automatic import of python-bsboltopeneuler20.03

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diff --git a/.gitignore b/.gitignore
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+/bsbolt-1.6.0.tar.gz
diff --git a/python-bsbolt.spec b/python-bsbolt.spec
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+%global _empty_manifest_terminate_build 0
+Name:		python-bsbolt
+Version:	1.6.0
+Release:	1
+Summary:	Bisulfite Sequencing Processing Platform
+License:	MIT
+URL:		https://github.com/NuttyLogic/BSBolt
+Source0:	https://mirrors.nju.edu.cn/pypi/web/packages/ca/64/b923da8df7f3e3887fafa6d8a94c0f8c38b785be60aa725c5f0f614b6226/bsbolt-1.6.0.tar.gz
+BuildArch:	noarch
+
+Requires:	python3-pysam
+Requires:	python3-numpy
+Requires:	python3-tqdm
+Requires:	python3-setuptools
+
+%description
+# **BSBolt (BiSulfite Bolt)**
+
+## A fast and safe bisulfite sequencing analysis platform
+
+[BiSuflite Bolt (BSBolt)](https://github.com/NuttyLogic/BSBolt); a fast and scalable bisulfite sequencing
+analysis platform. BSBolt is an integrated analysis platform that offers support for bisulfite sequencing
+read simulation, alignment, methylation calling, data aggregation, and data imputation. BSBolt has been validated
+to work with a wide array of bisulfite sequencing data,including whole genome bisulfite sequencing (WGBS),
+reduced representative bisulfite sequencing data (RRBS), and targeted methylation sequencing data.
+BSBolt utilizes forked versions of [BWA](https://github.com/lh3/bwa)
+and [WGSIM](https://github.com/lh3/wgsim) for read alignment and read simulation respectively.
+BSBolt is released under the MIT license.
+
+## Publication
+
+[Farrell, C., Thompson, M., Tosevska, A., Oyetunde, A. & Pellegrini, M. 
+**BiSulfite Bolt: A BiSulfite Sequencing Analysis Platform.** 2020.10.06.328559 (2020). 
+doi:10.1101/2020.10.06.328559](https://academic.oup.com/gigascience/article/10/5/giab033/6272610)
+
+## Documentation
+
+Documentation can be found at [https://bsbolt.readthedocs.io](https://bsbolt.readthedocs.io/en/latest/).
+
+## Release Notes
+- v1.6.0
+  - MethyDackel compatibility 
+  - Option to output alignment to stdout
+- v1.5.0
+  - Improved thread handling for methylation / variant calling.
+  - Experimental bisulfite aware SNP caller. 
+- v1.4.8
+  - Fixed bug ending alignment when the reference template end greater than reference boundary.
+- v1.4.7
+  - Alignment stats fix.
+- v1.4.6
+  - Alignment statistics now output as generated.
+  - Fixed bug where alignment would stop when observed mappability was low.
+- v1.4.5
+  - Fixed maximum read depth bug that prevented methylation call on site covered by greater than 8000 reads
+  - Refactored build script, with experimental support for M1 Macs
+- v1.4.4
+  - The default entry point for BSBolt has changed from **BSBolt** to **bsbolt** for conda compatibility
+
+## **Installation**
+
+### **PyPi Installation**
+
+Pre-compiled binaries can be installed using PyPi. Binaries are available for python >=3.6
+on unix like systems (macOS >=10.15 and linux).
+
+```shell
+pip3 install bsbolt --user
+```
+
+### **Conda Installation**
+
+BSBolt can be installed using the conda package manager using the instructions below.
+
+```shell
+conda config --add channels bioconda
+conda config --add channels conda-forge
+conda install -c cpfarrell bsbolt
+```
+
+### **Installing from Source**
+
+Dependencies
+
+* zlib-devel >= 1.2.3-29
+* GCC >= 8.3.1
+
+```shell
+# clone the repository
+git clone https://github.com/NuttyLogic/BSBolt.git
+cd bsbolt
+# compile and install package
+pip3 install .
