Nothing
SENSE <- 0
ANTISENSE <- 1
ALLELE_A <- 0
ALLELE_B <- 1
## setPageSizeSql <- ('
## pragma page_size = 8192;
## ')
## dbsnp_rs_id could be integer if we strip the leading 'rs' Also, chrom could
## be integer and we could have a separate mapping tabel to the cromosome label
## (so that names are more meaningful).
# NB -- VC added cytoband
createSnpFeatureSetSql <- ('
create table featureSet (
fsetid integer primary key,
man_fsetid text,
dbsnp_rs_id text,
chrom text,
physical_pos integer,
strand integer,
cytoband text,
allele_a text,
allele_b text,
gene_assoc text,
dbsnp integer,
cnv text)
')
createSnp6FeatureSetSql <- ('
create table featureSet (
fsetid integer primary key,
man_fsetid text,
affy_snp_id integer,
dbsnp_rs_id text,
chrom text,
physical_pos integer,
strand integer,
cytoband text,
allele_a text,
allele_b text,
gene_assoc text,
dbsnp integer,
cnv text)
')
createSnpFeatureSql <- ('
create table %s (
fid integer primary key,
strand integer,
allele integer,
fsetid integer not null references "featureSet" ("fsetid"),
pos integer,
x integer,
y integer)
')
createSnpPm_MmSql <- ('
create table %s (
pm_fid integer primary key references "pmfeature" ("fid"),
mm_fid integer references "mmfeature" ("fid"))
')
createSnpSequenceSql <- ('
create table sequence (
fid integer primary key,
offset integer,
tstrand text,
tallele text,
seq text)
')
createCnvFeatureSetSql <- ('
create table featureSetCNV (
fsetid integer primary key,
man_fsetid text,
chrom text,
chrom_start integer,
chrom_stop integer,
strand integer,
cytoband text,
gene_assoc text,
xpar integer,
cnv text)
')
createCnv6FeatureSetSql <- ('
create table featureSetCNV (
fsetid integer primary key,
man_fsetid text,
chrom text,
chrom_start integer,
chrom_stop integer,
strand integer,
cytoband text,
gene_assoc text,
xpar integer,
cnv text)
')
createCnvFeatureSql <- ('
create table %s (
fid integer primary key,
strand integer,
fsetid integer not null references "featureSetCNV" ("fsetid"),
x integer,
y integer)
')
createCnvSequenceSql <- ('
create table sequenceCNV (
fid integer primary key,
offset integer,
tstrand text,
seq text)
')
createSnpFragmentLengthSql <- ('
create table fragmentLength (
fsetid integer not null references "featureSet" ("fsetid"),
enzyme text,
length integer,
start integer,
stop integer)
')
createCnvFragmentLengthSql <- ('
create table fragmentLengthCNV (
fsetid integer not null references "featureSetCNV" ("fsetid"),
enzyme text,
length integer,
start integer,
stop integer)
')
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