int main(int argc, char *argv[])
/* Process command line. */
{
char *command;
bzpTime(NULL);
dnaUtilOpen();
setMaxAlloc(2LL*1024LL*1024LL*1024LL);
optionInit(&argc, argv, options);
port = optionInt("port", port);
host = optionVal("host", host);
netParseSubnet(optionVal("subnet", NULL), subnet);
cpuCount = optionInt("cpu", cpuCount);
if (argc < 2)
usage();
command = argv[1];
if (sameWord(command, "start"))
{
if (argc < 3)
usage();
serverStart(argv+2, argc-2);
}
else if (sameWord(command, "stop"))
{
serverStop();
}
else if (sameWord(command, "status"))
{
serverStatus();
}
else
usage();
return 0;
}
void serverStart(char *files[], int fileCount)
/* Load DNA. Build up indexes, set up listing port, and fall into
* accept loop. */
{
struct blatzIndex *indexList = NULL;
int i;
int acceptor;
struct bzp *bzp = bzpDefault();
/* Daemonize self. */
bzpSetOptions(bzp);
/* Load up all sequences. */
for (i=0; i<fileCount; ++i)
{
struct dnaLoad *dl = dnaLoadOpen(files[i]);
struct blatzIndex *oneList = blatzIndexDl(dl, bzp->weight, bzp->unmask);
indexList = slCat(indexList, oneList);
dnaLoadClose(&dl);
}
bzpTime("Loaded and indexed %d sequences", slCount(indexList));
verbose(1, "Ready for queries\n");
/* Turn self into proper daemon. */
logDaemonize("blatzServer");
acceptor = netAcceptingSocket(port, 100);
serviceLoop(acceptor, bzp, indexList);
}
static void loadAndAlignAll(struct bzp *bzp,
char *target, char *query, char *output)
/* blatz - Align genomic dna across species. */
{
struct dnaLoad *queryDl = dnaLoadOpen(query);
struct dnaLoad *targetDl = dnaLoadOpen(target);
struct blatzIndex *indexList = blatzIndexDl(targetDl, bzp->weight, bzp->unmask);
bzpTime("loaded and indexed target DNA");
// LX BEG
if (bzp->dynaWordCoverage > 0)
{
dynaNumWords = (pow(4,bzp->weight)); // ?? check with Jim if this is correct
AllocArray(dynaWordCount,dynaNumWords);
printf("Allocated word count table of size %d\n",dynaNumWords);
dynaWordLimit = bzp->dynaWordCoverage; // cheating, should be more like:
//dynaWordLimit = bzp->dynaWordCoverage*dynaSequenceSize/dynaNumWords;
printf("Set word limit to %d\n",dynaWordLimit);
}
// LX END
verbose(2, "Loaded %d in %s, opened %s\n", slCount(indexList), target,
query);
alignAll(bzp, indexList, queryDl, output);
}
int main(int argc, char *argv[])
/* Process command line. */
{
bzpTime(NULL);
dnaUtilOpen();
optionInit(&argc, argv, options);
port = optionInt("port", port);
host = optionVal("host", host);
if (argc != 3)
usage();
blatzClient(argv[1], argv[2]);
return 0;
}
int main(int argc, char *argv[])
/* Process command line. */
{
struct bzp *bzp = bzpDefault();
/* Do initialization. */
bzpTime(NULL);
dnaUtilOpen();
optionInit(&argc, argv, options);
if (argc != 4)
usage(bzp);
/* Fill in parameters from command line options. */
bzpSetOptions(bzp);
loadAndAlignAll(bzp, argv[1], argv[2], argv[3]);
/* If you were a turtle you'd be home right now. */
return 0;
}
void queryResponse(int sd, struct bzp *bzp, struct blatzIndex *indexList)
/* Respond to query message - read options and dna from socket,
* and do alignment. */
{
struct bzp lbzp = *bzp;
struct dnaSeq *seq = NULL;
char buf[256], *line, *word;
char *out = NULL, *mafT = NULL, *mafQ = NULL;
/* First get options - overriding what got set at startup. */
for (;;)
{
if ((line = netGetString(sd, buf)) == NULL)
{
truncatedQuery(1);
return;
}
word = nextWord(&line);
line = skipLeadingSpaces(line);
if (sameString(word, "seq"))
break;
else if (sameString(word, "rna"))
lbzp.rna = TRUE;
else if (sameString(word, "minScore"))
lbzp.minScore = atoi(line);
else if (sameString(word, "minGapless"))
lbzp.minGapless = atoi(line);
else if (sameString(word, "multiHits"))
lbzp.multiHits = atoi(line);
else if (sameString(word, "minChain"))
lbzp.minChain = atoi(line);
else if (sameString(word, "maxExtend"))
lbzp.maxExtend = atoi(line);
else if (sameString(word, "maxBandGap"))
lbzp.maxBandGap = atoi(line);
else if (sameString(word, "minExpand"))
lbzp.minExpand = atoi(line);
else if (sameString(word, "expandWindow"))
lbzp.expandWindow = atoi(line);
else if (sameString(word, "out"))
lbzp.out = out = cloneString(line);
else if (sameString(word, "mafQ"))
lbzp.mafQ = mafQ = cloneString(line);
else if (sameString(word, "mafT"))
lbzp.mafT = mafT = cloneString(line);
}
/* Get DNA into seq*/
{
char *name = netGetString(sd, buf);
char *dna;
if (name == NULL)
{
truncatedQuery(2);
return;
}
dna = netGetHugeString(sd);
if (dna == NULL)
{
truncatedQuery(3);
return;
}
AllocVar(seq);
seq->dna = dna;
seq->size = strlen(dna);
seq->name = cloneString(name);
bzpTime("Received %d bases in %s", seq->size, seq->name);
if (lbzp.rna)
maskTailPolyA(seq->dna, seq->size);
}
/* Create alignments into chainList and write results. */
{
FILE *f = netFileFromSocket(sd);
struct chain *chainList = blatzAlign(&lbzp, indexList, seq);
blatzWriteChains(&lbzp, &chainList, seq, 0, seq->size, seq->size, indexList, f);
bzpTime("sent result - %d chains", slCount(chainList));
carefulClose(&f);
}
dnaSeqFree(&seq);
freez(&out);
freez(&mafQ);
freez(&mafT);
}
void serviceLoop(int acceptor, struct bzp *bzp, struct blatzIndex *indexList)
/* Wait for requests on acceptor socket. */
{
for (;;)
{
int sd;
char buf[256];
char *command;
/* Wait for previous processes */
{
int options = 0;
int w, status;
for (;;)
{
if (cpusUsed < cpuCount)
options = WNOHANG;
w = waitpid(-1, &status, options);
if (w > 0)
{
--cpusUsed;
if (!WIFEXITED(status))
++crashCount;
else if (WEXITSTATUS(status) != 0)
++badQueryCount;
else
++goodQueryCount;
}
else
break;
}
}
sd = netAcceptFrom(acceptor, subnet);
bzpTime("Since last query");
command = netGetString(sd, buf);
if (command != NULL)
{
verbose(2, "servicing %s\n", command);
if (sameString(command, "stop"))
break;
else
{
int pid;
++cpusUsed;
pid = mustFork();
if (pid == 0)
{
if (command != NULL)
{
if (sameString(command, "status"))
statusResponse(sd, bzp, indexList);
else if (sameString(command, "query"))
queryResponse(sd, bzp, indexList);
}
exit(0);
}
}
}
close(sd);
}
}
