Metadata-Version: 2.1
Name: bam2html
Version: 1.0.5
Summary: View Bam in Highlighted HTML
Home-page: https://github.com/suqingdong/bam2html
Author: suqingdong
Author-email: 1078595229@qq.com
License: BSD License
Project-URL: Documentation, https://bam2html.readthedocs.io
Project-URL: Tracker, https://github.com/suqingdong/bam2html/issues
Description: [![DOI](https://zenodo.org/badge/291003590.svg)](https://doi.org/10.5281/zenodo.4005607)
        ![GitHub (Pre-)Release Date](https://img.shields.io/github/release-date-pre/suqingdong/bam2html)
        
        # Generate Highlighted HTML of Bam
        > highlight the specific sites of bam with `samtools tview`
        
        
        ## Dependencies
        - Linux/Unix
        - Python2/Python3
        - samtools
        - tar/gzip/zip [optional for compressing]
        
        
        ## Installation
        ```bash
        pip install bam2html
        ```
        
        
        ## Usage
        ```bash
        bam2html -b <input.bam> chrom:pos           # single position
        bam2html -b <input.bam> chrom:pos1,pos2...  # multiple positions
        bam2html -b <input.bam> chrom:start-end     # a region of positions
        bam2html -b <input.bam> chrom:pos -r /path/to/reference.fa # with reference
        bam2html -b <input.bam> chrom:pos -c 300    # set the width of window
        bam2html -b <input.bam> chrom:pos -color pink -bg green    # set colors
        bam2html -bl bam_list pos_list                             # batch mode
        bam2html -bl bam_list pos_list -s                          # generate summary.html
        bam2html -bl bam_list pos_list -s -x zip                   # compress the result with zip
        bam2html -bl bam_list pos_list -s -x tar.gz                # compress the result with tar/gzip
        ```
        
        
        ### Example Results
        - single position: [demo.1_985460.html](https://suqingdong.github.io/bam2html/example/demo.1_985460.html)
        - multiple positions: [demo.1_985460,985463,985469.html](https://suqingdong.github.io/bam2html/example/demo.1_985460,985463,985469.html)
        - region positions: [demo.1_985461-985465.html](https://suqingdong.github.io/bam2html/example/demo.1_985461-985465.html)
        - summary result: [summary.html](https://suqingdong.github.io/bam2html/example/summary.html)
        
        
        ## Meaning of Base's Colors
        | Color | Mapping Quality | Selector |
        | - | - | - |
        | Blue | 0-9 | .tviewcu1 |
        | Green | 10-19 | .tviewc2 |
        | Yellow | 20-29 | .tviewc3 |
        | Black |>=30 | .tviewc4 |
        
        > Underline: Secondary or orphan
        
        ---
        ## Documents
        https://bam2html.readthedocs.io
        
Platform: UNKNOWN
Classifier: Development Status :: 5 - Production/Stable
Classifier: Operating System :: OS Independent
Classifier: Intended Audience :: Developers
Classifier: License :: OSI Approved :: BSD License
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 2
Classifier: Programming Language :: Python :: 2.7
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.6
Classifier: Topic :: Software Development :: Libraries
Description-Content-Type: text/markdown
