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+/HiNT-Package-2.2.8.tar.gz
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+%global _empty_manifest_terminate_build 0
+Name:		python-HiNT-Package
+Version:	2.2.8
+Release:	1
+Summary:	HiNT -- HiC for copy number vairations and translocations detection
+License:	MIT License
+URL:		https://github.com/suwangbio/HiNT_py3
+Source0:	https://mirrors.nju.edu.cn/pypi/web/packages/ff/a1/f1d40fad4546763d4df8b02aea3d07454d55a865c418c8163b1b124cbb6b/HiNT-Package-2.2.8.tar.gz
+BuildArch:	noarch
+
+Requires:	python3-h5py
+Requires:	python3-numpy
+Requires:	python3-cooler
+Requires:	python3-pypairix
+Requires:	python3-pairtools
+Requires:	python3-scipy
+Requires:	python3-pandas
+Requires:	python3-scikit-learn
+Requires:	python3-multiprocess
+Requires:	python3-argparse
+Requires:	python3-pytabix
+
+%description
+# HiNT 
+## A computational method for detecting copy number variations and translocations from Hi-C data
+
+## Summary
+**HiNT** (**Hi**-C for copy **N**umber variation and **T**ranslocation detection), a computational method to detect CNVs and Translocations from Hi-C data. HiNT has three main components: **HiNT-PRE**, **HiNT-CNV**, and **HiNT-TL**. HiNT-PRE preprocesses Hi-C data and computes the contact matrix, which stores contact frequencies between any two genomic loci; both HiNT-CNV and HiNT-TL starts with HI-C contact matrix, predicts copy number segments, and inter-chromosomal translocations, respectively 
+
+#### Overview of HiNT workflow: 
+<img src="https://github.com/suwangbio/HiNT/blob/master/images/HiNT_workflow.png" width="800">
+
+## Installation
+
+### Dependencies
+R and R packages
+
+1. [R >= 3.4](https://www.r-project.org/)
+2. [mgcv](https://cran.r-project.org/web/packages/mgcv/index.html), [strucchange](https://cran.r-project.org/web/packages/strucchange/index.html), [doParallel](https://www.rdocumentation.org/packages/parallel/versions/3.4.1), [Cairo](https://cran.r-project.org/web/packages/Cairo/index.html), [foreach](https://cran.r-project.org/web/packages/optparse/index.html)
+
+Python and Python packages
+
+1. [python >= 3.5](https://www.python.org/)
+2. [pyparix >= 0.3.0](https://github.com/4dn-dcic/pairix#pypairix), [cooler >= 0.7.4](https://github.com/mirnylab/cooler), [pairtools >= 0.2.2](https://github.com/mirnylab/pairtools), [numpy](https://www.scipy.org/install.html), [scipy](https://www.scipy.org/install.html), [pandas](https://pandas.pydata.org/), [sklearn](https://scikit-learn.org/stable/install.html), [multiprocessing](https://pypi.org/project/multiprocess/)
+
+Java and related tools (Optional: required when want to process Hi-C data with juicer tools)
+
+1. [Java (version >= 1.7)](https://www.java.com/en/download/)
+2. [Juicer tools (1.8.9 is recommended)](https://github.com/aidenlab/juicer/wiki/Download) 
+
+Perl
+
+1. [Perl (version >= 5)](https://www.perl.org/)
+
+
+Other dependencies
+
+1. [samtools](http://www.htslib.org/doc/) (1.3.1+)
+2. [BIC-seq2](http://www.math.pku.edu.cn/teachers/xirb/downloads/software/BICseq2/BICseq2/BICseq2-seg_v0.7.3.tar.gz) (0.7.3) ! This is optional: if you don't want to run HiNT-CNV, you don't need this package. [Download BICseq2, unzip it, and give the path of BICseq2-seg_v0.7.3 (/path/to/BICseq2-seg_v0.7.3)].
+3. [bwa](https://sourceforge.net/projects/bio-bwa/files/) (0.7.16+) ! This is optional: required only when your input is fastq
+4. [tabix](https://sourceforge.net/projects/samtools/files/tabix/) (0.2.6)
+
+### Install HiNT
+
+* Method1: Install using conda (highly recommended)
+
+	``` $ conda install -c su hint```
+
+	or
+
+	``` $ conda install hint```
+
+* Method2: Install from PyPI using pip.
