diff bwa-0.6.2/QSufSort.h @ 2:a294fbfcb1db draft default tip

Uploaded BWA

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bwa-0.6.2/QSufSort.h	Fri Jul 18 07:55:59 2014 -0400
@@ -0,0 +1,45 @@
+/* QSufSort.h
+
+   Header file for QSufSort.c
+
+   This file contains an implementation of the algorithm presented in "Faster
+   Suffix Sorting" by N. Jesper Larsson ([e-mail]) and Kunihiko
+   Sadakane ([e-mail]).
+
+   This software may be used freely for any purpose. However, when distributed,
+   the original source must be clearly stated, and, when the source code is
+   distributed, the copyright notice must be retained and any alterations in
+   the code must be clearly marked. No warranty is given regarding the quality
+   of this software.
+
+   Modified by Wong Chi-Kwong, 2004
+
+   Changes summary:	- Used long variable and function names
+					- Removed global variables
+					- Replace pointer references with array references
+					- Used insertion sort in place of selection sort and increased insertion sort threshold
+					- Reconstructing suffix array from inverse becomes an option
+					- Add handling where end-of-text symbol is not necessary < all characters
+					- Removed codes for supporting alphabet size > number of characters
+  
+  No warrenty is given regarding the quality of the modifications.
+
+*/
+
+#ifndef __QSUFSORT_H__
+#define __QSUFSORT_H__
+
+#include <stdint.h>
+
+#define KEY(V, I, p, h)					( V[ I[p] + h ] )
+#define INSERT_SORT_NUM_ITEM	16
+
+typedef int64_t qsint_t;
+#define QSINT_MAX INT64_MAX
+
+void QSufSortSuffixSort(qsint_t* __restrict V, qsint_t* __restrict I, const qsint_t numChar, const qsint_t largestInputSymbol, 
+						const qsint_t smallestInputSymbol, const int skipTransform);
+void QSufSortGenerateSaFromInverse(const qsint_t *V, qsint_t* __restrict I, const qsint_t numChar);
+
+
+#endif