Metadata-Version: 2.4
Name: cutehap
Version: 1.0.0
Summary: Haplotype-resolved genomic structural variation detection with cuteHap
Home-page: https://github.com/Meltpinkg/cuteHap
Author: Shuqi Cao
Author-email: sqcao@stu.hit.edu.cn
License: MIT
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: scipy
Requires-Dist: pysam
Requires-Dist: Biopython
Requires-Dist: Cigar
Requires-Dist: numpy
Requires-Dist: Cython
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# cuteHap

A haplotype-resolved SV detector in phased long read sequencing data.

---
### Installation
We recommand the installation via conda or pip:
```
    The installation via conda and pypi is now in construction.
```
Alternatively, installing from source with:
```
    git clone https://github.com/Meltpinkg/cuteHap.git
    cd cuteHap
    CFLAGS="-std=c99" python setup.py install
```

---	
### Introduction
cuteHap detects germline or mosaic structural variations (SVs) through phased long reads sequencing alignments. 

---
### Dependence
	
	1. python3
 	2. scipy
	2. pysam
	3. Biopython
	4. cigar
	5. numpy
	6. Cython

---
### Quick Start
```
cuteHap <phased.bam> <reference.fa> <output.vcf> <workdir>
```

---
### Changelog
    cuteHap (v1.0.0)
    1. the initial version of cuteHap

---
### Contact
For advising, bug reporting and requiring help, please post on [Github Issue](https://github.com/Meltpinkg/cuteHap/issues) or contact sqcao@stu.hit.edu.cn.