+
+	``` $ pip install HiNT-Packages```
+
+* Method3: Install manually 
+  1. Install HiNT dependencies
+  2. Download HiNT ```git clone https://github.com/parklab/HiNT.git```
+  3. Go to HiNT directory, install it by ```$ python setup.py install ```
+
+  *** Type ```$ hint``` to test if HiNT successfully installed
+
+* Method 4: Run HiNT in a Docker container (highly recommended)
+
+	``` $ docker pull suwangbio/hint```
+
+	``` $ docker run suwangbio/hint hint```
+
+	See details of the usage on HiNT page at [docker hub](https://hub.docker.com/r/suwangbio/hint) 
+
+### Download reference files used in HiNT [HERE](https://www.dropbox.com/sh/2ufsyu4wvrboxxp/AABk5-_Fwy7jdM_t0vIsgYf4a?dl=0)
+
+1. Download HiNT references [HERE](https://www.dropbox.com/sh/qas48d7409t2syz/AACk5G2ngZ0vylLXsLFZXif_a?dl=0). Only hg19, hg38 and mm10 are available currently. Unzip it ```$ unzip hg19.zip ```
+2. Download HiNT background matrices [HERE](https://www.dropbox.com/sh/fyxx9u5g5vn57ez/AAAx-DtByKaU6HvTYyEUvCzRa?dl=0). Only hg19, hg38 and mm10 are available currently. Unzip it ```$ unzip hg19.zip ```
+3. Download BWA index files [HERE](https://www.dropbox.com/sh/l004df4108s6d3c/AAB6qtS95mBK_MdDZYlo2V-pa?dl=0). Only hg19, hg38 and mm10 are available currently. Unzip it ```$ unzip hg19.zip ```
+
+## Quick Start
+
+* Download the test datasets from [HERE](https://www.dropbox.com/sh/z1rceh8ddnsdtj7/AAC0VuDu48eh_RtzKHipztkLa?dl=0)
+
+### HiNT-PRE
+HiNT pre: Preprocessing Hi-C data. HiNT pre does alignment, contact matrix creation and normalization in one command line.
+
+```$ hint pre -d /path/to/hic_1.fastq.gz,/path/to/hic_2.fastq.gz -i /path/to/bwaIndex/hg19/hg19.fa --refdir /path/to/refData/hg19 --informat fastq --outformat cooler -g hg19 -n test -o /path/to/outputdir --pairtoolspath /path/to/pairtools --samtoolspath /path/to/samtools --coolerpath /path/to/cooler```
+
+```$ hint pre -d /path/to/test.bam --refdir /path/to/refData/hg19 --informat bam --outformat juicer -g hg19 -n test -o /path/to/outputdir --pairtoolspath /path/to/pairtools --samtoolspath /path/to/samtools --juicerpath /path/to/juicer_tools.1.8.9_jcuda.0.8.jar```
+
+use ```$ which samtools ``` ```$ which pairtools ``` ```$ which cooler ``` to get the absolute path of these tools, and ```/path/to/juicer_tools.1.8.9_jcuda.0.8.jar``` should be the path where you store this file
+
+see details and more options
+
+```$ hint pre -h ```
+
+### HiNT-CNV
+HiNT cnv: prediction of copy number information, as well as segmentation from Hi-C.
+
+```$ hint cnv -m contactMatrix.cool -f cooler --refdir /path/to/refDir/hg19 -r 50 -g hg19 -n test -o /path/to/outputDir --bicseq /path/to/BICseq2-seg_v0.7.3 -e MboI```
+
+```$ hint cnv -m /path/to/4DNFIS6HAUPP.mcool::/resolutions/50000 -f cooler --refdir /path/to/refDir/hg38 -r 50 -g hg38 -n HepG2 --bicseq /path/to/BICseq2-seg_v0.7.3 -e DpnII```
+
+```$ hint cnv -m /path/to/4DNFICSTCJQZ.hic -f juicer --refdir /path/to/refDir/hg38 -r 50 -g hg38 -n HepG2 --bicseq /path/to/BICseq2-seg_v0.7.3 -e DpnII```
+
+```$ hint cnv -m /path/to/4DNFICSTCJQZ.hic -f juicer --refdir /path/to/refDir/hg38 -r 50 -g hg38 -n HepG2 --bicseq /path/to/BICseq2-seg_v0.7.3 -e DpnII --doiter```
+
+```/path/to/BICseq2-seg_v0.7.3``` should be the path where you store this package
+
+see details and more options
+
+```$ hint cnv -h ```
+
+### HiNT-TL
+HiNT tl: interchromosomal translocations and breakpoints detection from
+Hi-C inter-chromosomal interaction matrices.
