Description of SweepFileConversion.java 

The program gets the phased haplotypes from HapMap and converts them into .emphase and .snp (input files for Sweep)

1) You need an input file (all_stopsnps_input.txt) with SNP name, chromosome, position pos_start and pos_end 
(this is the selected region, I used the SNP position and calculated 100 kb on each side to get this). 
This input file should look like this (tab del): 
marker id	chromosome	position	pos_start	pos_end
rs1001586	chr22	40994791	40894791	41094791
rs10237332	chr7	62973419	62873419	63073419
rs10250779	chr7	43878136	43778136	43978136
rs10430458	chr1	156612881	156512881	156712881
rs1043261	chr3	53874316	53774316	53974316
etc.

2) You need to keep 3 files in the same folder as the input file to run the program: 
#ostermiller_utils-1.05.jar
#SweepFileConversion.class
#sweep.bat (if you have a different input file name you need to change it in this file)

3) Go to command prompt (run - cmd)
Cd down the folder containing the files. 
Type sweep.bat

--> The program will create an .emphase and .snp file for each SNP for each population and put them in separate population folder.
It will also create .many file for each population (containing all SNP files)
The program takes into account that males for X chromosome SNPs are missing the U chromosome and adds the U chromosome with allele = 5.


