{
    "info": {
        "author": "Daniel Rice",
        "author_email": "daniel.rice@sanger.ac.uk",
        "bugtrack_url": null,
        "classifiers": [
            "Development Status :: 4 - Beta",
            "License :: OSI Approved :: GNU General Public License (GPL)",
            "Topic :: Scientific/Engineering :: Bio-Informatics",
            "Topic :: Scientific/Engineering :: Visualization"
        ],
        "description": "# shabam\nA python tool to plot BAM or CRAM sequence reads.\n\n## Installation\ninstall [cairo](https://www.cairographics.org/download/) if not already\ninstalled:\n```sh\n# macOS via conda, or via homebrew (choose one, then set the library path)\nconda install cairo pkgconfig\nbrew install cairo pkg-config\n```\n\nInstall shabam:\n```sh\npip install shabam\n```\n\n## The dream\n```py\nfrom shabam import seqplot\nseqplot('example.bam', chrom='1', start=30243, end=30321,\n    fastafile='reference.fasta', out='plot.svg')\n```\n\n![Reality](/tests/data/reality.svg)\n\n### Plotting options\n- shade reads by strand with `by_strand=True`\n- plot multiple sequence files together with a list of paths e.g.\n  `['child.bam', 'mom.bam', 'dad.bam']`\n- export PDF, PNG, SVG or PS formatted plots with matching filename extensions\n\n### Command line version\n```sh\nshabam \\\n  --seqfiles tests/data/example.bam \\\n  --chrom 1 \\\n  --start 30243 \\\n  --end 30321 \\\n  --fastafile tests/data/reference.fasta \\\n  --out plot.svg\n```\n\n## Further improvements to the dream\n- [ ] Use consensus sequence when we don't provide a reference sequence\n- [ ] Allow custom colors\n- [ ] Compute proportion of variants at any site\n- [ ] Plot read depth\n- [ ] At positions with proportion of variants > threshold, reflect proportion\n  with base colors\n- [ ] Option to scale plotted base size, currently at 10 pixels per base\n- [ ] Optionally shade plots deepVariant style:\n    - red channel: nucleotide\n    - blue channel: read strand\n    - green channel: base quality\n    - alpha: base supports ref or alt\n- [ ] Flatten vertical plotting in high depth sequence data\n- [ ] Down-sample reads for extremely high depth sequence data (>1000X)\n\n## Credit\nInitial cigar parsing code lifted with permission from\n[pybamview](https://github.com/mgymrek/pybamview).",
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        "name": "shabam",
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