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IO

Detailed Description

Modules

 FM-Index I/O
 
 Read data input
 
 Sequence Data Input
 
 Output
 
 Utils
 

Namespaces

 nvbio::io
 

Classes

struct  nvbio::io::Cigar
 
struct  nvbio::io::Alignment
 
struct  nvbio::io::AlignmentCompare
 
struct  nvbio::io::BestAlignments
 
struct  nvbio::io::PairedAlignments
 
struct  nvbio::io::BestPairedAlignments
 
struct  nvbio::io::has_second
 
struct  nvbio::io::has_second_paired
 
struct  nvbio::io::has_second_unpaired
 
struct  nvbio::io::is_paired
 
struct  nvbio::io::is_unpaired
 
struct  nvbio::io::is_concordant
 
struct  nvbio::io::is_discordant
 
struct  nvbio::io::is_not_concordant
 
struct  nvbio::io::is_aligned
 
class  nvbio::io::BufferedTextFile
 
struct  nvbio::OutputStream
 
struct  nvbio::GZOutputFile
 
struct  nvbio::LZ4OutputFile
 

Enumerations

enum  nvbio::io::MDS_OP {
  nvbio::io::MDS_MATCH = 0, nvbio::io::MDS_MISMATCH = 1, nvbio::io::MDS_INSERTION = 2, nvbio::io::MDS_DELETION = 3,
  nvbio::io::MDS_INVALID = 4
}
 

Functions

NVBIO_FORCEINLINE
NVBIO_HOST_DEVICE bool 
nvbio::io::distinct_alignments (const uint32 pos1, const bool rc1, const uint32 pos2, const bool rc2, const uint32 dist)
 
NVBIO_FORCEINLINE
NVBIO_HOST_DEVICE bool 
nvbio::io::distinct_alignments (const uint32 apos1, const uint32 opos1, const bool arc1, const bool orc1, const uint32 apos2, const uint32 opos2, const bool arc2, const bool orc2, const uint32 dist)
 
NVBIO_FORCEINLINE
NVBIO_HOST_DEVICE bool 
nvbio::io::distinct_alignments (const Alignment &p1, const Alignment &p2, const uint32 dist=1)
 
NVBIO_FORCEINLINE
NVBIO_HOST_DEVICE bool 
nvbio::io::distinct_alignments (const PairedAlignments &p1, const PairedAlignments &p2)
 
NVBIO_FORCEINLINE
NVBIO_HOST_DEVICE bool 
nvbio::io::distinct_alignments (const PairedAlignments &p1, const PairedAlignments &p2, const uint32 dist)
 
 nvbio::io::BufferedTextFile::BufferedTextFile (const char *fname, char record_separator= '\n', size_t buffer_size=256 *1024)
 
 nvbio::io::BufferedTextFile::~BufferedTextFile ()
 
bool nvbio::io::BufferedTextFile::fill_buffer (void)
 
bool nvbio::io::BufferedTextFile::buffer_full (void)
 
bool nvbio::io::BufferedTextFile::buffer_empty (void)
 
char * nvbio::io::BufferedTextFile::next_record (char **line_end)
 
OutputStream * nvbio::open_output_file (const char *file_name, const char *compressor, const char *options)
 

Enumeration Type Documentation

The list of MD string operations

Enumerator
MDS_MATCH 
MDS_MISMATCH 
MDS_INSERTION 
MDS_DELETION 
MDS_INVALID 

Definition at line 46 of file alignments.h.

Function Documentation

bool nvbio::io::BufferedTextFile::buffer_empty ( void  )
inline

Definition at line 116 of file bufferedtextfile.h.

bool nvbio::io::BufferedTextFile::buffer_full ( void  )
inline

Definition at line 111 of file bufferedtextfile.h.

nvbio::io::BufferedTextFile::BufferedTextFile ( const char *  fname,
char  record_separator = '\n',
size_t  buffer_size = 256 * 1024 
)
inline

Definition at line 58 of file bufferedtextfile.h.

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool nvbio::io::distinct_alignments ( const uint32  pos1,
const bool  rc1,
const uint32  pos2,
const bool  rc2,
const uint32  dist 
)

Definition at line 35 of file alignments_inl.h.

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool nvbio::io::distinct_alignments ( const uint32  apos1,
const uint32  opos1,
const bool  arc1,
const bool  orc1,
const uint32  apos2,
const uint32  opos2,
const bool  arc2,
const bool  orc2,
const uint32  dist 
)

Definition at line 66 of file alignments_inl.h.

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool nvbio::io::distinct_alignments ( const Alignment &  p1,
const Alignment &  p2,
const uint32  dist = 1 
)

Definition at line 90 of file alignments_inl.h.

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool nvbio::io::distinct_alignments ( const PairedAlignments &  p1,
const PairedAlignments &  p2 
)

Definition at line 105 of file alignments_inl.h.

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool nvbio::io::distinct_alignments ( const PairedAlignments &  p1,
const PairedAlignments &  p2,
const uint32  dist 
)

Definition at line 121 of file alignments_inl.h.

bool nvbio::io::BufferedTextFile::fill_buffer ( void  )
inline

Definition at line 81 of file bufferedtextfile.h.

char* nvbio::io::BufferedTextFile::next_record ( char **  line_end)
inline

Definition at line 122 of file bufferedtextfile.h.

OutputStream * nvbio::open_output_file ( const char *  file_name,
const char *  compressor,
const char *  options 
)

output file factory method

Definition at line 140 of file output_stream.cpp.

nvbio::io::BufferedTextFile::~BufferedTextFile ( )
inline

Definition at line 71 of file bufferedtextfile.h.