void cgapSageBedAddFreqs(char *oldBedFile, char *freqFile, char *libsFile, char *newBedFile)
/* cgapSageBedAddFreqs - Add frequency data to the bed. */
{
struct hash *totTagsHash;
struct bed *mappings;
struct hash *freqHash;
struct cgapSage *sageList;
verbose(1, "Loading libraries...\n");
totTagsHash = getTotTagsHash(libsFile);
verbose(1, "Loaded libraries.\n");
verbose(1, "Loading mappings...\n");
mappings = bedLoadNAll(oldBedFile, 8);
verbose(1, "Loaded mappings.\n");
verbose(1, "Loading frequencies...\n");
freqHash = getFreqHash(freqFile);
verbose(1, "Loaded frequencies.\n");
verbose(1, "Building new bed list...\n");
sageList = makeCgapSageList(freqHash, totTagsHash, mappings);
verbose(1, "Built new bed list.\n");
verbose(1, "Writing output...\n");
writeCgapSageFile(sageList, newBedFile);
verbose(1, "Wrote output. All done!\n");
freeFreqHash(&freqHash);
hashFree(&totTagsHash);
cgapSageFreeList(&sageList);
slFreeList(&mappings);
}
struct hash *getTotTagsHashFromTable(struct sqlConnection *conn)
/* Load the cgapSageLib table for the db then call getTotTagsHash. */
{
struct cgapSageLib *libs = cgapSageLibLoadByQuery(conn, "NOSQLINJ select * from cgapSageLib");
struct hash *libTotHash = getTotTagsHash(libs);
cgapSageLibFreeList(&libs);
return libTotHash;
}
