bam-viewer

BAM alignment viewer with BGZF decompression, FLAG decoding, CIGAR visualization, and MAPQ filtering.

Features

• BGZF block decompression via pako.js
• BAM binary header and alignment record parsing
• FLAG bitfield decoding with colored badges (paired, mapped, reverse, etc.)
• CIGAR string visualization with color-coded operations (M, I, D, S, H, N)
• MAPQ score display with quality indicator
• Reference sequence list from header (@SQ lines)
• Read group and program metadata display
• Chromosome and MAPQ filters
• Pagination for large files (100 reads per page, first 2000 reads max)

Supported Extensions

• .bam

Installation

Install from the Plugins tab in the AutoPipe desktop app.