5">
<span class="deleted-file">
−
3rdparty/cmph/fch_buckets.h
</span>
</a>
</li>
<li class="file-stats">
<a href="#19d9ea41599d50bdb370fc1a5d652285fd485637">
<span class="deleted-file">
−
3rdparty/cmph/fch_structs.h
</span>
</a>
</li>
<li class="file-stats">
<a href="#9aefac64e9f8d4086822ffa5252526000d40aa7f">
<span class="deleted-file">
−
3rdparty/cmph/graph.c
</span>
</a>
</li>
<li class="file-stats">
<a href="#6e70ae289e5ecd8863f537835ff208ccf7d44e6a">
<span class="deleted-file">
−
3rdparty/cmph/graph.h
</span>
</a>
</li>
<li class="file-stats">
<a href="#709298ced821f9c1bc2d06a4272b105b8a319bb5">
<span class="deleted-file">
−
3rdparty/cmph/hash.c
</span>
</a>
</li>
<li class="file-stats">
<a href="#94e7ad72ddb4038cfd8b1a0564f9948aea036b68">
<span class="deleted-file">
−
3rdparty/cmph/hash.h
</span>
</a>
</li>
<li class="file-stats">
<a href="#f3a9189139fd7ae992e75bd71b55c38c9fa947e2">
<span class="deleted-file">
−
3rdparty/cmph/hash_state.h
</span>
</a>
</li>
<li class="file-stats">
<a href="#3ead2090df35f14359d2a65db892011119dc201b">
<span class="deleted-file">
−
3rdparty/cmph/jenkins_hash.c
</span>
</a>
</li>
<li class="file-stats">
<a href="#1e82783563faeeb22d616d9d549a25c0f8c7d2d2">
<span class="deleted-file">
−
3rdparty/cmph/jenkins_hash.h
</span>
</a>
</li>
<li class="file-stats">
<a href="#640d775b6f3c15886e79d810d61b3cd1c631d483">
<span class="deleted-file">
−
3rdparty/cmph/miller_rabin.c
</span>
</a>
</li>
<li class="file-stats">
<a href="#ef4449878e8240b80b9391c251b360d76b0fa777">
<span class="deleted-file">
−
3rdparty/cmph/miller_rabin.h
</span>
</a>
</li>
<li class="file-stats">
<a href="#5cee896012f0bba07bbf36e7bfe08cd3f97b7189">
<span class="deleted-file">
−
3rdparty/cmph/select.c
</span>
</a>
</li>
<li class="file-stats">
<a href="#6ecd2a1783186d0b64882e11bbf30e1822b529df">
<span class="deleted-file">
−
3rdparty/cmph/select.h
</span>
</a>
</li>
<li class="file-stats">
<a href="#8d3005561c6fa7ee969a07be02ec6056ad75bc6c">
<span class="deleted-file">
−
3rdparty/cmph/select_lookup_tables.h
</span>
</a>
</li>
<li class="file-stats">
<a href="#a856acc71458c073dc11655c47be18b3164e804b">
<span class="deleted-file">
−
3rdparty/cmph/vqueue.c
</span>
</a>
</li>
<li class="file-stats">
<a href="#b9ffe27d23a70d7f799197645fb1c7a72103430c">
<span class="deleted-file">
−
3rdparty/cmph/vqueue.h
</span>
</a>
</li>
<li class="file-stats">
<a href="#cb1951735cfd3053f15cc079d3f6154a7f36b61c">
<span class="deleted-file">
−
3rdparty/cmph/vstack.c
</span>
</a>
</li>
<li class="file-stats">
<a href="#8f9eb9d2e7397d4a1d1737e78205989b619e45f6">
<span class="deleted-file">
−
3rdparty/cmph/vstack.h
</span>
</a>
</li>
<li class="file-stats">
<a href="#9a2aa4db38d3115ed60da621e012c0efc0172aae">
CMakeLists.txt
</a>
</li>
<li class="file-stats">
<a href="#f0cbc676dbcedaa2eb3debb256d34cfd1c889d9d">
CMakePresets.json
</a>
</li>
<li class="file-stats">
<a href="#6651ddff6eb82c840ced7c1dddee15c6e1913dd4">
Dockerfile
</a>
</li>
<li class="file-stats">
<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
README.md
</a>
</li>
<li class="file-stats">
<a href="#eade553d6e721bf11082bd8726a6a8553747ab5a">
<span class="new-file">
+
cmake/bundle_static_libs.cmake
</span>
</a>
</li>
<li class="file-stats">
<a href="#d86c803c1dc3b432debdc25ae66f94ae54906e0b">
<span class="new-file">
+
cmake/conda_tc.cmake
</span>
</a>
</li>
<li class="file-stats">
<a href="#3916f7fbb6b50c8568c46fd5c37701245396b98c">
cmake/presets/CMakePresets_rocksdb.json
</a>
</li>
<li class="file-stats">
