SamFileReader Class Reference

Child class of SamFile for reading files. More...

#include <SamFile.h>

Inheritance diagram for SamFileReader:

Collaboration diagram for SamFileReader:

Public Member Functions
	SamFileReader ()
	Default Constructor.
	SamFileReader (const char *filename)
	Constructor that opens the specified file for read.
	SamFileReader (const char *filename, ErrorHandler::HandlingType errorHandlingType)
	Constructor that opens the specified file for read.
	SamFileReader (const char *filename, SamFileHeader *header)
	Constructor that opens the specified file for read and reads the header from the file.
	SamFileReader (const char *filename, ErrorHandler::HandlingType errorHandlingType, SamFileHeader *header)
	Constructor that opens the specified file for read and reads the header from the file.
Public Member Functions inherited from SamFile
	SamFile ()
	Default Constructor, initializes the variables, but does not open any files.
	SamFile (ErrorHandler::HandlingType errorHandlingType)
	Constructor that sets the error handling type.
	SamFile (const char *filename, OpenType mode)
	Constructor that opens the specified file based on the specified mode (READ/WRITE), aborts if the file could not be opened.
	SamFile (const char *filename, OpenType mode, ErrorHandler::HandlingType errorHandlingType)
	Constructor that opens the specified file based on the specified mode (READ/WRITE) and handles errors per the specified handleType.
	SamFile (const char *filename, OpenType mode, SamFileHeader *header)
	Constructor that opens the specified file based on the specified mode (READ/WRITE) and reads the header, aborts if the file could not be opened or the header not read.
	SamFile (const char *filename, OpenType mode, ErrorHandler::HandlingType errorHandlingType, SamFileHeader *header)
	Constructor that opens the specified file based on the specified mode (READ/WRITE) and reads the header, handling errors per the specified handleType.
virtual	~SamFile ()
	Destructor.
bool	OpenForRead (const char *filename, SamFileHeader *header=NULL)
	Open a sam/bam file for reading with the specified filename, determing the type of file and SAM/BAM by reading the file (if not stdin).
bool	OpenForWrite (const char *filename, SamFileHeader *header=NULL)
	Open a sam/bam file for writing with the specified filename, determining SAM/BAM from the extension (.bam = BAM).
bool	ReadBamIndex (const char *filename)
	Read the specified bam index file.
bool	ReadBamIndex ()
	Read the bam index file using the BAM filename as a base.
void	SetReference (GenomeSequence *reference)
	Sets the reference to the specified genome sequence object.
void	SetReadSequenceTranslation (SamRecord::SequenceTranslation translation)
	Set the type of sequence translation to use when reading the sequence.
void	SetWriteSequenceTranslation (SamRecord::SequenceTranslation translation)
	Set the type of sequence translation to use when writing the sequence.
void	Close ()
	Close the file if there is one open.
bool	IsOpen ()
	Returns whether or not the file has been opened successfully.
bool	IsEOF ()
	Returns whether or not the end of the file has been reached.
bool	IsStream ()
	Returns whether or not the file has been opened for streaming input/output.
bool	ReadHeader (SamFileHeader &header)
	Reads the header section from the file and stores it in the passed in header.
bool	WriteHeader (SamFileHeader &header)
	Writes the specified header into the file.
bool	ReadRecord (SamFileHeader &header, SamRecord &record)
	Reads the next record from the file & stores it in the passed in record.
bool	WriteRecord (SamFileHeader &header, SamRecord &record)
	Writes the specified record into the file.
void	setSortedValidation (SortedType sortType)
	Set the flag to validate that the file is sorted as it is read/written.
uint32_t	GetCurrentRecordCount ()
	Return the number of records that have been read/written so far.
SamStatus::Status	GetFailure ()
	Deprecated, get the Status of the last call that sets status.
SamStatus::Status	GetStatus ()
	Get the Status of the last call that sets status.
const char *	GetStatusMessage ()
	Get the Status Message of the last call that sets status.
bool	SetReadSection (int32_t refID)
	Sets which reference id (index into the BAM list of reference information) of the BAM file should be read.
bool	SetReadSection (const char *refName)
	Sets which reference name of the BAM file should be read.
bool	SetReadSection (int32_t refID, int32_t start, int32_t end, bool overlap=true)
	Sets which reference id (index into the BAM list of reference information) & start/end positions of the BAM file should be read.
bool	SetReadSection (const char *refName, int32_t start, int32_t end, bool overlap=true)
	Sets which reference name & start/end positions of the BAM file should be read.
void	SetReadFlags (uint16_t requiredFlags, uint16_t excludedFlags)
	Specify which reads should be returned by ReadRecord.
int32_t	getNumMappedReadsFromIndex (int32_t refID)
	Get the number of mapped reads in the specified reference id.
int32_t	getNumUnMappedReadsFromIndex (int32_t refID)
	Get the number of unmapped reads in the specified reference id.
int32_t	getNumMappedReadsFromIndex (const char *refName, SamFileHeader &header)
	Get the number of mapped reads in the specified reference name.
int32_t	getNumUnMappedReadsFromIndex (const char *refName, SamFileHeader &header)
	Get the number of unmapped reads in the specified reference name.
uint32_t	GetNumOverlaps (SamRecord &samRecord)
	Returns the number of bases in the passed in read that overlap the region that is currently set.
void	GenerateStatistics (bool genStats)
	Whether or not statistics should be generated for this file.
const BamIndex *	GetBamIndex ()
	Return the bam index if one has been opened.
int64_t	GetCurrentPosition ()
	Get the current file position.
void	DisableBuffering ()
	Turn off file read buffering.
void	PrintStatistics ()
	Print the statistics that have been recorded due to a call to GenerateStatistics.
bool	attemptRecoverySync (bool(*checkSignature)(void *data), int length)
void	setAttemptRecovery (bool flag=false)

