本文整理汇总了C++中Genome::Open方法的典型用法代码示例。如果您正苦于以下问题：C++ Genome::Open方法的具体用法？C++ Genome::Open怎么用？C++ Genome::Open使用的例子？那么, 这里精选的方法代码示例或许可以为您提供帮助。您也可以进一步了解该方法所在类Genome的用法示例。
在下文中一共展示了Genome::Open方法的2个代码示例，这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞，您的评价将有助于系统推荐出更棒的C++代码示例。
示例1: main
int main( int argc, char *argv[] )
{
Alignments alignments ;
Genome genome ;
std::vector<int> rascafFileId ;
char line[2048] ;
char prefix[512] = "rascaf_scaffold" ;
int rawAssemblyInd = 1 ;
FILE *rascafFile ;
bool contigLevel = false ;
int i ;
FILE *outputFile ;
FILE *infoFile ;
breakN = 1 ;
if ( argc < 2 )
{
fprintf( stderr, "%s", usage ) ;
exit( 1 ) ;
}
for ( i = 1 ; i < argc ; ++i )
{
if ( !strcmp( "-o", argv[i] ) )
{
strcpy( prefix, argv[i + 1 ] ) ;
++i ;
}
else if ( !strcmp( "-ms", argv[i] ) )
{
minSupport = atoi( argv[i + 1] ) ;
++i ;
}
else if ( !strcmp( "-ignoreGap", argv[i] ) )
{
ignoreGap = true ;
}
else if ( !strcmp( "-r", argv[i] ) )
{
rascafFileId.push_back( i + 1 ) ;
++i ;
}
else
{
fprintf( stderr, "Unknown option: %s\n", argv[i] ) ;
exit( EXIT_FAILURE ) ;
}
}
if ( rascafFileId.size() == 0 )
{
fprintf( stderr, "Must use -r to specify rascaf output file.\n" ) ;
exit( EXIT_FAILURE ) ;
}
MAX_NEIGHBOR = 1 + rascafFileId.size() ;
// Get the bam file.
rascafFile = fopen( argv[ rascafFileId[0] ], "r" ) ;
while ( fgets( line, sizeof( line ), rascafFile ) != NULL )
{
if ( strstr( line, "command line:" ) )
{
char *p ;
char buffer[512] ;
p = strstr( line, "-breakN" ) ;
if ( p != NULL )
{
p += 7 ;
while ( *p == ' ' )
++p ;
for ( i = 0 ; *p && *p != ' ' ; ++p, ++i )
buffer[i] = *p ;
buffer[i] = '\0' ;
breakN = atoi( buffer ) ;
}
p = strstr( line, "-b" ) ;
if ( p == NULL )
{
fprintf( stderr, "Could not find the bam file specified by -b in Rascaf.\n" ) ;
exit( 1 ) ;
}
p += 2 ;
while ( *p == ' ' )
++p ;
for ( i = 0 ; *p && *p != ' ' ; ++p, ++i )
buffer[i] = *p ;
buffer[i] = '\0' ;
alignments.Open( buffer ) ;
p = strstr( line, "-f") ;
if ( p == NULL )
{
fprintf( stderr, "Could not find the raw assembly file specified by -f in Rascaf.\n" ) ;
exit( 1 ) ;
}
//.........这里部分代码省略.........
示例2: main
int main( int argc, char *argv[] )
{
int i ;
int ret ;
Alignments alignments ;
Alignments clippedAlignments ;
Blocks blocks ;
Genome genome ;
char *genomeFile = NULL ;
if ( argc < 2 )
{
printf( "%s", usage ) ;
exit( 0 ) ;
}
minimumSupport = 2 ;
minimumEffectiveLength = 200 ;
kmerSize = 23 ;
breakN = 1 ;
minContigSize = 200 ;
prefix = NULL ;
VERBOSE = false ;
outputConnectionSequence = false ;
aggressiveMode = false ;
for ( i = 1 ; i < argc ; ++i )
{
if ( !strcmp( "-b", argv[i] ) )
{
alignments.Open( argv[i + 1]) ;
++i ;
}
else if ( !strcmp( "-o", argv[i] ) )
{
prefix = argv[i + 1] ;
++i ;
}
else if ( !strcmp( "-f", argv[i] ) )
{
genomeFile = argv[i + 1] ;
++i ;
}
else if ( !strcmp( "-ms", argv[i] ) )
{
minimumSupport = atoi( argv[i + 1] ) ;
++i ;
}
else if ( !strcmp( "-ml", argv[i] ) )
{
minimumEffectiveLength = atoi( argv[i + 1] ) ;
++i ;
}
else if ( !strcmp( "-k", argv[i] ) )
{
kmerSize = atoi( argv[i + 1] ) ;
++i ;
}
else if ( !strcmp( "-breakN", argv[i] ) )
{
breakN = atoi( argv[i + 1] ) ;
++i ;
}
else if ( !strcmp( "-minContigSize", argv[i] ) )
{
minContigSize = atoi( argv[i + 1] ) ;
++i ;
}
else if ( !strcmp( "-v", argv[i] ) )
{
VERBOSE = true ;
}
else if ( !strcmp( "-cs", argv[i] ) )
{
outputConnectionSequence = true ;
}
/*else if ( !strcmp( "-aggressive", argv[i] ) )
{
aggressiveMode = true ;
}*/
else if ( !strcmp( "-bc", argv[i] ) )
{
// So far, assume the input is from BWA mem
clippedAlignments.Open( argv[i + 1] ) ;
clippedAlignments.SetAllowSupplementary( true ) ;
++i ;
}
else
{
fprintf( stderr, "Unknown parameter: %s\n", argv[i] ) ;
exit( 1 ) ;
}
}
if ( !alignments.IsOpened() )
{
printf( "Must use -b to specify the bam file." ) ;
return 0 ;
}
//.........这里部分代码省略.........