+
+```$ hint tl -m /path/to/data_1Mb.cool,/path/to/data_100kb.cool --chimeric /path/to/test_chimeric.sorted.pairsam.gz --refdir /path/to/refDir/hg19 --backdir /path/to/backgroundMatrices/hg19 --ppath /path/to/pairix -f cooler -g hg19 -n test -o /path/to/outputDir```
+
+```$ hint tl -m /path/to/4DNFIS6HAUPP.mcool::/resolutions/1000000,/path/to/4DNFIS6HAUPP.mcool::/resolutions/100000 -f cooler --refdir /path/to/refDir/hg38 --backdir /path/to/backgroundMatrices/hg38 -g hg38 -n 4DNFICSTCJQZ -c 0.05 --ppath /path/to/pairix -p 12```
+
+```$ hint tl -m /path/to/4DNFICSTCJQZ.hic -f juicer --refdir /path/to/refData/hg38 --backdir /path/to/backgroundMatrices/hg38 -g hg38 -n 4DNFICSTCJQZ -c 0.05 --ppath /path/to/pairix -p 12 -o HiNTtransl_juicerOUTPUT```
+
+use ```$ which pairix ``` to get the absolute path of pairix
+
+see details and more options
+
+```$ hint tl -h ```
+
+## Output of HiNT
+### HiNT-PRE output
+In the HiNT-PRE output directory, you will find
+
+1. ```jobname.bam``` aligned lossless file in bam format
+2. ```jobname_merged_valid.pairs.gz``` reads pairs in pair format
+3. ```jobname_chimeric.sorted.pairsam.gz``` ambiguous chimeric read pairs used for breakpoint detection in [pairsam](https://github.com/mirnylab/pairtools) format
+4. ```jobname_valid.sorted.deduped.pairsam.gz``` valid read pairs used for Hi-C contact matrix creation in [pairsam](https://github.com/mirnylab/pairtools) format
+5. ```jobname.mcool``` Hi-C contact matrix in [cool](https://github.com/mirnylab/cooler) format
+6. ```jobname.hic``` Hi-C contact matrix in [hic](https://github.com/aidenlab/juicer) format
+
+### HiNT-CNV output
+In the HiNT-CNV output directory, you will find
+
+1. ```jobname_GAMPoisson.pdf``` the GAM regression result
+2. ```segmentation/jobname_bicsq_allchroms.txt``` CNV segments with log2 copy ratio and p-values in txt file
+3. ```segmentation/jobname_resolution_CNV_segments.png``` figure to visualize CNV segments
+4. ```segmentation/jobname_bicseq_allchroms.l2r.pdf``` figure to visualize log2 copy ration in each bin (bin size = resolution you set)
+5. ```segmentation/other_files``` intermediate files used to run BIC-seq
+6. ```jonname_dataForRegression/*``` data used for regression as well as residuals after removing Hi-C biases
+
+### HiNT-TL output
+In the HiNT-TL output directory, you will find
+
+1. ```jobname_Translocation_IntegratedBP.txt``` the final integrated translocation breakpoint
+2. ```jobname_chrompairs_rankProduct.txt``` rank product predicted potential translocated chromosome pairs
+3. ```otherFolders``` intermediate files used to identify the translocation breakpoints
+
+
+
+
+%package -n python3-HiNT-Package
+Summary:	HiNT -- HiC for copy number vairations and translocations detection
+Provides:	python-HiNT-Package
+BuildRequires:	python3-devel
+BuildRequires:	python3-setuptools
+BuildRequires:	python3-pip
+%description -n python3-HiNT-Package
+# HiNT 
+## A computational method for detecting copy number variations and translocations from Hi-C data
+
+## Summary
+**HiNT** (**Hi**-C for copy **N**umber variation and **T**ranslocation detection), a computational method to detect CNVs and Translocations from Hi-C data. HiNT has three main components: **HiNT-PRE**, **HiNT-CNV**, and **HiNT-TL**. HiNT-PRE preprocesses Hi-C data and computes the contact matrix, which stores contact frequencies between any two genomic loci; both HiNT-CNV and HiNT-TL starts with HI-C contact matrix, predicts copy number segments, and inter-chromosomal translocations, respectively 
+
+#### Overview of HiNT workflow: 
+<img src="https://github.com/suwangbio/HiNT/blob/master/images/HiNT_workflow.png" width="800">
+
+## Installation
+
+### Dependencies
+R and R packages
+
+1. [R >= 3.4](https://www.r-project.org/)
+2. [mgcv](https://cran.r-project.org/web/packages/mgcv/index.html), [strucchange](https://cran.r-project.org/web/packages/strucchange/index.html), [doParallel](https://www.rdocumentation.org/packages/parallel/versions/3.4.1), [Cairo](https://cran.r-project.org/web/packages/Cairo/index.html), [foreach](https://cran.r-project.org/web/packages/optparse/index.html)
+
+Python and Python packages
+
+1. [python >= 3.5](https://www.python.org/)
+2. [pyparix >= 0.3.0](https://github.com/4dn-dcic/pairix#pypairix), [cooler >= 0.7.4](https://github.com/mirnylab/cooler), [pairtools >= 0.2.2](https://github.com/mirnylab/pairtools), [numpy](https://www.scipy.org/install.html), [scipy](https://www.scipy.org/install.html), [pandas](https://pandas.pydata.org/), [sklearn](https://scikit-learn.org/stable/install.html), [multiprocessing](https://pypi.org/project/multiprocess/)
+
+Java and related tools (Optional: required when want to process Hi-C data with juicer tools)
+
+1. [Java (version >= 1.7)](https://www.java.com/en/download/)
+2. [Juicer tools (1.8.9 is recommended)](https://github.com/aidenlab/juicer/wiki/Download) 
+
+Perl
+
+1. [Perl (version >= 5)](https://www.perl.org/)
+
+
+Other dependencies
+
+1. [samtools](http://www.htslib.org/doc/) (1.3.1+)
+2. [BIC-seq2](http://www.math.pku.edu.cn/teachers/xirb/downloads/software/BICseq2/BICseq2/BICseq2-seg_v0.7.3.tar.gz) (0.7.3) ! This is optional: if you don't want to run HiNT-CNV, you don't need this package. [Download BICseq2, unzip it, and give the path of BICseq2-seg_v0.7.3 (/path/to/BICseq2-seg_v0.7.3)].
+3. [bwa](https://sourceforge.net/projects/bio-bwa/files/) (0.7.16+) ! This is optional: required only when your input is fastq
+4. [tabix](https://sourceforge.net/projects/samtools/files/tabix/) (0.2.6)
+
+### Install HiNT
+
+* Method1: Install using conda (highly recommended)
+
+	``` $ conda install -c su hint```
+
+	or
+
+	``` $ conda install hint```
+
+* Method2: Install from PyPI using pip.
+
+	``` $ pip install HiNT-Packages```
+
+* Method3: Install manually 
+  1. Install HiNT dependencies
+  2. Download HiNT ```git clone https://github.com/parklab/HiNT.git```
+  3. Go to HiNT directory, install it by ```$ python setup.py install ```
+
+  *** Type ```$ hint``` to test if HiNT successfully installed
+
+* Method 4: Run HiNT in a Docker container (highly recommended)
+
+	``` $ docker pull suwangbio/hint```
+
+	``` $ docker run suwangbio/hint hint```
+
+	See details of the usage on HiNT page at [docker hub](https://hub.docker.com/r/suwangbio/hint) 
+
+### Download reference files used in HiNT [HERE](https://www.dropbox.com/sh/2ufsyu4wvrboxxp/AABk5-_Fwy7jdM_t0vIsgYf4a?dl=0)
+
+1. Download HiNT references [HERE](https://www.dropbox.com/sh/qas48d7409t2syz/AACk5G2ngZ0vylLXsLFZXif_a?dl=0). Only hg19, hg38 and mm10 are available currently. Unzip it ```$ unzip hg19.zip ```
+2. Download HiNT background matrices [HERE](https://www.dropbox.com/sh/fyxx9u5g5vn57ez/AAAx-DtByKaU6HvTYyEUvCzRa?dl=0). Only hg19, hg38 and mm10 are available currently. Unzip it ```$ unzip hg19.zip ```
+3. Download BWA index files [HERE](https://www.dropbox.com/sh/l004df4108s6d3c/AAB6qtS95mBK_MdDZYlo2V-pa?dl=0). Only hg19, hg38 and mm10 are available currently. Unzip it ```$ unzip hg19.zip ```
+
+## Quick Start
+
+* Download the test datasets from [HERE](https://www.dropbox.com/sh/z1rceh8ddnsdtj7/AAC0VuDu48eh_RtzKHipztkLa?dl=0)
+
+### HiNT-PRE
+HiNT pre: Preprocessing Hi-C data. HiNT pre does alignment, contact matrix creation and normalization in one command line.