+```
+
+### **Installing from Source on macOS**
+
+Dependencies 
+
+- autoconf
+- automake
+- homebrew
+- xcode
+
+Installation from source requires xcode command line utilities, [homebrew](https://brew.sh/) macOS package manager, 
+autoconf, python (>=3.6), and automake.The full installation process is outlined below.
+
+```shell
+# install xcode utilities
+xcode-select --install
+# install homebrew
+/bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"
+# install autoconf
+brew install autoconf
+# install automake
+brew install automake
+# optionally install python > 3.5
+brew install python3.8
+# clone the repository
+git clone https://github.com/NuttyLogic/BSBolt.git
+cd BSBolt
+# compile and install package
+pip3 install -e .
+```
+## Usage
+
+Following installation BSBolt can be called using **bsbolt Module**.
+
+```shell
+python3 -m bsbolt
+```
+
+```shell
+bsbolt Module
+
+Align               Alignment
+Index               Index Generation
+CallMethylation     Methylation Calling
+AggregateMatrix     CGmap Matrix Aggregation
+Simulate            bsbolt Illumina Read Simulation
+Impute              kNN Imputation
+Sort                Sort BAM File
+BamIndex            Index BAM file
+```
+
+
+%package -n python3-bsbolt
+Summary:	Bisulfite Sequencing Processing Platform
+Provides:	python-bsbolt
+BuildRequires:	python3-devel
+BuildRequires:	python3-setuptools
+BuildRequires:	python3-pip
+%description -n python3-bsbolt
+# **BSBolt (BiSulfite Bolt)**
+
+## A fast and safe bisulfite sequencing analysis platform
+
+[BiSuflite Bolt (BSBolt)](https://github.com/NuttyLogic/BSBolt); a fast and scalable bisulfite sequencing
+analysis platform. BSBolt is an integrated analysis platform that offers support for bisulfite sequencing
+read simulation, alignment, methylation calling, data aggregation, and data imputation. BSBolt has been validated
+to work with a wide array of bisulfite sequencing data,including whole genome bisulfite sequencing (WGBS),
+reduced representative bisulfite sequencing data (RRBS), and targeted methylation sequencing data.
+BSBolt utilizes forked versions of [BWA](https://github.com/lh3/bwa)
+and [WGSIM](https://github.com/lh3/wgsim) for read alignment and read simulation respectively.
+BSBolt is released under the MIT license.
+
+## Publication
+
+[Farrell, C., Thompson, M., Tosevska, A., Oyetunde, A. & Pellegrini, M. 
+**BiSulfite Bolt: A BiSulfite Sequencing Analysis Platform.** 2020.10.06.328559 (2020). 
+doi:10.1101/2020.10.06.328559](https://academic.oup.com/gigascience/article/10/5/giab033/6272610)
+
+## Documentation
+
+Documentation can be found at [https://bsbolt.readthedocs.io](https://bsbolt.readthedocs.io/en/latest/).
+
+## Release Notes
+- v1.6.0
+  - MethyDackel compatibility 
+  - Option to output alignment to stdout
+- v1.5.0
+  - Improved thread handling for methylation / variant calling.
+  - Experimental bisulfite aware SNP caller. 
+- v1.4.8
+  - Fixed bug ending alignment when the reference template end greater than reference boundary.
+- v1.4.7
+  - Alignment stats fix.
+- v1.4.6
+  - Alignment statistics now output as generated.
+  - Fixed bug where alignment would stop when observed mappability was low.
+- v1.4.5
+  - Fixed maximum read depth bug that prevented methylation call on site covered by greater than 8000 reads
+  - Refactored build script, with experimental support for M1 Macs
+- v1.4.4
+  - The default entry point for BSBolt has changed from **BSBolt** to **bsbolt** for conda compatibility
+
+## **Installation**
+
+### **PyPi Installation**
+
+Pre-compiled binaries can be installed using PyPi. Binaries are available for python >=3.6
+on unix like systems (macOS >=10.15 and linux).
+
+```shell
+pip3 install bsbolt --user
+```
+
+### **Conda Installation**
+
+BSBolt can be installed using the conda package manager using the instructions below.