Additional Inherited Members
Public Types inherited from SamFile
enum	OpenType { READ , WRITE }
	Enum for indicating whether to open the file for read or write. More...
enum	SortedType { UNSORTED = 0 , FLAG , COORDINATE , QUERY_NAME }
	Enum for indicating the type of sort expected in the file. More...
Protected Member Functions inherited from SamFile
void	init ()
void	init (const char *filename, OpenType mode, SamFileHeader *header)
void	resetFile ()
	Resets the file prepping for a new file.
bool	validateSortOrder (SamRecord &record, SamFileHeader &header)
	Validate that the record is sorted compared to the previously read record if there is one, according to the specified sort order.
SortedType	getSortOrderFromHeader (SamFileHeader &header)
bool	processNewSection (SamFileHeader &header)
bool	ensureIndexedReadPosition ()
bool	checkRecordInSection (SamRecord &record)
Protected Attributes inherited from SamFile
IFILE	myFilePtr
GenericSamInterface *	myInterfacePtr
bool	myIsOpenForRead
	Flag to indicate if a file is open for reading.
bool	myIsOpenForWrite
	Flag to indicate if a file is open for writing.
bool	myHasHeader
	Flag to indicate if a header has been read/written - required before being able to read/write a record.
SortedType	mySortedType
int32_t	myPrevCoord
	Previous values used for checking if the file is sorted.
int32_t	myPrevRefID
String	myPrevReadName
uint32_t	myRecordCount
	Keep a count of the number of records that have been read/written so far.
SamStatistics *	myStatistics
	Pointer to the statistics for this file.
SamStatus	myStatus
	The status of the last SamFile command.
bool	myIsBamOpenForRead
	Values for reading Sorted BAM files via the index.
bool	myNewSection
bool	myOverlapSection
int32_t	myRefID
int32_t	myStartPos
int32_t	myEndPos
uint64_t	myCurrentChunkEnd
SortedChunkList	myChunksToRead
BamIndex *	myBamIndex
GenomeSequence *	myRefPtr
SamRecord::SequenceTranslation	myReadTranslation
SamRecord::SequenceTranslation	myWriteTranslation
std::string	myRefName

Detailed Description

Child class of SamFile for reading files.

Definition at line 460 of file SamFile.h.

Constructor & Destructor Documentation

SamFileReader() [1/5]

SamFileReader::SamFileReader

(

)

Default Constructor.

Definition at line 1373 of file SamFile.cpp.

    : SamFile()
{
}

References SamFile::SamFile().

SamFileReader() [2/5]

SamFileReader::SamFileReader

(

const char *

filename

)

Constructor that opens the specified file for read.

Definition at line 1380 of file SamFile.cpp.

    : SamFile(filename, READ)
{
}

References SamFile::SamFile(), and SamFile::READ.

SamFileReader() [3/5]

SamFileReader::SamFileReader	(	const char *	filename,
		ErrorHandler::HandlingType	errorHandlingType )

Constructor that opens the specified file for read.

Definition at line 1389 of file SamFile.cpp.

    : SamFile(filename, READ, errorHandlingType)
{
}

References SamFile::SamFile(), and SamFile::READ.

SamFileReader() [4/5]

SamFileReader::SamFileReader	(	const char *	filename,
		SamFileHeader *	header )

Constructor that opens the specified file for read and reads the header from the file.

Definition at line 1397 of file SamFile.cpp.

    : SamFile(filename, READ, header)
{
}

References SamFile::SamFile(), and SamFile::READ.

SamFileReader() [5/5]

SamFileReader::SamFileReader	(	const char *	filename,
		ErrorHandler::HandlingType	errorHandlingType,
		SamFileHeader *	header )

Constructor that opens the specified file for read and reads the header from the file.

Definition at line 1405 of file SamFile.cpp.

    : SamFile(filename, READ, errorHandlingType, header)
{
}

References SamFile::SamFile(), and SamFile::READ.

~SamFileReader()

SamFileReader::~SamFileReader ( )

virtual

Definition at line 1413 of file SamFile.cpp.

{
}

---

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

• bam/SamFile.h
• bam/SamFile.cpp