+
+```$ hint pre -d /path/to/hic_1.fastq.gz,/path/to/hic_2.fastq.gz -i /path/to/bwaIndex/hg19/hg19.fa --refdir /path/to/refData/hg19 --informat fastq --outformat cooler -g hg19 -n test -o /path/to/outputdir --pairtoolspath /path/to/pairtools --samtoolspath /path/to/samtools --coolerpath /path/to/cooler```
+
+```$ hint pre -d /path/to/test.bam --refdir /path/to/refData/hg19 --informat bam --outformat juicer -g hg19 -n test -o /path/to/outputdir --pairtoolspath /path/to/pairtools --samtoolspath /path/to/samtools --juicerpath /path/to/juicer_tools.1.8.9_jcuda.0.8.jar```
+
+use ```$ which samtools ``` ```$ which pairtools ``` ```$ which cooler ``` to get the absolute path of these tools, and ```/path/to/juicer_tools.1.8.9_jcuda.0.8.jar``` should be the path where you store this file
+
+see details and more options
+
+```$ hint pre -h ```
+
+### HiNT-CNV
+HiNT cnv: prediction of copy number information, as well as segmentation from Hi-C.
+
+```$ hint cnv -m contactMatrix.cool -f cooler --refdir /path/to/refDir/hg19 -r 50 -g hg19 -n test -o /path/to/outputDir --bicseq /path/to/BICseq2-seg_v0.7.3 -e MboI```
+
+```$ hint cnv -m /path/to/4DNFIS6HAUPP.mcool::/resolutions/50000 -f cooler --refdir /path/to/refDir/hg38 -r 50 -g hg38 -n HepG2 --bicseq /path/to/BICseq2-seg_v0.7.3 -e DpnII```
+
+```$ hint cnv -m /path/to/4DNFICSTCJQZ.hic -f juicer --refdir /path/to/refDir/hg38 -r 50 -g hg38 -n HepG2 --bicseq /path/to/BICseq2-seg_v0.7.3 -e DpnII```
+
+```$ hint cnv -m /path/to/4DNFICSTCJQZ.hic -f juicer --refdir /path/to/refDir/hg38 -r 50 -g hg38 -n HepG2 --bicseq /path/to/BICseq2-seg_v0.7.3 -e DpnII --doiter```
+
+```/path/to/BICseq2-seg_v0.7.3``` should be the path where you store this package
+
+see details and more options
+
+```$ hint cnv -h ```
+
+### HiNT-TL
+HiNT tl: interchromosomal translocations and breakpoints detection from
+Hi-C inter-chromosomal interaction matrices.
+
+```$ hint tl -m /path/to/data_1Mb.cool,/path/to/data_100kb.cool --chimeric /path/to/test_chimeric.sorted.pairsam.gz --refdir /path/to/refDir/hg19 --backdir /path/to/backgroundMatrices/hg19 --ppath /path/to/pairix -f cooler -g hg19 -n test -o /path/to/outputDir```
+
+```$ hint tl -m /path/to/4DNFIS6HAUPP.mcool::/resolutions/1000000,/path/to/4DNFIS6HAUPP.mcool::/resolutions/100000 -f cooler --refdir /path/to/refDir/hg38 --backdir /path/to/backgroundMatrices/hg38 -g hg38 -n 4DNFICSTCJQZ -c 0.05 --ppath /path/to/pairix -p 12```
+
+```$ hint tl -m /path/to/4DNFICSTCJQZ.hic -f juicer --refdir /path/to/refData/hg38 --backdir /path/to/backgroundMatrices/hg38 -g hg38 -n 4DNFICSTCJQZ -c 0.05 --ppath /path/to/pairix -p 12 -o HiNTtransl_juicerOUTPUT```
+
+use ```$ which pairix ``` to get the absolute path of pairix
+
+see details and more options
+
+```$ hint tl -h ```
+
+## Output of HiNT
+### HiNT-PRE output
+In the HiNT-PRE output directory, you will find
+
+1. ```jobname.bam``` aligned lossless file in bam format
+2. ```jobname_merged_valid.pairs.gz``` reads pairs in pair format
+3. ```jobname_chimeric.sorted.pairsam.gz``` ambiguous chimeric read pairs used for breakpoint detection in [pairsam](https://github.com/mirnylab/pairtools) format
+4. ```jobname_valid.sorted.deduped.pairsam.gz``` valid read pairs used for Hi-C contact matrix creation in [pairsam](https://github.com/mirnylab/pairtools) format
+5. ```jobname.mcool``` Hi-C contact matrix in [cool](https://github.com/mirnylab/cooler) format
+6. ```jobname.hic``` Hi-C contact matrix in [hic](https://github.com/aidenlab/juicer) format
+
+### HiNT-CNV output
