Read isoSeq alignments and compare to genome annotations. More...

#include <memory>
#include <utility>
#include <vector>
#include <array>
#include <set>
#include <unordered_map>
#include <string>
#include <filesystem>
#include "sam.h"
#include "bgzf.h"

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Classes
struct	isaSpace::BamAndGffFiles
	BAM and GFF file name pair. More...
struct	isaSpace::StatsAndFastqFiles
	Mismatch statistics and FASTQ file name pair. More...
struct	isaSpace::TokenAttibuteListPair
	Token name and GFF attribute list pair. More...
struct	isaSpace::MappedReadInterval
	Delineates an interval in a mapped read. More...
struct	isaSpace::MappedReadMatchStatus
	Read match and map start. More...
struct	isaSpace::BinomialWindowParameters
	Binomial window parameters. More...
struct	isaSpace::ReadExonCoverage
	Exons covered by a read. More...
struct	isaSpace::ReadPortion
	Read portion for re-mapping. More...
struct	isaSpace::BAMsecondary
	BAM secondary alignment. More...
struct	isaSpace::BAMheaderDeleter
	BAM header pointer deleter. More...
struct	isaSpace::BAMrecordDeleter
	BAM record pointer deleter. More...
struct	isaSpace::BGZFhandleDeleter
	BGZF handle pointer deleter. More...
class	isaSpace::BAMsafeReader
	BAM file safe reader. More...
class	isaSpace::ExonGroup
	Group of exons from the same gene. More...
class	isaSpace::ReadMatchWindowBIC
	Binomial BIC for a read window. More...
class	isaSpace::BAMrecord
	Summary of a BAM record set. More...
class	isaSpace::BAMtoGenome
	Relate BAM alignments to exons. More...
class	isaSpace::BAMfile
	Records from a BAM file. More...

Detailed Description

Read isoSeq alignments and compare to genome annotations.

Author: Anthony J. Greenberg and Rebekah Rogers

Version: 0.2

Interface definitions of classes that take .bam files with isoSeq alignments and identify potential fused transcripts.

Classes

Detailed Description