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README.md

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![Build Status](https://github.com/jslfree080/bamscope/actions/workflows/tests.yml/badge.svg?branch=main)
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[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://github.com/jslfree080/bamscope/blob/main/LICENSE)
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A command line tool (in Kotlin/JVM) for visualizing BAM alignments.
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A command line tool (in Kotlin/JVM) for intuitively visualizing BAM alignments.
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<img alt="demonstration" src="https://github.com/jslfree080/jslfree080/blob/main/example2.png" width=550>
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## Interpretation of Output Image
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The images produced display the alignment of the bases using colored blocks. 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.
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The images produced display the alignment of the bases using colored blocks. 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.
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## Prerequisites
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