Added a method to read in the non-RLE BWT from a binary bwt file.

jts · Nov 19, 2010 · 74149fe · 74149fe
1 parent 737df47
commit 74149fe
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Showing 5 changed files with 24 additions and 4 deletions.
diff --git a/src/SGA/rmdup.cpp b/src/SGA/rmdup.cpp
@@ -121,7 +121,7 @@ void rmdup()
     delete pBWT; 
     delete pRBWT;
     delete pTimer;
-
+    
     std::string out_prefix = stripFilename(opt::outFile);
     std::string dupsFile = parseDupHits(hitsFilenames, out_prefix);
 

diff --git a/src/SuffixTools/BWTReaderBinary.cpp b/src/SuffixTools/BWTReaderBinary.cpp
@@ -35,6 +35,22 @@ void BWTReaderBinary::read(RLBWT* pRLBWT)
     //pRLBWT->print();
 }
 
+void BWTReaderBinary::read(SBWT* pSBWT)
+{
+    BWFlag flag;
+    size_t numSymbols;
+    readHeader(pSBWT->m_numStrings, numSymbols, flag);
+    size_t numRead = 0;
+    pSBWT->m_bwStr.resize(numSymbols);
+    while(numRead < numSymbols)
+    {
+        char b = readBWChar();
+        pSBWT->m_bwStr.set(numRead++, b);
+    }
+
+    assert(m_numRunsOnDisk > 0);
+}
+
 //
 void BWTReaderBinary::readHeader(size_t& num_strings, size_t& num_symbols, BWFlag& flag)
 {

diff --git a/src/SuffixTools/BWTReaderBinary.h b/src/SuffixTools/BWTReaderBinary.h
@@ -27,6 +27,8 @@ class BWTReaderBinary : public IBWTReader
 
         //
         virtual void read(RLBWT* pRLBWT);
+        virtual void read(SBWT* pSBWT);
+
         virtual void readHeader(size_t& num_strings, size_t& num_symbols, BWFlag& flag);
         virtual char readBWChar();
         virtual void readRuns(RLVector& out, size_t numRuns);

diff --git a/src/SuffixTools/SBWT.cpp b/src/SuffixTools/SBWT.cpp
@@ -9,6 +9,7 @@
 #include "SBWT.h"
 #include "Timer.h"
 #include "BWTReaderAscii.h"
+#include "BWTReaderBinary.h"
 #include "BWTWriterAscii.h"
 #include <istream>
 #include <queue>
@@ -21,7 +22,7 @@
 // Parse a BWT from a file
 SBWT::SBWT(const std::string& filename, int sampleRate)
 {
-    BWTReaderAscii reader(filename);
+    BWTReaderBinary reader(filename);
     reader.read(this);
     initializeFMIndex(sampleRate);
 }
@@ -136,5 +137,5 @@ void SBWT::printInfo() const
     printf("Sample rate: %zu\n", m_occurrence.getSampleRate());
     printf("Memory -- OCC: %zu C: %zu Str: %zu Misc: %zu TOTAL: %zu (%lf MB)\n",
             o_size, p_size, bwStr_size, offset_size, total_size, total_mb);
-    printf("N: %zu Bytes per suffix: %lf\n", m_bwStr.length(), (double)total_size / m_bwStr.length());
+    printf("N: %zu Bytes per symbol: %lf\n", m_bwStr.length(), (double)total_size / m_bwStr.length());
 }
diff --git a/src/SuffixTools/SBWT.h b/src/SuffixTools/SBWT.h
@@ -76,7 +76,8 @@ class SBWT
         friend class BWTReaderAscii;
         friend class BWTWriterAscii;
 
-        static const int DEFAULT_SAMPLE_RATE = 64;
+        static const int DEFAULT_SAMPLE_RATE = 128;
+        static const int DEFAULT_SAMPLE_RATE_SMALL = DEFAULT_SAMPLE_RATE;
 
     private: