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comparison pyPRADA_1.2/tools/bwa-0.5.7-mh/bwt_gen/QSufSort.h @ 0:acc2ca1a3ba4

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author siyuan
date Thu, 20 Feb 2014 00:44:58 -0500
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1 /* QSufSort.h
2
3 Header file for QSufSort.c
4
5 This file contains an implementation of the algorithm presented in "Faster
6 Suffix Sorting" by N. Jesper Larsson (jesper@cs.lth.se) and Kunihiko
7 Sadakane (sada@is.s.u-tokyo.ac.jp).
8
9 This software may be used freely for any purpose. However, when distributed,
10 the original source must be clearly stated, and, when the source code is
11 distributed, the copyright notice must be retained and any alterations in
12 the code must be clearly marked. No warranty is given regarding the quality
13 of this software.
14
15 Modified by Wong Chi-Kwong, 2004
16
17 Changes summary: - Used long variable and function names
18 - Removed global variables
19 - Replace pointer references with array references
20 - Used insertion sort in place of selection sort and increased insertion sort threshold
21 - Reconstructing suffix array from inverse becomes an option
22 - Add handling where end-of-text symbol is not necessary < all characters
23 - Removed codes for supporting alphabet size > number of characters
24
25 No warrenty is given regarding the quality of the modifications.
26
27 */
28
29 #ifndef __QSUFSORT_H__
30 #define __QSUFSORT_H__
31
32 #define KEY(V, I, p, h) ( V[ I[p] + h ] )
33 #define INSERT_SORT_NUM_ITEM 16
34
35 void QSufSortSuffixSort(int* __restrict V, int* __restrict I, const int numChar, const int largestInputSymbol,
36 const int smallestInputSymbol, const int skipTransform);
37 void QSufSortGenerateSaFromInverse(const int *V, int* __restrict I, const int numChar);
38
39
40 #endif