getChrNames.sh now uses the neighborhood executable bundled in the script directory, so users no longer need to install it manually. Resolution order is $PATH → script directory → error.
getChrNames.sh check_dependencies now correctly reports missing mashmap, seqtk, or neighborhood instead of silently passing when which returns empty.
getChrNames.sh: hoisted isHIC / isRUK detection out of the cache-guarded block. On re-runs where unitigs.hpc.mashmap.out already exists, the variables are now defined when later code symlinks the homopolymer-compressed .noseq.gfa, fixing a stale-cache failure.
getChrNames.sh: the reference FASTA argument is now validated; an empty or missing --reference exits with a clear error.
getChrNames.sh: realpath arguments are now quoted (realpath -- "$1"), so reference paths containing spaces are handled correctly.
getChrNames.sh: verbose set -x tracing is now opt-in via DEBUG=1 instead of being on by default.
getChrNames.sh: minor cleanups — removed dead ref=$1 at top of file, fixed echo "Examples:\n" so it no longer prints a literal \n.
