User:Lindenb/Notebook/UMR915/20100629

=creating table for degenerate base= will help to map degenerate prediction (sift/pph2) to the pileup calling.

create table deg2base(symbol char(1) not null, base enum ('A','T','G','C') not null, index(symbol), constraint unique index(symbol,base)); insert into deg2base(symbol,base) values ('A','A'),('C','C'),('G','G'),('T','T'); insert into deg2base(symbol,base) values ('N','A'),('N','C'),('N','G'),('N','T'); (...)

symbol	base A	A B	T B	G B	C C	C D	A D	T D	G G	G H	A H	T H	C K	T K	G M	A M	C N	A N	T N	G N	C R	A R	G S	G S	C T	T V	A V	G V	C W	A W	T Y	T Y	C =Format FAIDX= example: chr9_random	1146434	2938571700	50	51 chrM	16571	2939741069	50	51 chrX	154913754	2939757978	50	51 chrX_random	1719168	3097770021	50	51 chrY	57772954	3099523579	50	51


 * column 1: sequence name
 * column 2: sequence length
 * column 3: file offset for the first base in the file
 * column 4: fasta one line size
 * column 5: column 4 +1 ?? (CRLF would be 52 ??)