File yaha.spec of Package yaha

#
# spec file for package yaha
#
# Copyright (c) 2024 SUSE LLC
#
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# upon. The license for this file, and modifications and additions to the
# file, is the same license as for the pristine package itself (unless the
# license for the pristine package is not an Open Source License, in which
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# license that conforms to the Open Source Definition (Version 1.9)
# published by the Open Source Initiative.

# Please submit bugfixes or comments via https://bugs.opensuse.org/
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Name:           yaha
Version:        0.1.83
Release:        0
Summary:        Flexible, sensitive and accurate DNA aligner designed for single-end reads
License:        MIT
Group:          Productivity/Scientific/Other
URL:            https://github.com/GregoryFaust/yaha
Source:         https://github.com/GregoryFaust/yaha/archive/refs/tags/v%{version}.tar.gz#/yaha-%{version}.tar.gz
# Fixing compilation of modern GCC-C++
Patch0:         yaha.diff
BuildRequires:  gcc
BuildRequires:  gcc-c++

%description
Yaha is a flexible, sensitive and accurate DNA alignment tool designed to find optimal split-read mappings on single-end queries from 100bp to 32kb. It supports three major modes of operation:
1. The default “Optimal Query Coverage” (-OQC) mode reports the best set of alignments that cover the length of each query.
2. Using “Filter By Similarity” (-FBS), along with the best set of alignments, yaha will also output alignments that are highly similar to an alignment in the best set.
3. Finally, yaha can output all the alignments found for each query.
The -OQC and -FBS modes are specifically tuned to form split read mappings that can be used to accurately identify structural variation events (deletions, duplications, insertions or inversions) between the subject query and the reference genome.

%package doc
Summary:        Yaha documentation and examples
Group:          Productivity/Scientific/Other
BuildArch:      noarch

%description doc
Yaha is a flexible, sensitive and accurate DNA alignment tool designed to find optimal split-read mappings on single-end queries from 100bp to 32kb. Documentation and examples.

%prep
%setup -q
%patch -P 0

%build
%make_build
sed -i 's/\r$//' README.md

%install
install -d %{buildroot}%{_bindir}
install -D -m 0755 bin/yaha %{buildroot}%{_bindir}

%check

%files
%license LICENSE.txt
%doc README.md
%{_bindir}/*

%files doc
%doc YAHA_User_Guide.0.1.83.pdf

%changelog