isaSpace::BAMtoGenome Class Reference

Relate BAM alignments to exons. More...

#include <isoseqAlgn.hpp>

Public Member Functions
	BAMtoGenome ()=default
	Default constructor.
	BAMtoGenome (const BamAndGffFiles &bamGFFfilePairNames)
	Constructor intersecting iso-Seq alignments and exons.
	BAMtoGenome (const BAMtoGenome &toCopy)=default
	Copy constructor.
BAMtoGenome &	operator= (const BAMtoGenome &toCopy)=default
	Copy assignment operator.
	BAMtoGenome (BAMtoGenome &&toMove) noexcept=default
	Move constructor.
BAMtoGenome &	operator= (BAMtoGenome &&toMove) noexcept=default
	Move assignment operator.
	~BAMtoGenome ()=default
	Destructor.
size_t	nChromosomes () const noexcept
	Number of chromosomes/scaffolds/linkage groups.
size_t	nExonSets () const noexcept
	Number of exon sets (genes with exons).
void	saveReadCoverageStats (const std::string &outFileName, const size_t &nThreads) const
	Save read coverage to file.
void	saveUnmappedRegions (const std::string &outFileName, const BinomialWindowParameters &windowParameters, const size_t &nThreads) const
	Save unmapped read statistics to file.
void	saveUnmappedRegions (const StatsAndFastqFiles &outFilePair, const BinomialWindowParameters &windowParameters, const size_t &nThreads) const
	Save unmapped statistics and read portions to files.

Detailed Description

Relate BAM alignments to exons.

Relates each BAM alignment to a gene and check which exons are covered by the read.

Constructor & Destructor Documentation

BAMtoGenome() [1/3]

isaSpace::BAMtoGenome::BAMtoGenome

(

const BamAndGffFiles &

bamGFFfilePairNames

)

Constructor intersecting iso-Seq alignments and exons.

Uses exon positions from the provided GFF file to find iso-Seq alignments from the provided BAM file that may have mis-mapped first exons.

Parameters

[in]

bamGFFfilePairNames

BAM and GFF file name pair

BAMtoGenome() [2/3]

isaSpace::BAMtoGenome::BAMtoGenome ( const BAMtoGenome & toCopy )

default

Copy constructor.

Parameters

[in]

toCopy

object to copy

BAMtoGenome() [3/3]

isaSpace::BAMtoGenome::BAMtoGenome ( BAMtoGenome && toMove )

defaultnoexcept

Move constructor.

Parameters

[in]

toMove

object to move

Member Function Documentation

nChromosomes()

size_t isaSpace::BAMtoGenome::nChromosomes ( ) const

nodiscardnoexcept

Number of chromosomes/scaffolds/linkage groups.

Counts the number of unique GFF seqid elements. These are typically chromosomes, scaffolds, or linkage groups.

Returns

number of chromosomes

nExonSets()

size_t isaSpace::BAMtoGenome::nExonSets ( ) const

nodiscardnoexcept

Number of exon sets (genes with exons).

Returns

number of exon sets

operator=() [1/2]

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

defaultnoexcept

Move assignment operator.

Parameters

[in]

toMove

object to move

Returns

BAMtoGenome object

operator=() [2/2]

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

default

Copy assignment operator.

Parameters

[in]

toCopy

object to copy

Returns

BAMtoGenome object

saveReadCoverageStats()

void isaSpace::BAMtoGenome::saveReadCoverageStats	(	const std::string &	outFileName,
		const size_t &	nThreads ) const

Save read coverage to file.

Saves the read coverage statistics to a file. If a file with the same name exists it is overwritten.

Parameters

[in]	outFileName	output file name
[in]	nThreads	number of concurrent threads

saveUnmappedRegions() [1/2]

void isaSpace::BAMtoGenome::saveUnmappedRegions	(	const StatsAndFastqFiles &	outFilePair,
		const BinomialWindowParameters &	windowParameters,
		const size_t &	nThreads ) const

Save unmapped statistics and read portions to files.

Only considers reads that are at least partially well mapped, but have some interval(s) with low alignment quality. Save unmapped portions to a FASTQ file. If files with the same names exist it is overwritten.

Parameters

[in]	outFilePair	output file name
[in]	windowParameters	sliding window parameters
[in]	nThreads	number of concurrent threads

saveUnmappedRegions() [2/2]

void isaSpace::BAMtoGenome::saveUnmappedRegions	(	const std::string &	outFileName,
		const BinomialWindowParameters &	windowParameters,
		const size_t &	nThreads ) const

Save unmapped read statistics to file.

Only considers reads that are at least partially well mapped, but have some interval(s) with low alignment quality. If a file with the same name exists it is overwritten.

Parameters

[in]	outFileName	output file name
[in]	windowParameters	sliding window parameters
[in]	nThreads	number of concurrent threads

---

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

• isoseqAlgn.hpp