/usr/include/mash/CommandFind.h is in libmash-dev 2.0-2.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 | // Copyright © 2015, Battelle National Biodefense Institute (BNBI);
// all rights reserved. Authored by: Brian Ondov, Todd Treangen,
// Sergey Koren, and Adam Phillippy
//
// See the LICENSE.txt file included with this software for license information.
#ifndef INCLUDED_CommandFind
#define INCLUDED_CommandFind
#include "Command.h"
#include "Sketch.h"
#include <string.h>
#include <queue>
namespace mash {
class CommandFind : public Command
{
public:
struct FindInput
{
FindInput
(
const Sketch & sketchNew,
const char * seqIdNew,
const char * seqNew,
uint32_t lengthNew,
float thresholdNew,
int bestNew,
bool selfMatchesNew
) :
sketch(sketchNew),
length(lengthNew),
threshold(thresholdNew),
seqId(seqIdNew),
best(bestNew),
selfMatches(selfMatchesNew)
{
seq = new char[strlen(seqNew) + 1];
strcpy(seq, seqNew);
}
~FindInput()
{
delete [] seq;
}
const Sketch & sketch;
std::string seqId;
char * seq;
uint32_t length;
float threshold;
int best;
bool selfMatches;
};
struct FindOutput
{
struct Hit
{
Hit(uint32_t refNew, uint32_t startNew, uint32_t endNew, bool minusStrandNew, float scoreNew)
:
ref(refNew),
start(startNew),
end(endNew),
minusStrand(minusStrandNew),
score(scoreNew)
{}
unsigned int ref;
unsigned int start;
unsigned int end;
bool minusStrand;
float score;
};
std::string seqId;
std::priority_queue<Hit> hits;
};
CommandFind();
int run() const; // override
private:
void writeOutput(const Sketch & sketch, FindOutput * output) const;
};
CommandFind::FindOutput * find(CommandFind::FindInput * data);
void findPerStrand(const CommandFind::FindInput * input, CommandFind::FindOutput * output, bool minusStrand);
bool operator<(const CommandFind::FindOutput::Hit & a, const CommandFind::FindOutput::Hit & b);
} // namespace mash
#endif
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