void appendNewExperiment(char *file, struct hash *bedHash, struct hash *pslHash, struct expRecord **erList, int expNum)
{
struct expRecord *er = NULL;
char buff[256];
int count = 0;
struct bed *bed = NULL;
struct stanMad *smList = NULL, *sm = NULL;
smList = stanMadLoadAll(file);
er = createExpRec(file, expNum);
slAddHead(erList, er);
for(sm = smList; sm != NULL; sm = sm->next)
{
count++;
snprintf(buff,sizeof(buff), "%d-%s-%d", sm->clid, sm->prow, sm->pcol);
bed = hashFindVal(bedHash, buff);
if(bed != NULL)
{
bed->expIds[expNum] = expNum;
bed->expScores[expNum] = safeLog2(sm->rat2n);
}
else
{
if(sm->clid != 0)
{
struct psl *psl = NULL;
snprintf(buff,sizeof(buff), "%d", sm->clid);
psl = hashFindVal(pslHash, buff);
if(psl != NULL)
errAbort("Counldn't find hash entry at line %d in %s for %s, %d, %d.\n", count, file, buff, sm->clid, sm->spot);
}
}
}
stanMadFreeList(&smList);
}
void findStanAlignments(char *db, char *stan, char *image, char *pslOut)
{
struct hash *iHash = newHash(5);
struct stanMad *smList = NULL, *sm = NULL;
FILE *out = mustOpen(pslOut, "w");
int count =0;
struct sqlConnection *conn = NULL;
warn("Getting sql Connection...");
conn = hAllocConn(db);
warn("Reading in image clones...");
readInImageHash(iHash, image);
warn("Loading Stanford Alignments..");
smList = stanMadLoadAll(stan);
warn("Finding best Alignments...");
for(sm = smList; sm != NULL; sm = sm->next)
{
if(differentString(sm->type,"Control"))
{
if((count++ % 10000) ==0)
{
printf(".");
fflush(stdout);
}
outputAlignmentForStan(conn, sm, iHash, out);
}
}
printf("\n");
warn("Done. Cleaning up...");
stanMadFreeList(&smList);
freeHash(&iHash);
hFreeConn(&conn);
}
void createBeds(struct hash *bedHash, struct hash *pslHash, char *file, int numExps)
{
struct stanMad *smList=NULL, *sm=NULL;
struct psl *psl = NULL;
struct bed *bed = NULL;
char buff[256];
warn("File is %s", file);
smList = stanMadLoadAll(file);
for(sm=smList; sm != NULL; sm = sm->next)
{
sprintf(buff, "%d", sm->clid);
psl = hashFindVal(pslHash, buff);
if(psl != NULL)
{
snprintf(buff,sizeof(buff), "%d-%s-%d", sm->clid, sm->prow, sm->pcol);
bed = pslToBed(psl);
bed->expCount = numExps;
bed->expIds = needMem(sizeof(int) * numExps);
bed->expScores = needMem(sizeof(float) * numExps);
hashAddUnique(bedHash, buff, bed);
}
}
}