isaSpace::BAMfile Class Reference

Records from a BAM file. More...

#include <isoseqAlgn.hpp>

Public Member Functions
	BAMfile ()=default
	Default constructor.
	BAMfile (const std::string &BAMfileName)
	Constructor with BAM file name.
	BAMfile (const BAMfile &toCopy)=delete
	Copy constructor.
BAMfile &	operator= (const BAMfile &toCopy)=delete
	Copy assignment operator.
	BAMfile (BAMfile &&toMove) noexcept=default
	Move constructor.
BAMfile &	operator= (BAMfile &&toMove) noexcept=default
	Move assignment operator.
	~BAMfile ()=default
	Destructor.
size_t	getPrimaryAlignmentCount () const noexcept
	Get the number of primary alignments.
void	addRemaps (const std::string &remapBAMfileName, const float &remapIdentityCutoff)
	Add re-mapped read regions.
std::vector< std::string >	saveRemappedBAM (const std::string &outputBAMfileName) const
	Save the reads with re-alignments to a BAM file.
std::vector< std::string >	saveSortedRemappedBAM (const std::string &outputBAMfileName) const
	Sort and save the reads with re-alignments to a BAM file.

Detailed Description

Records from a BAM file.

Primary records from a BAM file, including the header. Used to add realignments as secondary records.

Constructor & Destructor Documentation

BAMfile() [1/3]

isaSpace::BAMfile::BAMfile

(

const std::string &

BAMfileName

)

Constructor with BAM file name.

Parameters

[in]

BAMfileName

name of the input BAM file

BAMfile() [2/3]

isaSpace::BAMfile::BAMfile ( const BAMfile & toCopy )

delete

Copy constructor.

Parameters

[in]

toCopy

object to copy

BAMfile() [3/3]

isaSpace::BAMfile::BAMfile ( BAMfile && toMove )

defaultnoexcept

Move constructor.

Parameters

[in]

toMove

object to move

Member Function Documentation

addRemaps()

void isaSpace::BAMfile::addRemaps	(	const std::string &	remapBAMfileName,
		const float &	remapIdentityCutoff )

Add re-mapped read regions.

Add re-mapped read regions as secondary alignments, fixing CIGAR strings for the primaries.

Parameters

[in]	remapBAMfileName	name of the BAM file with re-mapped read portions
[in]	remapIdentityCutoff	fraction of sites in the remapped read that are identical to the reference

getPrimaryAlignmentCount()

size_t isaSpace::BAMfile::getPrimaryAlignmentCount ( ) const

nodiscardnoexcept

Get the number of primary alignments.

Returns

number of primary alignments

operator=() [1/2]

BAMfile & isaSpace::BAMfile::operator= ( BAMfile && toMove )

defaultnoexcept

Move assignment operator.

Parameters

[in]

toMove

object to move

Returns

BAMfile object

operator=() [2/2]

BAMfile & isaSpace::BAMfile::operator= ( const BAMfile & toCopy )

delete

Copy assignment operator.

Parameters

[in]

toCopy

object to copy

Returns

BAMfile object

saveRemappedBAM()

std::vector< std::string > isaSpace::BAMfile::saveRemappedBAM ( const std::string & outputBAMfileName ) const

nodiscard

Save the reads with re-alignments to a BAM file.

Parameters

[in]

outputBAMfileName

output BAM file name

Returns

names of reads that failed to be written

saveSortedRemappedBAM()

std::vector< std::string > isaSpace::BAMfile::saveSortedRemappedBAM ( const std::string & outputBAMfileName ) const

nodiscard

Sort and save the reads with re-alignments to a BAM file.

References saved in the order of the original BAM file. Reads sorted by start position (which is the gene end if mapped to the negative strand).

Parameters

[in]

outputBAMfileName

output BAM file name

Returns

names of reads that failed to be written

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

• isoseqAlgn.hpp