+
+```shell
+conda config --add channels bioconda
+conda config --add channels conda-forge
+conda install -c cpfarrell bsbolt
+```
+
+### **Installing from Source**
+
+Dependencies
+
+* zlib-devel >= 1.2.3-29
+* GCC >= 8.3.1
+
+```shell
+# clone the repository
+git clone https://github.com/NuttyLogic/BSBolt.git
+cd bsbolt
+# compile and install package
+pip3 install .
+```
+
+### **Installing from Source on macOS**
+
+Dependencies 
+
+- autoconf
+- automake
+- homebrew
+- xcode
+
+Installation from source requires xcode command line utilities, [homebrew](https://brew.sh/) macOS package manager, 
+autoconf, python (>=3.6), and automake.The full installation process is outlined below.
+
+```shell
+# install xcode utilities
+xcode-select --install
+# install homebrew
+/bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"
+# install autoconf
+brew install autoconf
+# install automake
+brew install automake
+# optionally install python > 3.5
+brew install python3.8
+# clone the repository
+git clone https://github.com/NuttyLogic/BSBolt.git
+cd BSBolt
+# compile and install package
+pip3 install -e .
+```
+## Usage
+
+Following installation BSBolt can be called using **bsbolt Module**.
+
+```shell
+python3 -m bsbolt
+```
+
+```shell
+bsbolt Module
+
+Align               Alignment
+Index               Index Generation
+CallMethylation     Methylation Calling
+AggregateMatrix     CGmap Matrix Aggregation
+Simulate            bsbolt Illumina Read Simulation
+Impute              kNN Imputation
+Sort                Sort BAM File
+BamIndex            Index BAM file
+```
+
+
+%package help
+Summary:	Development documents and examples for bsbolt
+Provides:	python3-bsbolt-doc
+%description help
+# **BSBolt (BiSulfite Bolt)**
+
+## A fast and safe bisulfite sequencing analysis platform
+
+[BiSuflite Bolt (BSBolt)](https://github.com/NuttyLogic/BSBolt); a fast and scalable bisulfite sequencing
+analysis platform. BSBolt is an integrated analysis platform that offers support for bisulfite sequencing
+read simulation, alignment, methylation calling, data aggregation, and data imputation. BSBolt has been validated
+to work with a wide array of bisulfite sequencing data,including whole genome bisulfite sequencing (WGBS),
+reduced representative bisulfite sequencing data (RRBS), and targeted methylation sequencing data.
+BSBolt utilizes forked versions of [BWA](https://github.com/lh3/bwa)
+and [WGSIM](https://github.com/lh3/wgsim) for read alignment and read simulation respectively.
+BSBolt is released under the MIT license.
+
+## Publication
+
+[Farrell, C., Thompson, M., Tosevska, A., Oyetunde, A. & Pellegrini, M. 
+**BiSulfite Bolt: A BiSulfite Sequencing Analysis Platform.** 2020.10.06.328559 (2020). 
+doi:10.1101/2020.10.06.328559](https://academic.oup.com/gigascience/article/10/5/giab033/6272610)
+
+## Documentation
+
+Documentation can be found at [https://bsbolt.readthedocs.io](https://bsbolt.readthedocs.io/en/latest/).
+
+## Release Notes
+- v1.6.0
+  - MethyDackel compatibility 
+  - Option to output alignment to stdout
+- v1.5.0
+  - Improved thread handling for methylation / variant calling.
+  - Experimental bisulfite aware SNP caller. 
+- v1.4.8
+  - Fixed bug ending alignment when the reference template end greater than reference boundary.
+- v1.4.7
+  - Alignment stats fix.
+- v1.4.6
+  - Alignment statistics now output as generated.
+  - Fixed bug where alignment would stop when observed mappability was low.
+- v1.4.5
+  - Fixed maximum read depth bug that prevented methylation call on site covered by greater than 8000 reads
+  - Refactored build script, with experimental support for M1 Macs
+- v1.4.4
+  - The default entry point for BSBolt has changed from **BSBolt** to **bsbolt** for conda compatibility
+
+## **Installation**
+
+### **PyPi Installation**
+
+Pre-compiled binaries can be installed using PyPi. Binaries are available for python >=3.6
+on unix like systems (macOS >=10.15 and linux).