<a href="#24010de985d08575ca45ca1c68f3a6f6cc2bfb05">
<span class="deleted-file">
−
cmake/sortmernaConfig.cmake.in
</span>
</a>
</li>
<li class="file-stats">
<a href="#8fef376fbf37bb8f19d9e8a5faffe89af941bbdc">
<span class="new-file">
+
conda_build_env.yaml
</span>
</a>
</li>
<li class="file-stats">
<a href="#1b753e335da548078b79fa22f9207a5415b23103">
<span class="new-file">
+
conda_run_env.yaml
</span>
</a>
</li>
<li class="file-stats">
<a href="#28e91c59ac5ed7ec5ee70a504c9d12546ed62813">
<span class="new-file">
+
copyright.tmpl
</span>
</a>
</li>
<li class="file-stats">
<a href="#18b7e2bab82b090db578519687e5cf1825c61b7b">
<span class="new-file">
+
docs/c_api.rst
</span>
</a>
</li>
<li class="file-stats">
<a href="#d0153cac95479af9bfb99b746b633bc8255bb53a">
docs/index.rst
</a>
</li>
<li class="file-stats">
<a href="#6e3a5acd9f36652777c70fa548686dfe935f5e40">
include/ThreadPool.hpp
</a>
</li>
<li class="file-stats">
<a href="#b4860b32f4a80b96c75e9c5963a80be63304cac5">
include/alignment.hpp
</a>
</li>
<li class="file-stats">
<a href="#302bf2ebbeeb92578426b41137339fea10b0e5a1">
include/baserec.hpp
</a>
</li>
<li class="file-stats">
<a href="#09e7dfdc4cef5c885f5e9f76add7fa6c50bb46ab">
include/bitvector.hpp
</a>
</li>
<li class="file-stats">
<a href="#3ce824bff15707960d9fba8513f22e8c14ec6524">
include/build_version.h
</a>
</li>
<li class="file-stats">
<a href="#37bb94a74929cecbc557272b1726d57014d98080">
include/cmd.hpp
</a>
</li>
<li class="file-stats">
<a href="#ff35dcdbf88c10200073b0872754929a17c68e29">
include/common.hpp
</a>
</li>
<li class="file-stats">
<a href="#9766850dd15eda814b4642d6fe752eb4f7de12c4">
include/config.h
</a>
</li>
<li class="file-stats">
<a href="#c8ab16776d22b8e61ae6b9434614c6b2f20cdbb2">
include/index.hpp
</a>
</li>
<li class="file-stats">
<a href="#13a0d1bb234ad42de4d2934b5ac06794599697e5">
include/indexdb.hpp
</a>
</li>
<li class="file-stats">
<a href="#d9ee123602b5b4a7d8c8e23900304cf182702dbd">
include/izlib.hpp
</a>
</li>
<li class="file-stats">
<a href="#2e99168c53e1d521ddcc1d1317d6e49eceef2b30">
include/kseq_load.hpp
</a>
</li>
<li class="file-stats">
<a href="#f01c12dadc7790fb7c5f60e63f7527c9b33513c8">
include/kvdb.hpp
</a>
</li>
<li class="file-stats">
<a href="#9e6a79b1b8fbefd86f1a802f5d112b90d405a326">
include/loadgenome.hpp
</a>
</li>
<li class="file-stats">
<a href="#4e38a515cb0b22169f28370c648721ecf644582b">
include/minoccur.hpp
</a>
</li>
<li class="file-stats">
<a href="#1ecbec90a961dc3bfd1c2fc9bdc23013f9499f0b">
include/options.hpp
</a>
</li>
<li class="file-stats">
<a href="#d94fc1ce9ff47afa5c59c6efb73f4c9d0cdfaced">
include/otumap.h
</a>
</li>
<li class="file-stats">
<a href="#1bfef381baacd1f70c8067fa2351bde4d423f63d">
include/output.hpp
</a>
</li>
<li class="file-stats">
<a href="#39b9014931ac0bf9dfd48e142d12553be8322b4a">
include/paralleltraversal.hpp
</a>
</li>
<li class="file-stats">
<a href="#c9e553a1365a342a2fdeafc48824f028d6011aeb">
include/processor.hpp
</a>
</li>
<li class="file-stats">
<a href="#521b1b3525a3cc8f78e2dc541e561a8907095abd">
include/read.hpp
</a>
</li>
<li class="file-stats">
<a href="#bde4e46a971ca1c609595f9355cb5fdf9a8dc16d">
include/readfeed.hpp
</a>
</li>
<li class="file-stats">
<a href="#791d447902a107e4ad558232e67ee400d6a95e74">
include/readfile.h
</a>
</li>
<li class="file-stats">
<a href="#efd9d6b84f141d436efe7d8b2c37cf5ae75b6157">
<span class="deleted-file">
−
include/readsqueue.hpp
</span>
</a>
</li>
<li class="file-stats">
<a href="#a25c35836e3da1d3ab8cc0b6ca48775a8d4c2cec">
include/readstate.h
</a>
