methyl-seq-level.C ReadMe

The C++ program calculates CpG site methylation across the entire genome based on a pileup file
compiling:
g++ methyl-seq-level.C

usage:
methyl-seq-level hg19/hg19.CpG.sites.list out2  /scratch/users/lxm416/RAROproject_Methylome/583266_1-TN/583266_1-TN.1million.pileup TN 20

The file lists CpG site position across the entire genome
$ head hg19/hg19.CpG.sites.list
chr	pos	base
chr10	60025	CG
chr10	60089	CG
chr10	60109	CG

out2 is an output file name. It lists methylation for every CpG site across the entire genome.  
TN
0.5
NA (not available)
0.95
0.95
.9
0.8
0
1.1


The pileup file:
chr1	9999	N	1	^~c	?
chr1	10000	N	9	c^~C^~C^~A^~A^~A^~A^~A^~A	8C>>&!>5!
chr1	10001	t	11	,.......C^~.^~.	1C?>&!<5!%/
chr1	10002	a	16	,...GT..G..^~T^~T^~.^~G^~.	?CCC&!?5!%/!!!$B
chr1	10003	a	17	,........TCTTG..^~.	9FFF0%D6+%/!!!0C!
chr1	10004	c	19	,......G.....T..A^~,^~,	DFFF=CD37=899!@C!A?
 
 "TN" is a description for the sample name

20 coverage depth threshold.