README

Requirement
1.	Java 1.7.

Usage 
java -jar hapMap2JoinMap01.jar HapMap.hmp.txt momDataName dadDataName ToleranceThreshold MarkerSimilarity output.joinmap output.bad_loci output.stats outputThreshold.joinmap outputMarkerSimilarity.joinmap outputChisq.joinmap

Example of usage
java –jar hapMap2JoinMap01.jar HapMap.hmp.txt P1Su_HWI-Mom P2R_HWI-Dad 0.95 0.95 output.joinmap output.bad_loci output.stats  outputThreshold.joinmap outputMarkerSimilarity.joinmap outputChisq.joinmap

Input 1 file and 4 parameters
HapMap format file:  HapMap.hmp.txt (tab-delimited file) 
momDataName: momSampleName in HapmapFile
dadDataName: dadSampleName in HapmapFile
ToleranceThreshold: user specifies a number of 0~1
MarkerSimilarity: user specifies a number of 0~1  

Output 6 files
Joinmap format file: output.joinmap includes all good loci.
Bad loci file: output.bad_loci includes loci under the following conditions
•	Data where either parent is \"N\"
•	The loci where parents are both homogeneous(mom: A C G T, dad: A C G T)
•	Parents cannot account for child genotypes
Statistic file: output.stats provide the basic information for 
•	Number of loci of input hapmap file
•	Number of loci of Bad loci file 
•	Number of loci of output.joinmap
•	Number of loci of outputThreshold.joinmap
•	Number of loci of outputMarkerSimilarity.joinmap 
•	Number of loci of outputChisq.joinmap
Joinmap format file: outputThreshold.joinmap
•	Number of loci satisfy the tolerance threshold user specifies
Joinmap format file: outputMarkerSimilarity.joinmap
•	Number of loci satisfy tolerance threshold and marker similarity
Joinmap format file: outputChisq.joinmap
•	Number of loci satisfy tolerance threshold, marker similarity and significance level(0.0001) of Chi-sq distribution