</li>
<li class="file-stats">
<a href="#e50618b8cb0abe850cebe5565b131ef07f7d9d63">
include/readstats.hpp
</a>
</li>
<li class="file-stats">
<a href="#ea70ae6b41dac8e51bdf1b82f68b586e56970151">
include/references.hpp
</a>
</li>
<li class="file-stats">
<a href="#fabf1ae42341f1fae2e4b33c4333a1755572cabb">
include/refstats.hpp
</a>
</li>
<li class="file-stats">
<a href="#d1244561665c90fbcd229f5ff9649be04874bbd0">
include/report.h
</a>
</li>
<li class="file-stats">
<a href="#39b161dd42de3bf5a9baa018fd5778abae86238f">
include/report_biom.h
</a>
</li>
<li class="file-stats">
<a href="#203e7c9146984d0a3cf41d8b1aaa8d293ac13482">
include/report_blast.h
</a>
</li>
<li class="file-stats">
<a href="#920c4c1f3d3aa2cf9fdeb21b793ac8345bba5553">
include/report_denovo.h
</a>
</li>
<li class="file-stats">
<a href="#2ba0979d92567e1a9e71df062532d9327155ce42">
include/report_fastx.h
</a>
</li>
<li class="file-stats">
<a href="#372f4b1b8f3a72448572b6ca3f56d41f9f286f32">
include/report_fx_base.h
</a>
</li>
<li class="file-stats">
<a href="#756d338b1c3f234581b889413a867505b4012622">
include/report_fx_other.h
</a>
</li>
<li class="file-stats">
<a href="#f9456f7bd65feb0d291b7f827bb2a328bc850f20">
include/report_sam.h
</a>
</li>
<li class="file-stats">
<a href="#273cbb87ea41a94e51f5faf7587cfd2f5435e98d">
<span class="new-file">
+
include/restart.hpp
</span>
</a>
</li>
<li class="file-stats">
<a href="#36ab8127088f3547dd555e3342490a737ebc3327">
<span class="new-file">
+
include/smr_api.h
</span>
</a>
</li>
<li class="file-stats">
<a href="#177e7bba1794450710e3ce48f9d8ff1df0dc2fea">
<span class="deleted-file">
−
include/ssw.h
</span>
</a>
</li>
<li class="file-stats">
<a href="#ee649556f865f00c1190cdfe26e55e831316c870">
include/ssw.hpp
</a>
</li>
<li class="file-stats">
<a href="#9e11240b4f15ce8556d7647299994e979ecde8a6">
include/summary.hpp
</a>
</li>
<li class="file-stats">
<a href="#3e5e210c63dfd7fa0ea7c9db4009c98bf28a6dc0">
<span class="new-file">
+
include/thread_errors.hpp
</span>
</a>
</li>
<li class="file-stats">
<a href="#500543d65ed814c8128fc346103d7b2ac599aad2">
include/traverse_bursttrie.hpp
</a>
</li>
<li class="file-stats">
<a href="#4ca51e70eb2054db254d3241323b9a0ec8ea0320">
include/triestats.hpp
</a>
</li>
<li class="file-stats">
<a href="#c879736bc4600d92e5683925c65282a9ab8989b8">
include/version.h
</a>
</li>
<li class="file-stats">
<a href="#f0fb38cb13e113ebb3d5159d37a92164a3eb652a">
<span class="deleted-file">
−
include/writer.hpp
</span>
</a>
</li>
<li class="file-stats">
<a href="#051ccf7e31df4db8e0788c5f5e2c0207fa640d47">
scripts/env.jinja
</a>
</li>
<li class="file-stats">
<a href="#4354d406843cb3f412bd162afb1c622929158759">
<span class="new-file">
+
scripts/presets.tmpl.yaml
</span>
</a>
</li>
<li class="file-stats">
<a href="#8a3150135563589478ad1bf5c0d5d367af567448">
scripts/run.py
</a>
</li>
<li class="file-stats">
<a href="#ae356cb8c62345a7f1c533d8f0bc3af6aeb46f68">
<span class="new-file">
+
scripts/t18.jinja
</span>
</a>
</li>
<li class="file-stats">
<a href="#f2bb5a29d764e8c6dd89c7d629236883f37c0e8b">
<span class="new-file">
+
scripts/t18_1.jinja
</span>
</a>
</li>
<li class="file-stats">
<a href="#2ce078e2e0ebc6d1e84bf955a434286f103d9300">
<span class="new-file">
+
scripts/t18_6.jinja
</span>
</a>
</li>
<li class="file-stats">
<a href="#ebe78b37d6ef376faaba56ff9285eb6acdd4f722">
<span class="new-file">
+
scripts/t19.jinja
</span>
</a>
</li>
<li class="file-stats">
<a href="#868309133f0f20c8ea26025fd97f46b5efe434d7">
<span class="new-file">
+
scripts/t19_1.jinja
