methdup

methdup deduplicates complete, same-reference proper pairs from a coordinate-sorted BAM in one pass. By default it retains every record and sets the SAM duplicate bit (0x400) on the lower-quality pair in each duplicate group.

Install

cargo install --path .

Usage

methdup input.bam output.bam
methdup input.bam deduplicated.bam --remove-duplicates

On success it prints a summary to stderr and exits 0:

methdup: records=4 eligible_pairs=2 duplicate_pairs=1 flagged_records=2 removed_records=0 passthrough_records=0 peak_cache_records=4

Duplicate identity includes both read ends' start coordinates, orientations, and CIGAR strings, plus the pair's library resolved from its read group's LB field (RG tag → @RG). Records without a resolvable library all share an Unknown Library group, so they are compared against each other but never against records from a named library. The representative is the pair with the largest combined base-quality sum; input order breaks ties.

The command preserves coordinate order using a sliding cache. Set --max-cache-records N to bound that cache (default: 1,000,000); it fails safely if the bound is exceeded. It requires a BAM whose header declares coordinate sorting and verifies that the records actually obey that ordering.

Unmapped, secondary, supplementary, incomplete, and inter-reference records are passed through unchanged. No BAM index is created.