PlainMap: a lightweight, restartable mapping pipeline for ancient and modern DNA

Added

• Added opt-in --run-adaptclean for residual adapter cleanup of true single-end reads after fastp, with --adaptclean CMD for the external executable. Each processed chunk records its cycle length, adapter prefix, shortened-read count, and post-cleanup minimum-length removals in SAMPLE.adaptclean.tsv. Paired-end and merged reads are unchanged.
• AdaptClean now infers one cycle length per original SE FASTQ from the longest supported raw read length, so pre-trimmed variable-length reads and pre-fastp chunking work together. If the maximum is insufficiently supported, it warns and skips AdaptClean for that file without skipping fastp.

Fixed

• Resuming after an interruption during fastp preprocessing now rebuilds the complete pre-fastp chunk set before restarting preprocessing. Previously, delete-as-you-go could leave only unprocessed chunks, causing a resumed run to silently omit reads from chunks already trimmed before the interruption.