</span>
</a>
</li>
<li class="file-stats">
<a href="#9c890fb10bbf58a3a7376b2c2a03766fbf1ffedd">
<span class="new-file">
+
scripts/t19_3.jinja
</span>
</a>
</li>
<li class="file-stats">
<a href="#7f89c5caa45ee757da1468ea3aa903ea604cf1cb">
<span class="new-file">
+
scripts/t19_5.jinja
</span>
</a>
</li>
<li class="file-stats">
<a href="#a013efe24bb94d4097f4714cd84a18ec511a5689">
<span class="new-file">
+
scripts/t19_6.jinja
</span>
</a>
</li>
<li class="file-stats">
<a href="#6e8579c2cc07787a1f7c78ed899ab079adfa4045">
<span class="new-file">
+
scripts/t19_7.jinja
</span>
</a>
</li>
<li class="file-stats">
<a href="#e6b6dcabd22eee3c5a4a659c07f54e729d0e8b40">
<span class="new-file">
+
scripts/t2.jinja
</span>
</a>
</li>
<li class="file-stats">
<a href="#0b8771223798828873a053ae325cac0d67a7a775">
<span class="new-file">
+
scripts/t20.jinja
</span>
</a>
</li>
<li class="file-stats">
<a href="#da84ba33576e9f7f76da9ddcd55f7676595a3b93">
<span class="new-file">
+
scripts/t20_1.jinja
</span>
</a>
</li>
<li class="file-stats">
<a href="#d83bedae64e7b2e290764f0211c787d7836b12db">
<span class="new-file">
+
scripts/t20_5.jinja
</span>
</a>
</li>
<li class="file-stats">
<a href="#47af5b387e434a97342c492f284e22571261fde2">
<span class="new-file">
+
scripts/t20_6.jinja
</span>
</a>
</li>
<li class="file-stats">
<a href="#dd7f7d4de842bd75125798218c704228d1e3983b">
<span class="new-file">
+
scripts/t2_1.jinja
</span>
</a>
</li>
<li class="file-stats">
<a href="#d7dde2852f9dc82bbd4be8eb5b173d7bce63e67b">
<span class="new-file">
+
scripts/t3.jinja
</span>
</a>
</li>
<li class="file-stats">
<a href="#950633ffd1db8bbe9460b8949deba2c182fdeb3e">
<span class="new-file">
+
scripts/t38.jinja
</span>
</a>
</li>
<li class="file-stats">
<a href="#7b541b8bc8724c9c43bb877dac66756a4000ca40">
<span class="new-file">
+
scripts/t39.jinja
</span>
</a>
</li>
<li class="file-stats">
<a href="#3d017d154c1f24288c9abab0933221dbf8d8db12">
<span class="new-file">
+
scripts/t3_1.jinja
</span>
</a>
</li>
<li class="file-stats">
<a href="#82ddc22ab56537dd52eb3ac8b78a240b0fd15efd">
<span class="new-file">
+
scripts/t41.jinja
</span>
</a>
</li>
<li class="file-stats">
<a href="#84afbfb069741eb8a74fd46b25c9d5e9f75a6c0c">
<span class="new-file">
+
scripts/t43.jinja
</span>
</a>
</li>
<li class="file-stats">
<a href="#43882f1417120930ddd410eb74690988316a9e91">
<span class="new-file">
+
scripts/t46.jinja
</span>
</a>
</li>
<li class="file-stats">
<a href="#1e986502631d67ecad992e12cf70b0da3806c643">
<span class="new-file">
+
scripts/t52.jinja
</span>
</a>
</li>
<li class="file-stats">
<a href="#f3e17b783ca3bb65093e6fe6b2c950a77b97f12e">
<span class="new-file">
+
scripts/t53.jinja
</span>
</a>
</li>
<li class="file-stats">
<a href="#b2f0abd057808499212c2ee44340ae09578b1f8e">
<span class="new-file">
+
scripts/t54.jinja
</span>
</a>
</li>
<li class="file-stats">
<a href="#166058b2c22f9276a984a8852363a3774fe2723f">
<span class="new-file">
+
scripts/t54_1.jinja
</span>
</a>
</li>
<li class="file-stats">
<a href="#aed49e0554bff63ee5062b74d3ec4b3aa515a3c6">
<span class="new-file">
+
scripts/t55.jinja
</span>
</a>
</li>
<li class="file-stats">
<a href="#65625c367feee139516086130bd2166661311a4a">
<span class="new-file">
+
scripts/t55_1.jinja
</span>
</a>
</li>
<li class="file-stats">
<a href="#ac809cb46488af36ba405441477b3f8eac011afd">
<span class="new-file">
+
scripts/t56.jinja
</span>
</a>
</li>
<li class="file-stats">
<a href="#8206434137cae389c59c7d35dca88f96d1e42d81">
<span class="new-file">
+
scripts/t57.jinja
