Add index size logging with per-contig statistics

src/chain.cpp

@@ -210,6 +210,46 @@ bool ChainMap::interval_map_sanity_check() {
     return true;
 }
 
+/**
+ * @brief Logs statistics about the chain index.
+ *
+ * This function reports the number of contigs, intervals, bases, and average
+ * interval length present in the chain interval map. If a nonzero byte count is
+ * provided, it also logs the memory footprint in bytes. Per-contig statistics,
+ * such as the number of intervals and bases, as well as the average interval
+ * length, are reported for each contig.
+ *
+ * @param bytes (optional) The size in bytes of the loaded index to report.
+ */
+void ChainMap::log_index_size(size_t bytes) const {
+    size_t total_intervals = 0;
+    size_t total_bases = 0;
+    std::vector<std::pair<std::string, std::pair<size_t, size_t>>> stats;
+    stats.reserve(interval_map.size());
+    for (const auto &kv : interval_map) {
+        size_t n = kv.second.size();
+        size_t bases = 0;
+        for (const auto &intvl : kv.second) {
+            bases += static_cast<size_t>(intvl.source_end) -
+                     static_cast<size_t>(intvl.source_start);
+        }
+        total_intervals += n;
+        total_bases += bases;
+        stats.push_back({kv.first, {n, bases}});
+    }
+    size_t avg_len = total_intervals ? total_bases / total_intervals : 0;
+    std::cerr << "[I::chain::log_index_size] contigs=" << interval_map.size()
+              << " intervals=" << total_intervals << " bases=" << total_bases
+              << " avg_len=" << avg_len;
+    if (bytes) std::cerr << " bytes=" << bytes << "\n";
+    for (const auto &s : stats) {
+        size_t avg = s.second.first ? s.second.second / s.second.first : 0;
+        std::cerr << "[I::chain::log_index_size] " << s.first
+                  << ": intervals=" << s.second.first
+                  << " bases=" << s.second.second << " avg_len=" << avg << "\n";
+    }
+}
+
 /* Get the rank in the start bitvector at contig[pos]
  * If pos > len(contig): return rank(contig[-1])
  *

src/chain.hpp

@@ -63,6 +63,7 @@ class ChainMap {
     void debug_print_interval_map();
     void debug_print_intervals(std::string contig, const int n);
     bool interval_map_sanity_check();
+    void log_index_size(size_t bytes = 0) const;
     int get_start_rank(std::string contig, int pos);
     int get_end_rank(std::string contig, int pos);
     bool update_interval_indexes(const std::string contig, const int32_t pos,

src/leviosam.cpp

@@ -21,6 +21,7 @@
 #include <algorithm>
 #include <ctime>
 #include <vector>
+#include <fstream>
 
 #include "aln.hpp"
 #include "collate.hpp"
@@ -121,7 +122,8 @@ void serialize_run(lift_opts args) {
         chain::ChainMap cfp(args.chain_fname, args.verbose,
                             args.allowed_cigar_changes, args.length_map);
         std::ofstream o(fn_index, std::ios::binary);
-        cfp.serialize(o);
+        size_t bytes = cfp.serialize(o);
+        cfp.log_index_size(bytes);
         std::cerr << "[I::serialize_run] levioSAM ChainMap saved to "
                   << fn_index << "\n";
     } else {
@@ -299,14 +301,17 @@ std::map<std::string, std::string> load_fasta(std::string ref_name) {
 }
 
 void lift_run(lift_opts args) {
+    size_t chain_bytes = 0;
     chain::ChainMap chain_map = [&] {
         if (args.chainmap_fname != "") {
-            std::cerr << "[I::lift_run] Loading levioSAM index...";
+            std::cerr << "[I::lift_run] Loading levioSAM 2 index...";
             std::ifstream in(args.chainmap_fname, std::ios::binary);
+            std::ifstream fs(args.chainmap_fname, std::ios::binary | std::ios::ate);
+            chain_bytes = fs.tellg();
             return chain::ChainMap(in, args.verbose,
                                    args.allowed_cigar_changes);
         } else if (args.chain_fname != "") {
-            std::cerr << "[I::lift_run] Building levioSAM index...";
+            std::cerr << "[I::lift_run] Building levioSAM 2 index...";
             if (args.length_map.size() == 0) {
                 std::cerr << "[E::lift_run] No length map is found. Please "
                              "set -F properly.\n";
@@ -349,6 +354,8 @@ void lift_run(lift_opts args) {
         exit(1);
     }
     std::cerr << "done\n";
+    if (args.chainmap_fname != "" || args.chain_fname != "")
+        chain_map.log_index_size(chain_bytes);
 
     samFile *sam_fp = (args.sam_fname == "")
                           ? sam_open("-", "r")