isaSpace::ReadExonCoverage Struct Reference

Exons covered by a read. More...

#include <isoseqAlgn.hpp>

Collaboration diagram for isaSpace::ReadExonCoverage:

Public Attributes
std::string	chromosomeName
	Chromosome name.
std::string	readName
	Read name.
hts_pos_t	alignmentStart {0}
	Alignment start.
hts_pos_t	alignmentEnd {0}
	Alignment end.
hts_pos_t	bestAlignmentStart {0}
	Best alignment start.
hts_pos_t	bestAlignmentEnd {0}
	Best alignment end.
uint32_t	firstSoftClipLength {0}
	Length of the soft clip at read start.
uint16_t	nSecondaryAlignments {0}
	Number of secondary alignments.
uint16_t	nGoodSecondaryAlignments {0}
	Number of good secondary alignments.
uint16_t	nLocalReversedAlignments {0}
	Number of locally mapping reverse-complemented reads.
uint16_t	nExons {0}
	Number of exons.
std::string	geneName
	Gene name.
char	strand {'+'}
	Strand ID.
hts_pos_t	firstExonLength {-1}
	First exon length.
hts_pos_t	firstExonStart {-1}
	First exon start.
hts_pos_t	lastExonEnd {-1}
	Last exon end.
std::vector< float >	exonCoverageScores
	Exon coverage scores.
std::vector< float >	bestExonCoverageScores
	Best exon coverage scores.

Detailed Description

Exons covered by a read.

For a given alignment, stores information on exons covered by the read. All positions are 1-based, indexes are 0-based.

Member Data Documentation

alignmentEnd

hts_pos_t isaSpace::ReadExonCoverage::alignmentEnd {0}

Alignment end.

Base-1 position of the read end from the primary alignment. Never smaller than alignmentStart regardless of strand.

alignmentStart

hts_pos_t isaSpace::ReadExonCoverage::alignmentStart {0}

Alignment start.

Base-1 position of the read start from the primary alignment. Never larger than alignmentEnd regardless of strand.

bestAlignmentEnd

hts_pos_t isaSpace::ReadExonCoverage::bestAlignmentEnd {0}

Best alignment end.

Base-1 position of the latest read end from the primary and all good secondary alignments. Never smaller than bestAlignmentStart regardless of strand.

bestAlignmentStart

hts_pos_t isaSpace::ReadExonCoverage::bestAlignmentStart {0}

Best alignment start.

Base-1 position of the earliest read start from the primary and all good secondary alignments. Never larger than bestAlignmentEnd regardless of strand.

bestExonCoverageScores

std::vector<float> isaSpace::ReadExonCoverage::bestExonCoverageScores

Best exon coverage scores.

Fraction of reference bases in each exon covered by a matching base in the read from the best alignment for that exon among all alignments for the read.

chromosomeName

std::string isaSpace::ReadExonCoverage::chromosomeName

Chromosome name.

This can also be a linkage group or scaffold name, as listed in the GFF file in the seqid column.

exonCoverageScores

std::vector<float> isaSpace::ReadExonCoverage::exonCoverageScores

Exon coverage scores.

Fraction of reference bases in each exon covered by a matching base in the read from the primary alignment.

firstExonLength

hts_pos_t isaSpace::ReadExonCoverage::firstExonLength {-1}

First exon length.

Actual first exon, last in the sequence if the strand is negative.

firstExonStart

hts_pos_t isaSpace::ReadExonCoverage::firstExonStart {-1}

First exon start.

Base-1 position of the first exon start from the GFF file. End of the last exon if the strand negative.

firstSoftClipLength

uint32_t isaSpace::ReadExonCoverage::firstSoftClipLength {0}

Length of the soft clip at read start.

End of the CIGAR string if the read is reverse-complemented. Set to 0 if there is no soft clip.

geneName

std::string isaSpace::ReadExonCoverage::geneName

Gene name.

Set to no_overlap or past_last_mRNA if there is no gene in the GFF file that overlaps the alignment.

lastExonEnd

hts_pos_t isaSpace::ReadExonCoverage::lastExonEnd {-1}

Last exon end.

Base-1 position of the last exon end from the GFF file. Start of the first exon if the strand negative.

nGoodSecondaryAlignments

uint16_t isaSpace::ReadExonCoverage::nGoodSecondaryAlignments {0}

Number of good secondary alignments.

Secondary alignments that are on the same strand as the primary and overlap the same gene.

nLocalReversedAlignments

uint16_t isaSpace::ReadExonCoverage::nLocalReversedAlignments {0}

Number of locally mapping reverse-complemented reads.

Number of alignments on the opposite strand from the primary that overlap the same gene as the primary.

strand

char isaSpace::ReadExonCoverage::strand {'+'}

Strand ID.

Must be + or -.

---

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

• isoseqAlgn.hpp