{"id":33051296,"url":"https://github.com/jslfree080/bamscope","last_synced_at":"2025-11-18T21:00:57.285Z","repository":{"id":65916481,"uuid":"592049218","full_name":"jslfree080/bamscope","owner":"jslfree080","description":"A command line tool (in Kotlin/JVM) for intuitively visualizing BAM alignments. 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The opacity of each block reflects the quality score of the base, with blocks valued near 1 displayed for high-quality scores near 40 and those valued near 0 for low-quality scores close to 0. The strandedness of each read's alignment is indicated in both the leftmost and rightmost columns, where '→' indicates a forward strand alignment and '←' indicates a reverse strand alignment.\n\n## Prerequisites\n\nBamscope requires **Java 11** or later versions to build and run.\n\nAlso, [samtools](https://github.com/samtools/samtools) should be pre-installed to support accessing file formats such as BAM and FASTA.\n\n## Building\n\n* Clone the repo:\n```\n    git clone https://github.com/jslfree080/bamscope.git\n    cd bamscope/\n```\n\n* Build an executable Bamscope jar with all dependencies packaged:\n```\n    ./gradlew build\n```\n\n## Usage\n\n### Command line\n\nThe resulting jar will be in `build/libs`.\n\n```\nUsage: java -jar build/libs/bamscope.jar \u003cchrPos\u003e \u003cbamPath\u003e [options]\n\nParameters:\n      \u003cchrPos\u003e              Input chromosomal position       ex) (chr)N:XXXXXXXX\n                                 or path to a VCF file.         or path/to/x.vcf\n      \u003cbamPath\u003e             Path to an indexed BAM file.       ex) path/to/x.bam\n     \nOptions:\n  -f, --format=\u003cformat\u003e     File format of an output image.         default) png\n  -h, --help                Show this help message and exit.\n  -o, --outPath=\u003coutPath\u003e   Path to an output image.                  default) .\n  -r, --refPath=\u003crefPath\u003e   Path to a reference FASTA.  ex) path/to/x.fasta(.fa)\n  -s, --sPath=\u003csPath\u003e       Path to the samtools.    ex) /usr/local/bin/samtools\n  -w, --width=\u003cwidth\u003e       Width of start to interest position.     default) 50\n```\n\n* Example usage for a specific position:\n```\n    java -jar build/libs/bamscope.jar 18:53254446 ~/Downloads/x.bam -r ~/Downloads/x.fasta -o ~/Desktop/\n```\n\n* Example usage with VCF file (⚠️ This option may be computationally intensive):\n```\n    java -jar build/libs/bamscope.jar ~/Desktop/x.vcf ~/Downloads/x.bam -r ~/Downloads/x.fasta -o ~/Desktop/\n```\n\n## License\n\nCode and documentation released under the [MIT license](https://github.com/jslfree080/bamscope/blob/master/LICENSE).\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fjslfree080%2Fbamscope","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fjslfree080%2Fbamscope","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fjslfree080%2Fbamscope/lists"}