void usage()
/* Explain usage and exit. */
{
struct bzp *bzp = bzpDefault();
printf("blatzServer version %d - Set up in-memory server for\n", bzpVersion());
printf("cross-species DNA alignments\n");
printf("usage:\n");
printf(" blatzServer start file(s)\n");
printf("Starts up server. Files are either fasta files, nib files, 2bit files\n");
printf("or text files containing the names of the above files one per line.\n");
printf("It's important that the sequence be repeat masked with repeats in\n");
printf("lower case.\n");
printf("Options: (defaults are shown for numerical parameters)\n");
bzpServerOptionsHelp(bzp);
bzpClientOptionsHelp(bzp);
printf(" -debug Writes diagnostic output to console and no daemon fork\n");
printf(" -subnet=255.255.255.255 Restrict access to subnet\n");
printf(" -port=%d Use specified TCP/IP port\n", bzpDefaultPort);
printf(" -host=%s Query specified host\n", host);
printf(" -cpu=%d Use specified number of CPUs (processes)\n", cpuCount);
printf("Other uses:\n");
printf(" blatzServer stop\n");
printf(" this terminates server\n");
printf(" blatzServer status\n");
printf(" this prints status info including version\n");
noWarnAbort();
}
void statusResponse(int sd, struct bzp *bzp, struct blatzIndex *indexList)
/* Respond to status message. */
{
FILE *f = netFileFromSocket(sd);
fprintf(f, "version: %d\n", bzpVersion());
fprintf(f, "indexed sequences: %d\n", slCount(indexList));
fprintf(f, "bases indexed: %lld\n", basesInIndexList(indexList));
fprintf(f, "weight: %d\n", bzp->weight);
fprintf(f, "rna: %s\n", trueFalseString(bzp->rna));
fprintf(f, "minScore: %d\n", bzp->minScore);
fprintf(f, "minGapless: %d\n", bzp->minGapless);
fprintf(f, "multiHits: %d\n", bzp->multiHits);
fprintf(f, "minChain: %d\n", bzp->minChain);
fprintf(f, "maxExtend: %d\n", bzp->maxExtend);
fprintf(f, "maxBandGap: %d\n", bzp->maxBandGap);
fprintf(f, "minExpand: %d\n", bzp->minExpand);
fprintf(f, "expandWindow: %d\n", bzp->expandWindow);
fprintf(f, "out: %s\n", bzp->out);
fprintf(f, "good queries: %d\n", goodQueryCount);
fprintf(f, "bad queries: %d\n", badQueryCount);
fprintf(f, "crashes: %d\n", crashCount);
fprintf(f, "cpus used: %d\n", cpusUsed);
carefulClose(&f);
}
void usage(struct bzp *bzp)
/* Explain usage and exit. */
{
printf("blatz version %d - Align dna across species\n", bzpVersion());
printf("usage:\n");
printf(" blatz target query output\n");
printf("where target and query are either fasta files, nib files, 2bit files\n");
printf("or a text files containing the names of the above files one per line.\n");
printf("It's important that the sequence be repeat masked with repeats in\n");
printf("lower case.\n");
printf("Options: (defaults are shown for numerical parameters)\n");
bzpServerOptionsHelp(bzp);
bzpClientOptionsHelp(bzp);
noWarnAbort();
}
static void usage()
/* Explain usage and exit. */
{
struct bzp *bzp = bzpDefault();
printf("blatzClient version %d - Ask server to do\n", bzpVersion());
printf("cross-species DNA alignments and save results.\n");
printf("usage:\n");
printf(" blatzClient queryFile outputFile.\n");
printf("The queryFile can be in fasta, nib, or 2bit format or a \n");
printf("text file containing the names of the above files one per line.\n");
printf("It's important that the sequence be repeat masked with repeats in\n");
printf("lower case.\n");
printf("Options: (defaults are shown for numerical parameters)\n");
bzpClientOptionsHelp(bzp);
printf(" -port=%d Use specified TCP/IP port\n", bzpDefaultPort);
printf(" -host=%s Query specified host\n", host);
noWarnAbort();
}