a little bit code clean up

bwt_gen/bwt_gen.c

@@ -257,13 +257,11 @@ BWT *BWTCreate(const unsigned int textLength, unsigned int *decodeTable)
 	bwt = (BWT*)calloc(1, sizeof(BWT));
 
 	bwt->textLength = 0;
-	bwt->inverseSa = 0;
 
 	bwt->cumulativeFreq = (unsigned*)calloc((ALPHABET_SIZE + 1), sizeof(unsigned int*));
 	initializeVAL(bwt->cumulativeFreq, ALPHABET_SIZE + 1, 0);
 
 	bwt->bwtSizeInWord = 0;
-	bwt->saValueOnBoundary = NULL;
 
 	// Generate decode tables
 	if (decodeTable == NULL) {
@@ -279,14 +277,6 @@ BWT *BWTCreate(const unsigned int textLength, unsigned int *decodeTable)
 	bwt->occSizeInWord = 0;
 	bwt->occValue = NULL;
 
-	bwt->saInterval = ALL_ONE_MASK;
-	bwt->saValueSize = 0;
-	bwt->saValue = NULL;
-
-	bwt->inverseSaInterval = ALL_ONE_MASK;
-	bwt->inverseSaSize = 0;
-	bwt->inverseSa = NULL;
-
 	return bwt;
 }
 
@@ -1047,7 +1037,6 @@ void BWTGenerateOccValueFromBwt(const unsigned int*  bwt, unsigned int* __restri
 	wordBetweenOccValue = OCC_INTERVAL / CHAR_PER_WORD;
 
 	// Calculate occValue
-	// [lh3] by default: OCC_INTERVAL_MAJOR=65536, OCC_INTERVAL=256
 	numberOfOccValue = (textLength + OCC_INTERVAL - 1) / OCC_INTERVAL + 1;				// Value at both end for bi-directional encoding
 	numberOfOccIntervalPerMajor = OCC_INTERVAL_MAJOR / OCC_INTERVAL;
 	numberOfOccValueMajor = (numberOfOccValue + numberOfOccIntervalPerMajor - 1) / numberOfOccIntervalPerMajor;
@@ -1464,11 +1453,7 @@ void BWTFree(BWT *bwt)
 	free(bwt->bwtCode);
 	free(bwt->occValue);
 	free(bwt->occValueMajor);
-	free(bwt->saValue);
-	free(bwt->inverseSa);
 	free(bwt->decodeTable);
-	free(bwt->saIndexRange);
-	free(bwt->saValueOnBoundary);
 	free(bwt);
 }
 
@@ -1503,19 +1488,6 @@ void BWTSaveBwtCodeAndOcc(const BWT *bwt, const char *bwtFileName, const char *o
 	bwtLength = BWTFileSizeInWord(bwt->textLength);
 	fwrite(bwt->bwtCode, sizeof(unsigned int), bwtLength, bwtFile);
 	fclose(bwtFile);
-/*
-	occValueFile = (FILE*)fopen(occValueFileName, "wb");
-	if (occValueFile == NULL) {
-		fprintf(stderr, "BWTSaveBwtCodeAndOcc(): Cannot open occ value file!\n");
-		exit(1);
-	}
-
-	fwrite(&bwt->inverseSa0, sizeof(unsigned int), 1, occValueFile);
-	fwrite(bwt->cumulativeFreq + 1, sizeof(unsigned int), ALPHABET_SIZE, occValueFile);
-	fwrite(bwt->occValue, sizeof(unsigned int), bwt->occSizeInWord, occValueFile);
-	fwrite(bwt->occValueMajor, sizeof(unsigned int), bwt->occMajorSizeInWord, occValueFile);
-	fclose(occValueFile);
-*/
 }
 
 void bwt_bwtgen(const char *fn_pac, const char *fn_bwt)

bwt_gen/bwt_gen.h

@@ -25,6 +25,11 @@
 #ifndef BWT_GEN_H
 #define BWT_GEN_H
 
+#include <stdint.h>
+
+//typedef int64_t bgint_t;
+typedef unsigned bgint_t;
+
 #define ALPHABET_SIZE				4
 #define BIT_PER_CHAR				2
 #define CHAR_PER_WORD				16
@@ -56,32 +61,17 @@
 #define truncateRight(value, offset)			( (value) >> (offset) << (offset) )
 #define DNA_OCC_SUM_EXCEPTION(sum)			((sum & 0xfefefeff) == 0)
 
-typedef struct SaIndexRange {
-	unsigned int startSaIndex;
-	unsigned int endSaIndex;
-} SaIndexRange;
-
 typedef struct BWT {
-	unsigned int textLength;			// length of the text
-	unsigned int saInterval;			// interval between two SA values stored explicitly
-	unsigned int inverseSaInterval;		// interval between two inverse SA stored explicitly
-	unsigned int inverseSa0;			// SA-1[0]
-	unsigned int *cumulativeFreq;		// cumulative frequency
+	bgint_t textLength;					// length of the text
+	bgint_t inverseSa0;					// SA-1[0]
+	bgint_t *cumulativeFreq;			// cumulative frequency
 	unsigned int *bwtCode;				// BWT code
 	unsigned int *occValue;				// Occurrence values stored explicitly
-	unsigned int *occValueMajor;		// Occurrence values stored explicitly
-	unsigned int *saValue;				// SA values stored explicitly
-	unsigned int *inverseSa;			// Inverse SA stored explicitly
-	SaIndexRange *saIndexRange;			// SA index range
-	int saIndexRangeNumOfChar;			// Number of characters indexed in SA index range
-	unsigned int *saValueOnBoundary;	// Pre-calculated frequently referred data
+	bgint_t *occValueMajor;				// Occurrence values stored explicitly
 	unsigned int *decodeTable;			// For decoding BWT by table lookup
-	unsigned int decodeTableGenerated;	// == TRUE if decode table is generated on load and will be freed
 	unsigned int bwtSizeInWord;			// Temporary variable to hold the memory allocated
 	unsigned int occSizeInWord;			// Temporary variable to hold the memory allocated
 	unsigned int occMajorSizeInWord;	// Temporary variable to hold the memory allocated
-	unsigned int saValueSize;			// Temporary variable to hold the memory allocated
-	unsigned int inverseSaSize;			// Temporary variable to hold the memory allocated
 	unsigned int saIndexRangeSize;		// Temporary variable to hold the memory allocated
 } BWT;