libStatGen Software 1
genomeSequenceMmapHeader Class Reference
Inheritance diagram for genomeSequenceMmapHeader:
Collaboration diagram for genomeSequenceMmapHeader:

Static Public Member Functions

static size_t getHeaderSize (int chromosomeCount)
 

Friends

class GenomeSequence
 
std::ostream & operator<< (std::ostream &, genomeSequenceMmapHeader &)
 

Additional Inherited Members

- Public Member Functions inherited from MemoryMapArrayHeader
void constructorClear ()
 
void debugPrint (FILE *)
 
size_t getHeaderSize (int i)
 
void setApplication (const char *s)
 
void setCreationUser (const char *s)
 
void setCreationHost (const char *s)
 
- Public Attributes inherited from MemoryMapArrayHeader
uint32_t typeCookie
 
uint32_t typeVersion
 
uint32_t contentCookie
 
uint32_t contentVersion
 
size_t headerSize
 
time_t creationDate
 
char creationUser [32]
 
char creationHost [32]
 
char application [32]
 
size_t elementCount
 

Detailed Description

Definition at line 79 of file GenomeSequenceHelpers.h.

Member Function Documentation

◆ getHeaderSize()

static size_t genomeSequenceMmapHeader::getHeaderSize ( int  chromosomeCount)
inlinestatic

Definition at line 95 of file GenomeSequenceHelpers.h.

96 {
97 return sizeof(genomeSequenceMmapHeader) + sizeof(ChromosomeInfo[1]) * chromosomeCount;
98 }

Friends And Related Function Documentation

◆ GenomeSequence

friend class GenomeSequence
friend

Definition at line 81 of file GenomeSequenceHelpers.h.

◆ operator<<

std::ostream & operator<< ( std::ostream &  ,
genomeSequenceMmapHeader  
)
friend

Definition at line 1137 of file GenomeSequence.cpp.

1138{
1139 stream << (MemoryMapArrayHeader &) h;
1140 stream << "chromosomeCount: " << h._chromosomeCount << std::endl;
1141 stream << "isColorSpace: " << h._colorSpace << std::endl;
1142 stream << "chromosomeCount: " << h._chromosomeCount << std::endl;
1143 uint64_t totalSize = 0;
1144 for (uint32_t i=0; i < h._chromosomeCount; i++)
1145 {
1146 totalSize += h._chromosomes[i].size;
1147 stream << "Chromosome Index " << i << " name: " << h._chromosomes[i].name << std::endl;
1148 stream << "Chromosome Index " << i << " whole genome start: " << h._chromosomes[i].start << std::endl;
1149 stream << "Chromosome Index " << i << " whole genome size: " << h._chromosomes[i].size << std::endl;
1150 stream << "Chromosome Index " << i << " md5 checksum: " << h._chromosomes[i].md5 << std::endl;
1151 stream << "Chromosome Index " << i << " assemblyID: " << h._chromosomes[i].assemblyID << std::endl;
1152 stream << "Chromosome Index " << i << " species: " << h._chromosomes[i].species << std::endl;
1153 stream << "Chromosome Index " << i << " URI: " << h._chromosomes[i].uri << std::endl;
1154 }
1155 stream << "Total Genome Size: " << totalSize << " bases."<< std::endl;
1156 if (totalSize != h.elementCount)
1157 {
1158 stream << "Total Genome Size: does not match elementCount!\n";
1159 }
1160
1161 stream << std::endl;
1162 return stream;
1163}

The documentation for this class was generated from the following file: