int
main(int argc, char **argv)
{
if (argc != 3 || (nthreads = atoi(argv[1])) <= 0
|| strlen(argv[2]) != 16*2)
usage();
assert(nthreads > 0);
// Decode the MD5 hash from hex
unsigned char hash[16];
int i;
for (i = 0; i < 16; i++) {
int hi = hexdig(argv[2][i*2+0]);
int lo = hexdig(argv[2][i*2+1]);
if (hi < 0 || lo < 0)
usage();
hash[i] = (hi << 4) | lo;
}
// Search all strings of length 1, then of length 2, ...
int len;
for (len = 1; len < MAXLEN; len++) {
cprintf("Searching strings of length %d\n", len);
uint8_t str[len+1];
str[len] = 0; // Null terminate for printing match
memset(str, MINCHR, len);
if (psearch(str, len, hash)) {
printf("Match: '%s'\n", out);
exit(0);
}
}
cprintf("not found\n");
return 1;
}
//**********************************************************************************************************************
vector<string> AlignCommand::setParameters(){
try {
CommandParameter ptemplate("reference", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(ptemplate);
CommandParameter pcandidate("fasta", "InputTypes", "", "", "none", "none", "none","fasta-alignreport-accnos",false,true,true); parameters.push_back(pcandidate);
CommandParameter psearch("search", "Multiple", "kmer-blast-suffix", "kmer", "", "", "","",false,false,true); parameters.push_back(psearch);
CommandParameter pksize("ksize", "Number", "", "8", "", "", "","",false,false); parameters.push_back(pksize);
CommandParameter pmatch("match", "Number", "", "1.0", "", "", "","",false,false); parameters.push_back(pmatch);
CommandParameter palign("align", "Multiple", "needleman-gotoh-blast-noalign", "needleman", "", "", "","",false,false,true); parameters.push_back(palign);
CommandParameter pmismatch("mismatch", "Number", "", "-1.0", "", "", "","",false,false); parameters.push_back(pmismatch);
CommandParameter pgapopen("gapopen", "Number", "", "-5.0", "", "", "","",false,false); parameters.push_back(pgapopen);
CommandParameter pgapextend("gapextend", "Number", "", "-2.0", "", "", "","",false,false); parameters.push_back(pgapextend);
CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);
CommandParameter pflip("flip", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pflip);
CommandParameter pthreshold("threshold", "Number", "", "0.50", "", "", "","",false,false); parameters.push_back(pthreshold);
CommandParameter pseed("seed", "Number", "", "0", "", "", "","",false,false); parameters.push_back(pseed);
CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
return myArray;
}
catch(exception& e) {
m->errorOut(e, "AlignCommand", "setParameters");
exit(1);
}
}
//**********************************************************************************************************************
vector<string> ClassifySeqsCommand::setParameters(){
try {
CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(ptaxonomy);
CommandParameter ptemplate("reference", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(ptemplate);
CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","taxonomy",false,true,true); parameters.push_back(pfasta);
CommandParameter pname("name", "InputTypes", "", "", "NameCount", "none", "none","",false,false,true); parameters.push_back(pname);
CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "none", "none","",false,false,true); parameters.push_back(pcount);
CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "none", "none","",false,false,true); parameters.push_back(pgroup);
CommandParameter poutput("output", "Multiple", "simple-detail", "detail", "", "", "","",false,false, true); parameters.push_back(poutput);
CommandParameter psearch("search", "Multiple", "kmer-blast-suffix-distance-align", "kmer", "", "", "","",false,false); parameters.push_back(psearch);
CommandParameter pksize("ksize", "Number", "", "8", "", "", "","",false,false); parameters.push_back(pksize);
CommandParameter pmethod("method", "Multiple", "wang-knn-zap", "wang", "", "", "","",false,false); parameters.push_back(pmethod);
CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);
CommandParameter pmatch("match", "Number", "", "1.0", "", "", "","",false,false); parameters.push_back(pmatch);
CommandParameter pprintlevel("printlevel", "Number", "", "-1", "", "", "","",false,false); parameters.push_back(pprintlevel);
CommandParameter pmismatch("mismatch", "Number", "", "-1.0", "", "", "","",false,false); parameters.push_back(pmismatch);
CommandParameter pgapopen("gapopen", "Number", "", "-2.0", "", "", "","",false,false); parameters.push_back(pgapopen);
CommandParameter pgapextend("gapextend", "Number", "", "-1.0", "", "", "","",false,false); parameters.push_back(pgapextend);
CommandParameter pcutoff("cutoff", "Number", "", "80", "", "", "","",false,true); parameters.push_back(pcutoff);
CommandParameter pprobs("probs", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(pprobs);
CommandParameter piters("iters", "Number", "", "100", "", "", "","",false,true); parameters.push_back(piters);
CommandParameter pshortcuts("shortcuts", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(pshortcuts);
CommandParameter prelabund("relabund", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(prelabund);
CommandParameter pnumwanted("numwanted", "Number", "", "10", "", "", "","",false,true); parameters.push_back(pnumwanted);
CommandParameter pseed("seed", "Number", "", "0", "", "", "","",false,false); parameters.push_back(pseed);
CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
return myArray;
}
catch(exception& e) {
m->errorOut(e, "ClassifySeqsCommand", "setParameters");
exit(1);
}
}