</span>
</a>
</li>
<li class="file-stats">
<a href="#b916474de2fc63c88d4c4dac8023ab02f2fd90a2">
scripts/test.jinja
</a>
</li>
<li class="file-stats">
<a href="#308a17a75ad1135688d635deaaa9950ab1dc6b99">
<span class="new-file">
+
scripts/update_copyright_header.py
</span>
</a>
</li>
<li class="file-stats">
<a href="#8e2edce0d507e1297474f25c00cae94258db38d8">
setup.py
</a>
</li>
<li class="file-stats">
<a href="#1f55fba454d76567e8257fee5dad04f7d9f757a0">
<span class="new-file">
+
src/smr_api/CMakeLists.txt
</span>
</a>
</li>
<li class="file-stats">
<a href="#a1c630e00ee04dbb14dc02e0843d3964b6627f65">
<span class="new-file">
+
src/smr_api/smr_api.cpp
</span>
</a>
</li>
<li class="file-stats">
<a href="#31a9658c812c42235e70c41d2c95d333f250526f">
src/sortmerna/CMakeLists.txt
</a>
</li>
<li class="file-stats">
<a href="#e62e38daf3118dc90764ff6cfcfdb51090fc230a">
src/sortmerna/alignment.cpp
</a>
</li>
<li class="file-stats">
<a href="#ac487d02a447995910657266f7697167d600e3c0">
src/sortmerna/bitvector.cpp
</a>
</li>
<li class="file-stats">
<a href="#1344d01b5987019418cf2376f9ac8740940d1c00">
src/sortmerna/cmd.cpp
</a>
</li>
<li class="file-stats">
<a href="#59ef61626a24d6cb683cbcaa272e858825f41ea2">
src/sortmerna/index.cpp
</a>
</li>
<li class="file-stats">
<a href="#13cc7bb3704e808dc4e0910927969e5f71931735">
src/sortmerna/indexdb.cpp
</a>
</li>
<li class="file-stats">
<a href="#edb57ebb3730a7190c969b70d239a9ae7a041cc0">
src/sortmerna/izlib.cpp
</a>
</li>
<li class="file-stats">
<a href="#68af66743d8bdcc81ef159546b0155a69d0cabf9">
src/sortmerna/kseq_load.cpp
</a>
</li>
<li class="file-stats">
<a href="#9d476e474046263f066ee947f6f9aaaee2f72988">
src/sortmerna/kvdb.cpp
</a>
</li>
<li class="file-stats">
<a href="#859cabcfd50174da31866ca763321be57fc6ff15">
src/sortmerna/main.cpp
</a>
</li>
<li class="file-stats">
<a href="#94ee4a145120a99b9ba0e9b682ea17796851712f">
src/sortmerna/minoccur.cpp
</a>
</li>
<li class="file-stats">
<a href="#17d2386c3b6e144938752d248abb68e461a9314f">
src/sortmerna/options.cpp
</a>
</li>
<li class="file-stats">
<a href="#560b4d4991845de69095e065de65641b675f9066">
src/sortmerna/otumap.cpp
</a>
</li>
<li class="file-stats">
<a href="#f8978cd6271b51c1dd88253118a657c8db90b07f">
src/sortmerna/output.cpp
</a>
</li>
<li class="file-stats">
<a href="#bfd196ff030b8d9b7bdb7dfc994dbf8472ed0fc9">
src/sortmerna/paralleltraversal.cpp
</a>
</li>
<li class="file-stats">
<a href="#9a56cf64342e79fe62ab6f5e894e03c908f7f953">
src/sortmerna/processor.cpp
</a>
</li>
<li class="file-stats">
<a href="#5d4a6a46daf19bcd2b394016d0bb3f69a029cf88">
src/sortmerna/read.cpp
</a>
</li>
<li class="file-stats">
<a href="#437a786b9cdd4b5c16576defc43c22b71e9a62e8">
<span class="deleted-file">
−
src/sortmerna/read_control.cpp
</span>
</a>
</li>
<li class="file-stats">
<a href="#63a33e7cfd415f3217763120d32f0e6fb5eee134">
src/sortmerna/readfeed.cpp
</a>
</li>
<li class="file-stats">
<a href="#844832c4d105f9ec6ddd115f0a567a15f382fea4">
src/sortmerna/readstats.cpp
</a>
</li>
<li class="file-stats">
<a href="#360920ae0c36aec3125f9f96cced5033fee4ac12">
src/sortmerna/references.cpp
</a>
</li>
<li class="file-stats">
<a href="#c6b47873d70575669f7a4aef5e3af315449721ac">
src/sortmerna/refstats.cpp
</a>
</li>
<li class="file-stats">
<a href="#78121f48ad301e467c4119999673dcf60fd54eea">
src/sortmerna/report.cpp
</a>
</li>
<li class="file-stats">
<a href="#6436110a5ee909bc054ca4b7b7faae1d36d4f8a7">
src/sortmerna/report_biom.cpp
</a>
</li>
<li class="file-stats">
<a href="#4d64e361e15e60d642f9afea31801e98dd843a6c">
