Read alignment processing elements. More...

Classes
class	shore::alignment_queue
	Read alignment storage queue. More...

class	shore::alignment_3px
	Move the 3' end of alignments, but keep them sorted by position. More...

class	shore::poissonifier
	Adaptive duplicate read filtering. More...

class	shore::seqid_translator
	Transpose reference sequence IDs, e.g. for re-alignment in mapflowcell. More...

class	shore::besthit_filter
	Discards redundant or suboptimal alignments. More...

class	shore::alignment_statistic
	Collect statistics on alignments. More...

class	shore::hits_correction_single_pipe
	Set the number of hits to the number of entries in the alignment file. More...

class	shore::flatten_alignment_pipe
	Extract the read information from alignments. More...

class	shore::mapping_pair_finder_pipe
	Collect concordant or unique pairings from position-sorted and PE corrected map.lists. More...

class	shore::mapping_pair_joiner_pipe
	Join paired alignments into one. More...

class	shore::alignment_trimmer_pipe
	Trim alignments that overlap range boundaries. More...

class	shore::alignment_filter_pipe
	Combines various alignment filters. More...

class	shore::alignment_condenser_pipe
	Replaces 'match' streches in the alignment string with their length, and reduces their quality resolution. More...

Functions
std::ostream &	shore::operator<< (std::ostream &os, const poissonifier::pf_core::pos &p)

Detailed Description

Read alignment processing elements.

Classes