Creates a lightweight connection object that validates the BAM index,
probes the header for sequence names and lengths, and exposes a
$fetch(region, ...) method returning a GRanges of alignments.
Usage
open_bam(path, max_fetch_bp = 100000L)
Arguments
- path
Character. Path to an indexed BAM file (.bam).
- max_fetch_bp
Integer. Maximum genomic span per $fetch() call.
Default 1e5 (100 kb). BAM fetches over wide regions can be very
slow — keep this tight.
Value
A SeqBam S3 object with seqnames, seq_lengths,
max_fetch_bp, and a fetch(region, min_mapq, max_reads) closure.