forked from DaehwanKimLab/hisat2
/
diff_sample.cpp
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/
diff_sample.cpp
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/*
* Copyright 2011, Ben Langmead <langmea@cs.jhu.edu>
*
* This file is part of Bowtie 2.
*
* Bowtie 2 is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* Bowtie 2 is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with Bowtie 2. If not, see <http://www.gnu.org/licenses/>.
*/
#include "diff_sample.h"
struct sampleEntry clDCs[16];
bool clDCs_calced = false; /// have clDCs been calculated?
/**
* Entries 4-57 are transcribed from page 6 of Luk and Wong's paper
* "Two New Quorum Based Algorithms for Distributed Mutual Exclusion",
* which is also used and cited in the Burkhardt and Karkkainen's
* papers on difference covers for sorting. These samples are optimal
* according to Luk and Wong.
*
* All other entries are generated via the exhaustive algorithm in
* calcExhaustiveDC().
*
* The 0 is stored at the end of the sample as an end-of-list marker,
* but 0 is also an element of each.
*
* Note that every difference cover has a 0 and a 1. Intuitively,
* any optimal difference cover sample can be oriented (i.e. rotated)
* such that it includes 0 and 1 as elements.
*
* All samples in this list have been verified to be complete covers.
*
* A value of 0xffffffff in the first column indicates that there is no
* sample for that value of v. We do not keep samples for values of v
* less than 3, since they are trivial (and the caller probably didn't
* mean to ask for it).
*/
uint32_t dc0to64[65][10] = {
{0xffffffff}, // 0
{0xffffffff}, // 1
{0xffffffff}, // 2
{1, 0}, // 3
{1, 2, 0}, // 4
{1, 2, 0}, // 5
{1, 3, 0}, // 6
{1, 3, 0}, // 7
{1, 2, 4, 0}, // 8
{1, 2, 4, 0}, // 9
{1, 2, 5, 0}, // 10
{1, 2, 5, 0}, // 11
{1, 3, 7, 0}, // 12
{1, 3, 9, 0}, // 13
{1, 2, 3, 7, 0}, // 14
{1, 2, 3, 7, 0}, // 15
{1, 2, 5, 8, 0}, // 16
{1, 2, 4, 12, 0}, // 17
{1, 2, 5, 11, 0}, // 18
{1, 2, 6, 9, 0}, // 19
{1, 2, 3, 6, 10, 0}, // 20
{1, 4, 14, 16, 0}, // 21
{1, 2, 3, 7, 11, 0}, // 22
{1, 2, 3, 7, 11, 0}, // 23
{1, 2, 3, 7, 15, 0}, // 24
{1, 2, 3, 8, 12, 0}, // 25
{1, 2, 5, 9, 15, 0}, // 26
{1, 2, 5, 13, 22, 0}, // 27
{1, 4, 15, 20, 22, 0}, // 28
{1, 2, 3, 4, 9, 14, 0}, // 29
{1, 2, 3, 4, 9, 19, 0}, // 30
{1, 3, 8, 12, 18, 0}, // 31
{1, 2, 3, 7, 11, 19, 0}, // 32
{1, 2, 3, 6, 16, 27, 0}, // 33
{1, 2, 3, 7, 12, 20, 0}, // 34
{1, 2, 3, 8, 12, 21, 0}, // 35
{1, 2, 5, 12, 14, 20, 0}, // 36
{1, 2, 4, 10, 15, 22, 0}, // 37
{1, 2, 3, 4, 8, 14, 23, 0}, // 38
{1, 2, 4, 13, 18, 33, 0}, // 39
{1, 2, 3, 4, 9, 14, 24, 0}, // 40
{1, 2, 3, 4, 9, 15, 25, 0}, // 41
{1, 2, 3, 4, 9, 15, 25, 0}, // 42
{1, 2, 3, 4, 10, 15, 26, 0}, // 43
{1, 2, 3, 6, 16, 27, 38, 0}, // 44
{1, 2, 3, 5, 12, 18, 26, 0}, // 45
{1, 2, 3, 6, 18, 25, 38, 0}, // 46
{1, 2, 3, 5, 16, 22, 40, 0}, // 47
{1, 2, 5, 9, 20, 26, 36, 0}, // 48
{1, 2, 5, 24, 33, 36, 44, 0}, // 49
{1, 3, 8, 17, 28, 32, 38, 0}, // 50
{1, 2, 5, 11, 18, 30, 38, 0}, // 51
{1, 2, 3, 4, 6, 14, 21, 30, 0}, // 52
{1, 2, 3, 4, 7, 21, 29, 44, 0}, // 53
{1, 2, 3, 4, 9, 15, 21, 31, 0}, // 54
{1, 2, 3, 4, 6, 19, 26, 47, 0}, // 55
{1, 2, 3, 4, 11, 16, 33, 39, 0}, // 56
{1, 3, 13, 32, 36, 43, 52, 0}, // 57
// Generated by calcExhaustiveDC()
{1, 2, 3, 7, 21, 33, 37, 50, 0}, // 58
{1, 2, 3, 6, 13, 21, 35, 44, 0}, // 59
{1, 2, 4, 9, 15, 25, 30, 42, 0}, // 60
{1, 2, 3, 7, 15, 25, 36, 45, 0}, // 61
{1, 2, 4, 10, 32, 39, 46, 51, 0}, // 62
{1, 2, 6, 8, 20, 38, 41, 54, 0}, // 63
{1, 2, 5, 14, 16, 34, 42, 59, 0} // 64
};