+
+```shell
+pip3 install bsbolt --user
+```
+
+### **Conda Installation**
+
+BSBolt can be installed using the conda package manager using the instructions below.
+
+```shell
+conda config --add channels bioconda
+conda config --add channels conda-forge
+conda install -c cpfarrell bsbolt
+```
+
+### **Installing from Source**
+
+Dependencies
+
+* zlib-devel >= 1.2.3-29
+* GCC >= 8.3.1
+
+```shell
+# clone the repository
+git clone https://github.com/NuttyLogic/BSBolt.git
+cd bsbolt
+# compile and install package
+pip3 install .
+```
+
+### **Installing from Source on macOS**
+
+Dependencies 
+
+- autoconf
+- automake
+- homebrew
+- xcode
+
+Installation from source requires xcode command line utilities, [homebrew](https://brew.sh/) macOS package manager, 
+autoconf, python (>=3.6), and automake.The full installation process is outlined below.
+
+```shell
+# install xcode utilities
+xcode-select --install
+# install homebrew
+/bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"
+# install autoconf
+brew install autoconf
+# install automake
+brew install automake
+# optionally install python > 3.5
+brew install python3.8
+# clone the repository
+git clone https://github.com/NuttyLogic/BSBolt.git
+cd BSBolt
+# compile and install package
+pip3 install -e .
+```
+## Usage
+
+Following installation BSBolt can be called using **bsbolt Module**.
+
+```shell
+python3 -m bsbolt
+```
+
+```shell
+bsbolt Module
+
+Align               Alignment
+Index               Index Generation
+CallMethylation     Methylation Calling
+AggregateMatrix     CGmap Matrix Aggregation
+Simulate            bsbolt Illumina Read Simulation
+Impute              kNN Imputation
+Sort                Sort BAM File
+BamIndex            Index BAM file
+```
+
+
+%prep
+%autosetup -n bsbolt-1.6.0
+
+%build
+%py3_build
+
+%install
+%py3_install
+install -d -m755 %{buildroot}/%{_pkgdocdir}
+if [ -d doc ]; then cp -arf doc %{buildroot}/%{_pkgdocdir}; fi
+if [ -d docs ]; then cp -arf docs %{buildroot}/%{_pkgdocdir}; fi
+if [ -d example ]; then cp -arf example %{buildroot}/%{_pkgdocdir}; fi
+if [ -d examples ]; then cp -arf examples %{buildroot}/%{_pkgdocdir}; fi
+pushd %{buildroot}
+if [ -d usr/lib ]; then
+	find usr/lib -type f -printf "/%h/%f\n" >> filelist.lst
+fi
+if [ -d usr/lib64 ]; then
+	find usr/lib64 -type f -printf "/%h/%f\n" >> filelist.lst
+fi
+if [ -d usr/bin ]; then
+	find usr/bin -type f -printf "/%h/%f\n" >> filelist.lst
+fi
+if [ -d usr/sbin ]; then
+	find usr/sbin -type f -printf "/%h/%f\n" >> filelist.lst
+fi
+touch doclist.lst
+if [ -d usr/share/man ]; then
+	find usr/share/man -type f -printf "/%h/%f.gz\n" >> doclist.lst
+fi
+popd
+mv %{buildroot}/filelist.lst .
+mv %{buildroot}/doclist.lst .
+
+%files -n python3-bsbolt -f filelist.lst
+%dir %{python3_sitelib}/*
+
+%files help -f doclist.lst
+%{_docdir}/*
+
+%changelog
+* Wed May 10 2023 Python_Bot <Python_Bot@openeuler.org> - 1.6.0-1
+- Package Spec generated
diff --git a/sources b/sources
new file mode 100644
index 0000000..6dbd0ea
--- /dev/null
+++ b/sources
@@ -0,0 +1 @@
+dbcf41de517589ed80b4d88e13109eeb  bsbolt-1.6.0.tar.gz