void pslCoverage(char *inLst, char *inPsl, double aliRatio, int trimSize, char *outName,
char *misAsmName)
/* Analyse inName and put best alignments for eacmRNA in estAliName.
* Put repeat info in repName. */
{
struct lineFile *in = pslFileOpen(inPsl);
FILE *out = mustOpen(outName, "a");
FILE *misAsm = mustOpen(misAsmName, "w");
struct psl *pslList = NULL, *psl;
char lastName[256];
int threshold = round((1.0 - (1.0 - aliRatio)*2)*1000);
struct hash *probeHash;
struct probe *probeList;
readProbeList(inLst, &probeList, &probeHash);
printf("Found %d probes in %s\n", slCount(probeList), inLst);
printf("Processing %s percent ID %f%% threshold %d\n", inPsl, aliRatio*100, threshold);
strcpy(lastName, "");
while ((psl = pslNext(in)) != NULL)
{
if (!sameString(lastName, psl->qName))
{
doOneAcc(lastName, pslList, threshold, trimSize, probeHash, misAsm);
finishList(&pslList);
strcpy(lastName, psl->qName);
}
slAddHead(&pslList, psl);
}
doOneAcc(lastName, pslList, threshold, trimSize, probeHash, misAsm);
finishList(&pslList);
lineFileClose(&in);
summarizeProbeList(probeList, trimSize, aliRatio, out, misAsm);
fclose(out);
}
//----------------------------------------------------------
void PdBase::sendList(const std::string& dest, const List& list) {
PdContext& context = PdContext::instance();
if(context.bMsgInProgress) {
cerr << "Pd: Can not send list, message in progress" << endl;
return;
}
_LOCK();
libpd_start_message(list.len());
_UNLOCK();
context.bMsgInProgress = true;
// step through list
for(int i = 0; i < list.len(); ++i) {
if(list.isFloat(i))
addFloat(list.getFloat(i));
else if(list.isSymbol(i))
addSymbol(list.getSymbol(i));
}
finishList(dest);
}
PdBase& PdBase::operator<<(const FinishList& var) {
finishList(var.dest);
return *this;
}
