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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
@@ -22,20 +26,20 @@ bam2html -b <input.bam> chrom:start-end # a region of positions
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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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-
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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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+
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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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