File	Date	Author	Commit
bin	2017-04-10	Rastas Pasi M A	[42ad25] Support for phased data
src	2017-04-10	Rastas Pasi M A	[42ad25] Support for phased data
COPYING	2015-03-02	pmr47	[a10573] COPYING added
README	2015-11-25	pmr47	[574af3] Bug fix in markerClusters

Read Me

Lep-MAP2 (v. 0.2)

Linkage map construction suite

See Lep-MAP2 wiki on sourceforge for documentation

To run:
java -cp bin/ Filtering
java -cp bin/ SeparateChromosomes
java -cp bin/ JoinSingles
java -cp bin/ OrderMarkers
java -cp bin/ ParentCall

to compile:
javac src/*.java -d bin/

Changes from (v. 0.1)

New phasing algorithm: The old algorithm was not always 
working correctly with markers where both parents were 
informative

Used data phase is now in the output of OrderMarkers

Option markerClusters to manually set duplicated markes (allows speedups)

The option ignoreParentOrder in ParentCall is working (allows better linkage mapping on data without parental genotypes)