CN: per-probe heterozygous BAF spread from the batch reference; --mosaic-prior/--switch-distance; Pi memory guard

scripts/pi_run.sh runs heavy jobs in their own process group and stops them when
MemAvailable drops below a floor (Raspberry Pi OS boots with cgroup_disable=memory, so a
systemd MemoryMax cap is not available); a 360-sample genotype run with cohort QC had
exhausted memory and the OOM killer took down the desktop session.

Co-Authored-By: Claude Opus 5.5 <[email protected]>
Claude-Session: https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv

scripts/pi_run.sh

@@ -0,0 +1,30 @@
+#!/usr/bin/env bash
+# Run a heavy command on the 8 GB Pi with a memory guard. Raspberry Pi OS boots with cgroup_disable=memory, so
+# systemd MemoryMax cannot be used; instead the command runs in its own process group and is stopped (TERM, then
+# KILL) as soon as the system's MemAvailable drops below MIN_FREE_MB -- before the kernel OOM killer would pick
+# victims such as the desktop session. Prints the peak resident memory of the command's process tree.
+#   MIN_FREE_MB=1200 bash scripts/pi_run.sh <command...>
+set -uo pipefail
+MIN_FREE_MB=${MIN_FREE_MB:-1200}
+setsid "$@" &
+pid=$!
+peak=0
+tripped=0
+tree_rss() {  # kB, summed over the process group
+  ps -o rss= -g "$pid" 2>/dev/null | awk '{s+=$1} END {print s+0}'
+}
+while kill -0 "$pid" 2>/dev/null; do
+  rss=$(tree_rss); (( rss > peak )) && peak=$rss
+  avail=$(awk '/^MemAvailable:/ {print int($2/1024)}' /proc/meminfo)
+  if (( avail < MIN_FREE_MB )); then
+    echo "pi_run: MemAvailable ${avail} MiB < ${MIN_FREE_MB} MiB -- stopping the job (process group $pid)" >&2
+    kill -TERM -- "-$pid" 2>/dev/null; sleep 5; kill -KILL -- "-$pid" 2>/dev/null
+    tripped=1
+    break
+  fi
+  sleep 1
+done
+wait "$pid"; rc=$?
+(( tripped )) && rc=137
+echo "pi_run: exit $rc, peak RSS $((peak / 1024)) MiB, guard ${MIN_FREE_MB} MiB free" >&2
+exit $rc