Class List

Here are the classes, structs, unions and interfaces with brief descriptions:

BAMParser	Fills Fragment objects by parsing an input file in BAM format
BAMWriter	Writes Fragment objects back to file in BAM format with per-mapping probabilistic assignments, or by sampling a single mapping based on assignment probabilities
BiasBoss	Keeps track of sequence-specific and positional bias
Bundle	Keeps track of a group of targets that have shared ambiguous (multi-mapped) reads
BundleTable	Keeps track of the Bundle objects for a given run
CovarTable	The CovarTable is a sparse matrix for storing and updating pairwise covariances between targets
DirectionDetector	Keeps track of the observed fragment directions (forward-reverse or reverse-forward) and whether they are paired or single-end
FragHit	The FragHit struct stores the information for a single fragment alignment
Fragment	Stores information for all alignments of a single fragment
FrequencyMatrix< T >	Frequencymatrix.h express
HaplotypeHandler	Keeps track of sets of transcripts from different chromosomes
HitParams	The HitParams struct stores likelihood information for a single hit of a fragment
Indel	The Indel struct stores the information for a single insertion or deletion
LengthDistribution	Lengthdistribution.h express
Librarian	Keeps track of the different library objects for a run
Library	Library.h express
Logger	Logger.cpp express
MapParser	Meant to be run as a separate thread from the main processing
MarkovModel	Used to store transition probabilities of a Markov chain based on a nucleotide Sequence, which itself can be probabilistic
MismatchTable	Used to store and update mismatch and indel (error) parameters using a first-order Markov model based on nucleotide and position in a read
Parser	Abstract class for implementing a SAMParser or BAMParser
ParseThreadSafety	The ParseThreadSafety struct stores objects to allow for parsing to safely occur on a separate thread from processing
ReadHit	The ReadHit struct stores information for a single read alignment
Result
RobertsFilter	Implements a datastructure to test for repeats of a key with high probability, when repeats are most likely to be nearby
RoundParams	The RoundParams struct stores the target parameters unique to a given round (iteration) of EM
SAMParser	Fills Fragment objects by parsing an input in SAM format
SAMWriter	Writes Fragment objects back to file in SAM format with per-mapping probabilistic assignments, or by sampling a single mapping based on assignment probabilities
Sequence	Abstract class whose implmentations are used to store and access encoded nucleotide sequences
SequenceFwd	Implements the Sequence abstract class for storing the forward sequence
SequenceRev	Implements the Sequence abstract class for accessing the reverse sequence
SeqWeightTable	Keeps track of sequence-specific bias parameters
Target	Used to store objects for the targets being mapped to
TargetTable	Used to keep track of the Target objects for a run
ThreadSafeFragQueue	The ThreadSafeFragQueue is a threadsafe queue of Fragment pointers
Writer	Abstract class for implementing a SAMWriter or BAMWriter