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        "author": "Yuichi Shiraishi",
        "author_email": "friend1ws@gamil.com",
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        "classifiers": [
            "Development Status :: 4 - Beta",
            "Intended Audience :: Science/Research",
            "License :: OSI Approved :: GNU General Public License v3 (GPLv3)",
            "Operating System :: Unix",
            "Programming Language :: Python :: 2.7",
            "Programming Language :: Python :: 3.5",
            "Programming Language :: Python :: 3.6",
            "Topic :: Scientific/Engineering :: Bio-Informatics"
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        "description": "# chimera_utils\n\n[![License: GPL v3](https://img.shields.io/badge/License-GPL%20v3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0)\n[![Build Status](https://travis-ci.org/friend1ws/chimera_utils.svg?branch=devel)](https://travis-ci.org/friend1ws/chimera_utils)\n\n\n## Introduction \n\nThis is a suite of tools for processing chimeric reads generated at a STAR alignment step (Chimeric.out.sam files).\n\n## Dependency\n\n### Python\npysam, [annot_utils](https://github.com/friend1ws/annot_utils), [fusionfusion](https://github.com/Genomon-Project/fusionfusion)\n\n### Software\n[htslib](http://www.htslib.org), [bedtools](http://bedtools.readthedocs.io/en/latest/)\n\n\n## Install\n\n```\npip install chimera_utils\n```\n\nAlternatively you can download from the source code:\n```\nwget https://github.com/friend1ws/chimera_utils/archive/v0.5.0.tar.gz\ntar zxvf v0.6.0.tar.gz\ncd chimera_utils-0.6.0\npython setup.py build install\n```\n\nFor the last command, you may need to add --user if using a shared computing cluster.\n\n## Commands\n\n### count\nCount supporting read pairs for each chimera junction\n\n```\nchimera_utils count [-h] [--abnormal_insert_size ABNORMAL_INSERT_SIZE]\n                          [--min_major_clipping_size MIN_MAJOR_CLIPPING_SIZE]\n                          [--min_read_pair_num MIN_READ_PAIR_NUM]\n                          [--min_cover_size MIN_COVER_SIZE]\n                          [--anchor_size_thres ANCHOR_SIZE_THRES]\n                          [--min_chimeric_size MIN_CHIMERIC_SIZE] [--debug]\n                          Chimeric.out.sam output_file\n```\n\n### merge_control\nMerge chimeric junction cout file (generated by `count` command) of control data (typically) for later filtering\n\n```\nchimera_utils merge_control [-h] chimeric_count_list.txt output_file\n```\n\n### associate\nAssociate chimeric junctions with the output of GenomonSV\n\n```\nchimera_utils associate [-h] [--margin MARGIN]\n                               [--sv_margin_major SV_MARGIN_MAJOR]\n                               [--sv_margin_minor SV_MARGIN_MINOR]\n                               [--genome_id {hg19,hg38,mm10}] [--grc]\n                               [--debug]\n                               chimera.txt genomonSV.result.txt output.txt\n```",
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