Added RLCSA index option

[SXSI/TextCollection.git] / incbwt / read_bwt.cpp

diff --git a/incbwt/read_bwt.cpp b/incbwt/read_bwt.cpp
new file mode 100644 (file)
index 0000000..6b7b65e
--- /dev/null
+++ b/incbwt/read_bwt.cpp
@@ -0,0 +1,103 @@
+#include <cstdlib>
+#include <fstream>
+#include <iostream>
+
+#include "rlcsa.h"
+
+
+using namespace CSA;
+
+
+/*
+  This program writes run-length encoded PLCP of the collection into a file.
+*/
+
+
+usint
+countRuns(usint prev, uchar* buffer, usint length)
+{
+  usint runs = 0;
+
+  for(usint i = 0; i < length; i++)
+  {
+    if(buffer[i] != prev)
+    {
+      prev = buffer[i];
+      if(buffer[i] != 0) { runs++; }
+    }
+  }
+
+  return runs;
+}
+
+
+int
+main(int argc, char** argv)
+{
+  std::cout << "RLCSA to BWT converter" << std::endl;
+  if(argc < 2)
+  {
+    std::cout << "Usage: read_bwt base_name [buffer_size]" << std::endl;
+    return 1;
+  }
+
+  std::string base_name = argv[1];
+  std::string bwt_name = base_name + ".bwt";
+  std::cout << "BWT: " << bwt_name << std::endl;
+  std::ofstream bwt_file(bwt_name.c_str(), std::ios_base::binary);
+  if(!bwt_file)
+  {
+    std::cerr << "Error creating BWT file!" << std::endl;
+    return 2;
+  }
+  std::cout << std::endl;
+
+  RLCSA rlcsa(base_name);
+  clock_t start = clock();
+  usint buffer_size = 0;
+  if(argc > 2) { buffer_size = atoi(argv[2]); }
+  usint n = rlcsa.getSize() + rlcsa.getNumberOfSequences();
+
+  usint runs = 0, prev = CHARS;
+  if(buffer_size > 0)
+  {
+    for(usint i = 0; i < n; i += buffer_size)
+    {
+      pair_type range(i, std::min(i + buffer_size - 1, n - 1));
+      uchar* bwt = rlcsa.readBWT(range);
+      if(bwt != 0)
+      {
+        runs += countRuns(prev, bwt, length(range));
+        prev = bwt[length(range) - 1];
+        bwt_file.write((char*)bwt, length(range));
+        delete[] bwt;
+      }
+    }
+  }
+  else
+  {
+    uchar* bwt = rlcsa.readBWT();
+    if(bwt != 0)
+    {
+      runs = countRuns(prev, bwt, n);
+      bwt_file.write((char*)bwt, n);
+      delete[] bwt;
+    }
+  }
+
+  clock_t stop = clock();
+  double time = ((stop - start) / (double)CLOCKS_PER_SEC);
+  double megabytes = n / (double)MEGABYTE;
+  std::cout << megabytes << " megabytes in " << time << " seconds (" << (megabytes / time) << " MB/s)" << std::endl;
+  std::cout << std::endl;
+
+  // Testing direct reporting of the number of runs.
+  // This is as expensive as reading the BWT.
+  std::cout << "Number of runs: " << runs << std::endl;
+  runs = rlcsa.countRuns();
+  std::cout << "Number of runs (direct count): " << runs << std::endl;
+  std::cout << std::endl;
+
+  bwt_file.close();
+  return 0;
+}