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README.md

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[![DOI](https://zenodo.org/badge/291003590.svg)](https://doi.org/10.5281/zenodo.4005607)
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![GitHub (Pre-)Release Date](https://img.shields.io/github/release-date-pre/suqingdong/bam2html)
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# Generate Highlighted HTML of Bam
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> highlight the specific sites of html which output by `samtools tview`
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- tar/gzip/zip [optional for compressing]
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## Installation
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```bash
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pip install bam2html
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```
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## Usage
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```bash
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bam2html -b <input.bam> chrom:pos # single position
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bam2html -b <input.bam> chrom:pos -r /path/to/reference.fa # with reference
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bam2html -b <input.bam> chrom:pos -c 300 # set the width of window
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bam2html -b <input.bam> chrom:pos -color pink -bg green # set colors
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bam2html -bl bam_list pos_list # batch
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bam2html -bl bam_list pos_list # batch mode
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bam2html -bl bam_list pos_list -s # generate summary.html
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bam2html -bl bam_list pos_list -s -x zip # compress the result with zip
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bam2html -bl bam_list pos_list -s -x tar.gz # compress the result with tar/gzip
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```
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### Example Results
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- single position: [demo.1_985460.html](https://suqingdong.github.io/bam2html/example/demo.1_985460.html)
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- multiple positions: [demo.1_985460,985463,985469.html](https://suqingdong.github.io/bam2html/example/demo.1_985460,985463,985469.html)
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- region positions: [demo.1_985461-985465.html](https://suqingdong.github.io/bam2html/example/demo.1_985461-985465.html)
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- summary result: [summary.html](https://suqingdong.github.io/bam2html/example/summary.html)
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## Meaning of Base's Colors
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| Color | Mapping Quality | Selector |
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| - | - | - |
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> Underline: Secondary or orphan
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---
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## Documents
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https://bam2html.readthedocs.io

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