Crate rsomics_bam_to_bed 

Convert BAM alignments to BED6 format.

Algorithm

For each mapped alignment, emit one BED6 record: chrom start end name score strand

• start is 0-based (BED convention), sourced directly from the BAM pos field which is also 0-based.
• end = start + reference span of the alignment.
• score is the mapping quality (MAPQ) unless use_edit_distance is set, in which case the NM auxiliary tag value is used.
• strand is + for forward, - for reverse-complemented reads.

With split, any spliced alignment (containing N CIGAR operations) is broken into individual exon blocks — one BED record per block. The name and score come from the read; blocks are non-overlapping and non-adjacent.

Unmapped reads (FLAG & 0x4) are always skipped.

Reference

BEDTools bamtobed — Quinlan & Hall (2010). Bioinformatics 26(6): 841–842. DOI: 10.1093/bioinformatics/btq033

Structs

BamToBedOpts

Functions

bam_to_bed