+In the HiNT-CNV output directory, you will find
+
+1. ```jobname_GAMPoisson.pdf``` the GAM regression result
+2. ```segmentation/jobname_bicsq_allchroms.txt``` CNV segments with log2 copy ratio and p-values in txt file
+3. ```segmentation/jobname_resolution_CNV_segments.png``` figure to visualize CNV segments
+4. ```segmentation/jobname_bicseq_allchroms.l2r.pdf``` figure to visualize log2 copy ration in each bin (bin size = resolution you set)
+5. ```segmentation/other_files``` intermediate files used to run BIC-seq
+6. ```jonname_dataForRegression/*``` data used for regression as well as residuals after removing Hi-C biases
+
+### HiNT-TL output
+In the HiNT-TL output directory, you will find
+
+1. ```jobname_Translocation_IntegratedBP.txt``` the final integrated translocation breakpoint
+2. ```jobname_chrompairs_rankProduct.txt``` rank product predicted potential translocated chromosome pairs
+3. ```otherFolders``` intermediate files used to identify the translocation breakpoints
+
+
+
+
+%package help
+Summary:	Development documents and examples for HiNT-Package
+Provides:	python3-HiNT-Package-doc
+%description help
+# HiNT 
+## A computational method for detecting copy number variations and translocations from Hi-C data
+
+## Summary
+**HiNT** (**Hi**-C for copy **N**umber variation and **T**ranslocation detection), a computational method to detect CNVs and Translocations from Hi-C data. HiNT has three main components: **HiNT-PRE**, **HiNT-CNV**, and **HiNT-TL**. HiNT-PRE preprocesses Hi-C data and computes the contact matrix, which stores contact frequencies between any two genomic loci; both HiNT-CNV and HiNT-TL starts with HI-C contact matrix, predicts copy number segments, and inter-chromosomal translocations, respectively 
+
+#### Overview of HiNT workflow: 
+<img src="https://github.com/suwangbio/HiNT/blob/master/images/HiNT_workflow.png" width="800">
+
+## Installation
+
+### Dependencies
+R and R packages
+
+1. [R >= 3.4](https://www.r-project.org/)
+2. [mgcv](https://cran.r-project.org/web/packages/mgcv/index.html), [strucchange](https://cran.r-project.org/web/packages/strucchange/index.html), [doParallel](https://www.rdocumentation.org/packages/parallel/versions/3.4.1), [Cairo](https://cran.r-project.org/web/packages/Cairo/index.html), [foreach](https://cran.r-project.org/web/packages/optparse/index.html)
+
+Python and Python packages
+
+1. [python >= 3.5](https://www.python.org/)
+2. [pyparix >= 0.3.0](https://github.com/4dn-dcic/pairix#pypairix), [cooler >= 0.7.4](https://github.com/mirnylab/cooler), [pairtools >= 0.2.2](https://github.com/mirnylab/pairtools), [numpy](https://www.scipy.org/install.html), [scipy](https://www.scipy.org/install.html), [pandas](https://pandas.pydata.org/), [sklearn](https://scikit-learn.org/stable/install.html), [multiprocessing](https://pypi.org/project/multiprocess/)
+
+Java and related tools (Optional: required when want to process Hi-C data with juicer tools)
+
+1. [Java (version >= 1.7)](https://www.java.com/en/download/)
+2. [Juicer tools (1.8.9 is recommended)](https://github.com/aidenlab/juicer/wiki/Download) 
+
+Perl
+
+1. [Perl (version >= 5)](https://www.perl.org/)
+
+
+Other dependencies
+
+1. [samtools](http://www.htslib.org/doc/) (1.3.1+)
+2. [BIC-seq2](http://www.math.pku.edu.cn/teachers/xirb/downloads/software/BICseq2/BICseq2/BICseq2-seg_v0.7.3.tar.gz) (0.7.3) ! This is optional: if you don't want to run HiNT-CNV, you don't need this package. [Download BICseq2, unzip it, and give the path of BICseq2-seg_v0.7.3 (/path/to/BICseq2-seg_v0.7.3)].
