void affyTransLiftedToSample(int grouping, char *affyTransIn)
/* Top level function to run combine pairs and offset files to give sample. */
{
struct affyTransLifted *atl = NULL, *atlList = NULL;
struct sample *sampList = NULL, *samp = NULL;
struct sample *groupedList = NULL;
char *fileRoot = NULL;
char buff[10+strlen(affyTransIn)];
FILE *out = NULL;
char *fileNameCopy = cloneString(affyTransIn);
chopSuffix(fileNameCopy);
fprintf(stderr, ".");
fflush(stderr);
atlList = affyTransLiftedLoadAll(affyTransIn);
//warn("Creating samples.");
for(atl = atlList; atl != NULL; atl = atl->next)
{
samp = sampleFromAffyTransLifted(atl, fileNameCopy);
if(samp != NULL)
slAddHead(&sampList, samp);
}
//warn("Sorting Samples");
slSort(&sampList, sampleCoordCmp);
groupedList = groupByPosition(grouping, sampList);
//warn("Saving Samples.");
snprintf(buff, sizeof(buff), "%s.sample", affyTransIn);
out = mustOpen(buff, "w");
for(samp = groupedList; samp != NULL; samp = samp->next)
{
sampleTabOut(samp, out);
}
//warn("Cleaning up.");
freez(&fileNameCopy);
carefulClose(&out);
sampleFreeList(&sampList);
sampleFreeList(&groupedList);
affyTransLiftedFreeList(&atlList);
}
void affyPairsToSample(struct hash *liftHash, int grouping, char *pairsIn)
/* Top level function to run combine pairs and offset files to give sample. */
{
struct affyPairs *apList = NULL, *ap = NULL;
struct sample *sampList = NULL, *samp = NULL;
struct sample *groupedList = NULL;
char buff[10+strlen(pairsIn)];
FILE *out = NULL;
fprintf(stderr, ".");
fflush(stderr);
//warn("Loading Affy Pairs.");
apList = affyPairsLoadAll(pairsIn);
//warn("Creating samples.");
for(ap = apList; ap != NULL; ap = ap->next)
{
samp = sampFromAffyPair(ap, liftHash);
if(samp != NULL)
{
slAddHead(&sampList, samp);
}
}
//warn("Sorting Samples");
slSort(&sampList, sampleCoordCmp);
groupedList = groupByPosition(grouping, sampList);
//warn("Saving Samples.");
snprintf(buff, sizeof(buff), "%s.sample", pairsIn);
out = mustOpen(buff, "w");
for(samp = groupedList; samp != NULL; samp = samp->next)
{
sampleTabOut(samp, out);
}
//warn("Cleaning up.");
carefulClose(&out);
sampleFreeList(&sampList);
sampleFreeList(&groupedList);
affyPairsFreeList(&apList);
}
