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cnvCallerGPU
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gad-public
cnvCallerGPU
Commits
3b7da2fe
Commit
3b7da2fe
authored
Mar 04, 2025
by
Yannis Duffourd
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first implementation
parent
05411fd2
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Galacs.h
Galacs.h
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Galacs.h
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3b7da2fe
#ifndef _CNVCALLERGPU_H
#ifndef _CNVCALLERGPU_H
#define _CNVCALLERGPU_H
#define _CNVCALLERGPU_H
#include <vector>
#include <vector>
#include <map>
#include <map>
#include <string>
#include <string>
#include <htslib/sam.h>
#include <htslib/sam.h>
class
cnvCallerGPU
class
cnvCallerGPU
{
{
public
:
public
:
cnvCallerGPU
();
cnvCallerGPU
();
cnvCallerGPU
(
std
::
string
,
std
::
string
,
std
::
string
,
std
::
string
,
std
::
string
,
int
,
int
,
double
,
int
,
int
);
cnvCallerGPU
(
std
::
string
,
std
::
string
,
std
::
string
,
std
::
string
,
std
::
string
,
int
,
int
,
double
,
int
,
int
);
int
mainLoop
();
int
mainLoop
();
int
getNbThread
();
int
getNbThread
();
int
getWindowSize
();
int
getWindowSize
();
int
getStepSize
();
int
getStepSize
();
double
getZscore
();
double
getZscore
();
std
::
string
getOutputFilePairs
();
std
::
string
getOutputFilePairs
();
std
::
string
getOutputFileSplit
();
std
::
string
getOutputFileSplit
();
std
::
string
getOutputFile
();
std
::
string
getOutputFile
();
std
::
string
getReferenceFile
();
std
::
string
getReferenceFile
();
std
::
string
getBamFile
();
std
::
string
getBamFile
();
private
:
private
:
std
::
string
sampleName
;
std
::
string
sampleName
;
std
::
string
inputBamFile
;
std
::
string
inputBamFile
;
std
::
string
referenceFile
;
std
::
string
referenceFile
;
std
::
string
outputFile
;
std
::
string
outputFile
;
std
::
string
outputFilePairs
;
std
::
string
outputFilePairs
;
std
::
string
outputFileSplit
;
std
::
string
outputFileSplit
;
std
::
map
<
std
::
string
,
std
::
map
<
int32_t
,
std
::
map
<
int32_t
,
int32_t
>>>
rawCounts
;
std
::
map
<
std
::
string
,
std
::
map
<
int32_t
,
std
::
map
<
int32_t
,
int32_t
>>>
rawCounts
;
std
::
map
<
std
::
string
,
std
::
map
<
int32_t
,
std
::
map
<
int32_t
,
float
>>>
gcContent
;
std
::
map
<
std
::
string
,
std
::
map
<
int32_t
,
std
::
map
<
int32_t
,
float
>>>
gcContent
;
std
::
map
<
std
::
string
,
std
::
map
<
int32_t
,
int32_t
>>
refDict
;
std
::
map
<
std
::
string
,
std
::
map
<
int32_t
,
int32_t
>>
refDict
;
int
depthThreshold
;
int
depthThreshold
;
int
nbThread
;
int
nbThread
;
int
loggingLevel
;
int
loggingLevel
;
int
window
;
int
window
;
int
step
;
int
step
;
double
zscore
;
double
zscore
;
// method
// method
int
getGenome
();
int
getGenome
();
void
displayGenome
();
void
displayGenome
();
int
readBam
(
std
::
string
,
int32_t
,
int32_t
);
int
readBam
(
std
::
string
,
int32_t
,
int32_t
);
int
bamParsingLauncher
();
int
bamParsingLauncher
();
};
};
#endif
#endif
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