perf(build): enable geometric LCP memoization for genome indexing

CHANGELOG.md

@@ -13,6 +13,14 @@ Sections commonly used: Features, Bug fixes, Other changes.
 
 ### Other changes
 
+- Production genome indexing now enables caps-sa 0.7's bounded geometric LCP
+  memoization through its stable policy API. On the complete ruSTAR-shaped
+  GRCh38 plus GENCODE v50 fixture (6.56 billion symbols, 6.18 billion retained
+  suffixes, 1.40 million segments, 32 physical cores), the final caps-sa 0.7
+  implementation built the SA in 172.953 s versus 267.592 s for its original
+  0.7 baseline: 35.4% faster, with peak RSS reduced from 10,512,408 to
+  9,169,892 KiB. The complete output hash was unchanged.
+
 - `cluster_seeds` reuses its window-bin map across reads on a thread instead
   of rebuilding it per read. Merging two windows re-keys every bin in the
   merged span, so the per-read pre-sizing was only a floor and the map

Cargo.toml

@@ -46,7 +46,7 @@ chrono = "0.4"
 tempfile = "3"
 bitflags = { version = "2.12.1", features = ["std"] }
 shlex = "2.0.1"
-caps-sa = "0.6"
+caps-sa = "0.7"
 # mimalloc as the global allocator. Two reasons:
 #   1. **Memory return**: glibc malloc creates one arena per worker
 #      thread (rayon spawns ~num_cpus workers + sub-threads) and

src/index/sa_build.rs

@@ -633,7 +633,13 @@ fn dispatch_caps_sa_segmented(
     );
 
     if use_ext_mem(n) {
-        let opts = caps_sa_ext_mem_opts(temp_dir);
+        // The production segmented genome-plus-junction layout contains many
+        // long shared contexts across phase-4 partition merges. Enable caps-sa's
+        // bounded, partition-local geometric LCP memoization with its measured
+        // defaults. The policy remains explicit here: caps-sa itself defaults
+        // to the direct kernel for generic inputs.
+        let opts = caps_sa_ext_mem_opts(temp_dir)
+            .lcp_memoization(caps_sa::LcpMemoizationPolicy::geometric());
         // Predicate accepts ACGT only (rejects N at 4, spacer at 5).
         // Borrows `original` via `&[u8]` — `Send + Sync` is satisfied.
         let original_ref: &[u8] = original;