src/sortmerna/report_blast.cpp
</a>
</li>
<li class="file-stats">
<a href="#13c4aea8cfe3a691adbef396003206faed9c7a82">
src/sortmerna/report_denovo.cpp
</a>
</li>
<li class="file-stats">
<a href="#fcab626aea9656a15d3d2d5efba209d20701ff69">
src/sortmerna/report_fastx.cpp
</a>
</li>
<li class="file-stats">
<a href="#4e325cd22506d9d4b0f57af9e6601e0db07e2c81">
src/sortmerna/report_fx_base.cpp
</a>
</li>
<li class="file-stats">
<a href="#83598a525db4af5740bbf51553f35db778881e20">
src/sortmerna/report_fx_other.cpp
</a>
</li>
<li class="file-stats">
<a href="#227604ab698e2aa3655f592e8172dd8ab5889b04">
src/sortmerna/report_sam.cpp
</a>
</li>
<li class="file-stats">
<a href="#9e11cdefa1bc77e635d000058aed46590fab640c">
<span class="new-file">
+
src/sortmerna/restart.cpp
</span>
</a>
</li>
<li class="file-stats">
<a href="#d4f30ee637b0f2685c79ca1a726c5fe3907e68a1">
<span class="new-file">
+
src/sortmerna/smr_log.cpp
</span>
</a>
</li>
<li class="file-stats">
<a href="#7e4736ff323c741ed6640ae63b46f5d2c2ad9928">
<span class="deleted-file">
−
src/sortmerna/ssw.c
</span>
</a>
</li>
<li class="file-stats">
<a href="#0747d5a4a551733a063d90edee11038654a18a9e">
src/sortmerna/summary.cpp
</a>
</li>
<li class="file-stats">
<a href="#4fa575fd77961ea6aa93ed8504bf34f90caee1fb">
src/sortmerna/traverse_bursttrie.cpp
</a>
</li>
<li class="file-stats">
<a href="#5ee0886007aa991fe9f1840b24601c50a72eec2c">
src/sortmerna/util.cpp
</a>
</li>
<li class="file-stats">
<a href="#1f2d913d916ec00fb78ac8d627835ede150709ba">
<span class="deleted-file">
−
src/sortmerna/writer.cpp
</span>
</a>
</li>
<li class="file-stats">
<a href="#277843e365ce09d06783a15fe951b11bb4636309">
src/util/build_version.cpp.in
</a>
</li>
<li class="file-stats">
<a href="#90b829f742cbb603ffc792c41bd8318fc5c5165e">
<span class="deleted-file">
−
src/winapi/CMakeLists.txt
</span>
</a>
</li>
<li class="file-stats">
<a href="#fad2e56276a5b47b699152433b9c2e6d4dec830c">
<span class="deleted-file">
−
src/winapi/include/sys/time.h
</span>
</a>
</li>
<li class="file-stats">
<a href="#adf4124688d6e90689b5a659f172299cf1de1b24">
<span class="deleted-file">
−
src/winapi/include/unistd.h
</span>
</a>
</li>
<li class="file-stats">
<a href="#92764cd654f56c91a9b0e2340d1967c997f71616">
<span class="deleted-file">
−
src/winapi/unistd.cpp
</span>
</a>
</li>
<li class="file-stats">
<a href="#2f4f243f3d863ae8d6f1116146e6e7ef229ca545">
<span class="deleted-file">
−
src/winapi/wintime.cpp
</span>
</a>
</li>
<li class="file-stats">
<a href="#70a47bb4f8ad15834cc8968254be433e8e98bc77">
data/empty_file.fasta
→
test_data/empty_file.fasta
</a>
</li>
<li class="file-stats">
<a href="#1f64039ffc33afd66295d379ccfa3e4e859163b8">
data/gg_13_8_ref_set.fasta
→
test_data/gg_13_8_ref_set.fasta
</a>
</li>
<li class="file-stats">
<a href="#74bc7d3f5e2e4c5323d3c10829d9961a85b762c2">
data/illumina_GQ099317.fasta
→
test_data/illumina_GQ099317.fasta
</a>
</li>
<li class="file-stats">
<a href="#15bb468b04809f00e4f47b2b1d4b3ff6ff7854da">
data/ref_GQ099317_forward_and_rc.fasta
→
test_data/ref_GQ099317_forward_and_rc.fasta
</a>
</li>
<li class="file-stats">
<a href="#ceca70182d34d5a06e5c82fac877b4f7b972d4fb">
data/ref_short_seqs.fasta
→
test_data/ref_short_seqs.fasta
</a>
</li>
<li class="file-stats">
<a href="#11668889eb2ce666e66934c1bc07c28b209b00c7">
data/rRNA_databases/README.txt
→
test_data/refs/README.txt
</a>
</li>
<li class="file-stats">
<a href="#631c31f01acb90bc80762ec17e6c5f05c47f7caf">
data/rRNA_databases/rfam-5.8s-database-id98.fasta
→
