Package nix.affy.bpmap

For maping, filtering, and calculating statistics about text version bpmap files.

See:
Description

Class Summary

BlastFilterResult	Container for a blast result: chromosome, numMatches, exactMatches, oneBPMismatches, startExactMatch.
BPMapDuplicateFilter	For extracting duplicate oligo/ features from Affy's bpmap file, can be used as a stand alone but better to use BPMapProcessor.
BPMapFeature	Container for info about a particular oligo feature from a bpmap file, see LoadedOligo too.
BPMapLine	Minimal bpmap line, chrom, start, nothing else.
BPMapOligoBlastFilter	Application for remapping and filtering a text version bpmap file with BLAST.
BPMapProcessor	Combo app for processing a bpmap file, wraps the BPMapDuplicateFilter, MapSplitter, and WindowMaker scripts.
BPMapSort	This sorts a text version bpmap first by chromosome, second by base position.
BPMapStripHighLowGC	Strips a text version bpmap file of lines where the %GC is > 0.6 or < 0.4.
CollapseBPMap	Collapses a text version bpmap into a unique set of bpmap lines base on the oligo sequence.
MapSplitter	Splits a '.bpmap' text file into different chromosomes, helper script for BPMapProcessor.
MummerFilter	Application to remap and filter a ProbeExporter text bpmap file for exact matches useing MUMMER.
StatBPMap	Calculates simple stats on a bpmap text file, number unique oligos, number of lines.
WindowMaker	Creates Windows (start position, end position) of a given length, containing a given number of oligos/ features.

Package nix.affy.bpmap Description

For maping, filtering, and calculating statistics about text version bpmap files. Use the ProbeExporter application from Affy to convert your binary bpmap to a text version.