+3. [bwa](https://sourceforge.net/projects/bio-bwa/files/) (0.7.16+) ! This is optional: required only when your input is fastq
+4. [tabix](https://sourceforge.net/projects/samtools/files/tabix/) (0.2.6)
+
+### Install HiNT
+
+* Method1: Install using conda (highly recommended)
+
+	``` $ conda install -c su hint```
+
+	or
+
+	``` $ conda install hint```
+
+* Method2: Install from PyPI using pip.
+
+	``` $ pip install HiNT-Packages```
+
+* Method3: Install manually 
+  1. Install HiNT dependencies
+  2. Download HiNT ```git clone https://github.com/parklab/HiNT.git```
+  3. Go to HiNT directory, install it by ```$ python setup.py install ```
+
+  *** Type ```$ hint``` to test if HiNT successfully installed
+
+* Method 4: Run HiNT in a Docker container (highly recommended)
+
+	``` $ docker pull suwangbio/hint```
+
+	``` $ docker run suwangbio/hint hint```
+
+	See details of the usage on HiNT page at [docker hub](https://hub.docker.com/r/suwangbio/hint) 
+
+### Download reference files used in HiNT [HERE](https://www.dropbox.com/sh/2ufsyu4wvrboxxp/AABk5-_Fwy7jdM_t0vIsgYf4a?dl=0)
+
+1. Download HiNT references [HERE](https://www.dropbox.com/sh/qas48d7409t2syz/AACk5G2ngZ0vylLXsLFZXif_a?dl=0). Only hg19, hg38 and mm10 are available currently. Unzip it ```$ unzip hg19.zip ```
+2. Download HiNT background matrices [HERE](https://www.dropbox.com/sh/fyxx9u5g5vn57ez/AAAx-DtByKaU6HvTYyEUvCzRa?dl=0). Only hg19, hg38 and mm10 are available currently. Unzip it ```$ unzip hg19.zip ```
+3. Download BWA index files [HERE](https://www.dropbox.com/sh/l004df4108s6d3c/AAB6qtS95mBK_MdDZYlo2V-pa?dl=0). Only hg19, hg38 and mm10 are available currently. Unzip it ```$ unzip hg19.zip ```
+
+## Quick Start
+
+* Download the test datasets from [HERE](https://www.dropbox.com/sh/z1rceh8ddnsdtj7/AAC0VuDu48eh_RtzKHipztkLa?dl=0)
+
+### HiNT-PRE
+HiNT pre: Preprocessing Hi-C data. HiNT pre does alignment, contact matrix creation and normalization in one command line.
+
+```$ hint pre -d /path/to/hic_1.fastq.gz,/path/to/hic_2.fastq.gz -i /path/to/bwaIndex/hg19/hg19.fa --refdir /path/to/refData/hg19 --informat fastq --outformat cooler -g hg19 -n test -o /path/to/outputdir --pairtoolspath /path/to/pairtools --samtoolspath /path/to/samtools --coolerpath /path/to/cooler```
+
+```$ hint pre -d /path/to/test.bam --refdir /path/to/refData/hg19 --informat bam --outformat juicer -g hg19 -n test -o /path/to/outputdir --pairtoolspath /path/to/pairtools --samtoolspath /path/to/samtools --juicerpath /path/to/juicer_tools.1.8.9_jcuda.0.8.jar```
+
+use ```$ which samtools ``` ```$ which pairtools ``` ```$ which cooler ``` to get the absolute path of these tools, and ```/path/to/juicer_tools.1.8.9_jcuda.0.8.jar``` should be the path where you store this file
+
+see details and more options
+
+```$ hint pre -h ```
+
+### HiNT-CNV
+HiNT cnv: prediction of copy number information, as well as segmentation from Hi-C.
+
+```$ hint cnv -m contactMatrix.cool -f cooler --refdir /path/to/refDir/hg19 -r 50 -g hg19 -n test -o /path/to/outputDir --bicseq /path/to/BICseq2-seg_v0.7.3 -e MboI```
+
+```$ hint cnv -m /path/to/4DNFIS6HAUPP.mcool::/resolutions/50000 -f cooler --refdir /path/to/refDir/hg38 -r 50 -g hg38 -n HepG2 --bicseq /path/to/BICseq2-seg_v0.7.3 -e DpnII```
+
+```$ hint cnv -m /path/to/4DNFICSTCJQZ.hic -f juicer --refdir /path/to/refDir/hg38 -r 50 -g hg38 -n HepG2 --bicseq /path/to/BICseq2-seg_v0.7.3 -e DpnII```
+
+```$ hint cnv -m /path/to/4DNFICSTCJQZ.hic -f juicer --refdir /path/to/refDir/hg38 -r 50 -g hg38 -n HepG2 --bicseq /path/to/BICseq2-seg_v0.7.3 -e DpnII --doiter```
+
+```/path/to/BICseq2-seg_v0.7.3``` should be the path where you store this package
+
+see details and more options
+
+```$ hint cnv -h ```
+
+### HiNT-TL
+HiNT tl: interchromosomal translocations and breakpoints detection from
+Hi-C inter-chromosomal interaction matrices.