test_data/refs/rfam-5.8s-database-id98.fasta
</a>
</li>
<li class="file-stats">
<a href="#f445da0fb238a1d12b6259826b82e0bd2567915a">
data/rRNA_databases/rfam-5s-database-id98.fasta
→
test_data/refs/rfam-5s-database-id98.fasta
</a>
</li>
<li class="file-stats">
<a href="#d47eae376b7156bbf9f80e7e9e07eb94381d3cc3">
data/rRNA_databases/scripts/edit_U_to_T_rna.py
→
test_data/refs/scripts/edit_U_to_T_rna.py
</a>
</li>
<li class="file-stats">
<a href="#f4b0828587f8810749109dc4d8b67ac81a08e8a5">
data/rRNA_databases/scripts/generate_databases.sh
→
test_data/refs/scripts/generate_databases.sh
</a>
</li>
<li class="file-stats">
<a href="#dae92b486c2e838549f5274a0a8e0026220f4278">
data/rRNA_databases/scripts/hmmer_clean.sh
→
test_data/refs/scripts/hmmer_clean.sh
</a>
</li>
<li class="file-stats">
<a href="#a51928ed9e3269afb73815eb668624ba1b82dd52">
data/rRNA_databases/silva-arc-16s-id95.fasta
→
test_data/refs/silva-arc-16s-id95.fasta
</a>
</li>
<li class="file-stats">
<a href="#90ca2b131e1b30c4b9830778d7cd53fc46b80808">
data/rRNA_databases/silva-arc-23s-id98.fasta
→
test_data/refs/silva-arc-23s-id98.fasta
</a>
</li>
<li class="file-stats">
<a href="#f9e90d99647af72057ceff29567c5d86ac5b39c6">
data/rRNA_databases/silva-bac-16s-id90.fasta
→
test_data/refs/silva-bac-16s-id90.fasta
</a>
</li>
<li class="file-stats">
<a href="#1b619971a2fc4008adbf41fbbf1d6bf2c3ba39f3">
data/rRNA_databases/silva-bac-23s-id98.fasta
→
test_data/refs/silva-bac-23s-id98.fasta
</a>
</li>
<li class="file-stats">
<a href="#6ebabc99994d5168f8861420db2c9fbd299e2bce">
data/rRNA_databases/silva-euk-18s-id95.fasta
→
test_data/refs/silva-euk-18s-id95.fasta
</a>
</li>
<li class="file-stats">
<a href="#df4d3473c23caf3de4ae1baec2e5b1fdc845dac2">
data/rRNA_databases/silva-euk-28s-id98.fasta
→
test_data/refs/silva-euk-28s-id98.fasta
</a>
</li>
<li class="file-stats">
<a href="#8ec4a4702c666efd0ce278600a61ab361cea2970">
data/rRNA_databases/silva_ids_acc_tax.tar.gz
→
test_data/refs/silva_ids_acc_tax.tar.gz
</a>
</li>
<li class="file-stats">
<a href="#6db304ff98f5c4c6812590a9bfa9065d2db29845">
data/set2_environmental_study_550_amplicon.fasta
→
test_data/set2_environmental_study_550_amplicon.fasta
</a>
</li>
<li class="file-stats">
<a href="#7f7f082160f0aec8ff7cbbed1d8881c684d7a1e6">
data/set2_environmental_study_550_amplicon.fasta.gz
→
test_data/set2_environmental_study_550_amplicon.fasta.gz
</a>
</li>
<li class="file-stats">
<a href="#561cd27b3b95ea81845abbc89dde007f547696c4">
data/set4_mate_pairs_metatranscriptomics.fastq
→
test_data/set4_mate_pairs_metatranscriptomics.fastq
</a>
</li>
<li class="file-stats">
<a href="#d4b4602170cd077dad7e1a2a0a9c45d9a5098bbf">
data/set4_mate_pairs_metatranscriptomics_1.fastq
→
test_data/set4_mate_pairs_metatranscriptomics_1.fastq
</a>
</li>
<li class="file-stats">
<a href="#09acb25da405f56b1cf679fdbc2987aca785360c">
data/set4_mate_pairs_metatranscriptomics_1.fastq.gz
→
test_data/set4_mate_pairs_metatranscriptomics_1.fastq.gz
</a>
</li>
<li class="file-stats">
<a href="#26ce2f4024281ce91ee907cbf4df5fc01db396f9">
data/set4_mate_pairs_metatranscriptomics_2.fastq
→
test_data/set4_mate_pairs_metatranscriptomics_2.fastq
</a>
</li>
<li class="file-stats">
<a href="#e49e9560bc69fb08f85bae41b16cd7216ff6afa5">
data/set4_mate_pairs_metatranscriptomics_2.fastq.gz
→
test_data/set4_mate_pairs_metatranscriptomics_2.fastq.gz
</a>
</li>
<li class="file-stats">
<a href="#8e9488ab6fdd4b4197e8224b2435b58b22bdd320">
data/set5_simulated_amplicon_silva_bac_16s.fasta
→
test_data/set5_simulated_amplicon_silva_bac_16s.fasta
