User:Lindenb/Notebook/UMR915/20100629
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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 ??)