+
+```$ hint tl -m /path/to/data_1Mb.cool,/path/to/data_100kb.cool --chimeric /path/to/test_chimeric.sorted.pairsam.gz --refdir /path/to/refDir/hg19 --backdir /path/to/backgroundMatrices/hg19 --ppath /path/to/pairix -f cooler -g hg19 -n test -o /path/to/outputDir```
+
+```$ hint tl -m /path/to/4DNFIS6HAUPP.mcool::/resolutions/1000000,/path/to/4DNFIS6HAUPP.mcool::/resolutions/100000 -f cooler --refdir /path/to/refDir/hg38 --backdir /path/to/backgroundMatrices/hg38 -g hg38 -n 4DNFICSTCJQZ -c 0.05 --ppath /path/to/pairix -p 12```
+
+```$ hint tl -m /path/to/4DNFICSTCJQZ.hic -f juicer --refdir /path/to/refData/hg38 --backdir /path/to/backgroundMatrices/hg38 -g hg38 -n 4DNFICSTCJQZ -c 0.05 --ppath /path/to/pairix -p 12 -o HiNTtransl_juicerOUTPUT```
+
+use ```$ which pairix ``` to get the absolute path of pairix
+
+see details and more options
+
+```$ hint tl -h ```
+
+## Output of HiNT
+### HiNT-PRE output
+In the HiNT-PRE output directory, you will find
+
+1. ```jobname.bam``` aligned lossless file in bam format
+2. ```jobname_merged_valid.pairs.gz``` reads pairs in pair format
+3. ```jobname_chimeric.sorted.pairsam.gz``` ambiguous chimeric read pairs used for breakpoint detection in [pairsam](https://github.com/mirnylab/pairtools) format
+4. ```jobname_valid.sorted.deduped.pairsam.gz``` valid read pairs used for Hi-C contact matrix creation in [pairsam](https://github.com/mirnylab/pairtools) format
+5. ```jobname.mcool``` Hi-C contact matrix in [cool](https://github.com/mirnylab/cooler) format
+6. ```jobname.hic``` Hi-C contact matrix in [hic](https://github.com/aidenlab/juicer) format
+
+### HiNT-CNV output
+In the HiNT-CNV output directory, you will find
+
+1. ```jobname_GAMPoisson.pdf``` the GAM regression result
+2. ```segmentation/jobname_bicsq_allchroms.txt``` CNV segments with log2 copy ratio and p-values in txt file
+3. ```segmentation/jobname_resolution_CNV_segments.png``` figure to visualize CNV segments
+4. ```segmentation/jobname_bicseq_allchroms.l2r.pdf``` figure to visualize log2 copy ration in each bin (bin size = resolution you set)
+5. ```segmentation/other_files``` intermediate files used to run BIC-seq
+6. ```jonname_dataForRegression/*``` data used for regression as well as residuals after removing Hi-C biases
+
+### HiNT-TL output
+In the HiNT-TL output directory, you will find
+
+1. ```jobname_Translocation_IntegratedBP.txt``` the final integrated translocation breakpoint
+2. ```jobname_chrompairs_rankProduct.txt``` rank product predicted potential translocated chromosome pairs
+3. ```otherFolders``` intermediate files used to identify the translocation breakpoints
+
+
+
+
+%prep
+%autosetup -n HiNT-Package-2.2.8
+
+%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-HiNT-Package -f filelist.lst
+%dir %{python3_sitelib}/*
+
+%files help -f doclist.lst
+%{_docdir}/*
+
+%changelog
+* Mon May 29 2023 Python_Bot <Python_Bot@openeuler.org> - 2.2.8-1
+- Package Spec generated
diff --git a/sources b/sources
new file mode 100644
index 0000000..899b161
--- /dev/null
+++ b/sources
@@ -0,0 +1 @@
+f95b22f554010fd4f14bbf56c7dab3cf  HiNT-Package-2.2.8.tar.gz