</a>
</li>
<li class="file-stats">
<a href="#a726bebf807f9da4c1e2cae4d5cd29d28a0a8040">
data/set7_arc_bac_16S_database_match.fasta
→
test_data/set7_arc_bac_16S_database_match.fasta
</a>
</li>
<li class="file-stats">
<a href="#4e1812deee6d7475e1d1191ba9efd6e3b84d65e3">
data/silva-arc-16s-database-id95.fasta
→
test_data/silva-arc-16s-database-id95.fasta
</a>
</li>
<li class="file-stats">
<a href="#4e7b2dfde9f45efd560f167ff3c4fe3e248c9cb0">
<span class="new-file">
+
test_data/silva-arc-16s-database-id95_part.fasta
</span>
</a>
</li>
<li class="file-stats">
<a href="#dbf21d388207d3f9aaa9cf5fd40c4d59b868504e">
data/silva-bac-16s-database-id85.fasta
→
test_data/silva-bac-16s-database-id85.fasta
</a>
</li>
<li class="file-stats">
<a href="#3b2c828004384078e4a00da1d4a76801017b23db">
data/t0_expected_alignment.blast
→
test_data/t0_expected_alignment.blast
</a>
</li>
<li class="file-stats">
<a href="#1abd227eacffe8b46c5532885c5dc1c25eba091c">
data/test_read.fasta
→
test_data/test_read.fasta
</a>
</li>
<li class="file-stats">
<a href="#ed6163a09e8d0a6c93cf1871645166e398e05be5">
data/test_ref.fasta
→
test_data/test_ref.fasta
</a>
</li>
<li class="file-stats">
<a href="#966d957be8c262c6ab27bcd4815ea34134ff48a3">
<span class="new-file">
+
tests/golden/small/aligned.blast
</span>
</a>
</li>
<li class="file-stats">
<a href="#004faad613fdb958dfd91a4213584c0a34357af6">
<span class="new-file">
+
tests/golden/small/aligned.fa
</span>
</a>
</li>
<li class="file-stats">
<a href="#cf09e47404c7fc364cc51d94bcf34a688033480d">
<span class="new-file">
+
tests/golden/small/aligned.sam
</span>
</a>
</li>
<li class="file-stats">
<a href="#2ee001c6f26edd7e64c42214adcd31f424f32434">
<span class="new-file">
+
tests/golden/small/other.fa
</span>
</a>
</li>
<li class="file-stats">
<a href="#c59b84a89a8754309a70d87179448335cd10f299">
<span class="new-file">
+
tests/golden/tiny/aligned.blast
</span>
</a>
</li>
<li class="file-stats">
<a href="#3c56b126728bf8beb639634679c12aec23f793b5">
<span class="new-file">
+
tests/golden/tiny/aligned.fa
</span>
</a>
</li>
<li class="file-stats">
<a href="#ebf8d8378a5fe49e2ef0c99214401ba82edf9fe0">
<span class="new-file">
+
tests/golden/tiny/aligned.sam
</span>
</a>
</li>
<li class="file-stats">
<a href="#6c08eaa58fec89ee6cbc4a7b735732fe81babd6b">
<span class="new-file">
+
tests/smr_api/CMakeLists.txt
</span>
</a>
</li>
<li class="file-stats">
<a href="#a6f8871632b939540723852df7009fd3255dc596">
<span class="new-file">
+
tests/smr_api/test_harness.h
</span>
</a>
</li>
<li class="file-stats">
<a href="#acb78dd3f90b37a9aa478f34931e3486a95f77fa">
<span class="new-file">
+
tests/smr_api/test_link.c
</span>
</a>
</li>
<li class="file-stats">
<a href="#2368b783230fc57834b1c3c2713e20810c02326a">
<span class="new-file">
+
tests/smr_api/test_smoke.c
</span>
</a>
</li>
<li class="file-stats">
<a href="#2531c4996d9b27b587139554c3be0f3623e4dc00">
tests/sortmerna/CMakeLists.txt
</a>
</li>
<li class="file-stats">
<a href="#3186ebbf20fad35411503f1a715f27a2128e9adf">
tests/sortmerna/kvdb.cpp
</a>
</li>
<li class="file-stats">
<a href="#9e7edf1e775cbb09f5facafbbdefc2fe0c8c146c">
tests/sortmerna/main.cpp
</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/sortmerna/-/compare/cd8be11ffc474a61bfec3aa9837a00061aae2030...5f68260340054634d63601355c3bcd370c15f33a">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/sortmerna/-/compare/cd8be11ffc474a61bfec3aa9837a00061aae2030...5f68260340054634d63601355c3bcd370c15f33a at 1792414477
</span>
</p>
</div>
</body>
</html>