int main(int argc, char *argv[])
{
MyCmdLine(argc, argv);
if (argc < 2)
{
Usage();
return 0;
}
if (opt_version)
{
printf("uchime v" MY_VERSION ".%s\n", SVN_VERSION);
return 0;
}
printf("uchime v" MY_VERSION ".%s\n", SVN_VERSION);
printf("by Robert C. Edgar\n");
printf("http://drive5.com/uchime\n");
printf("This code is donated to the public domain.\n");
printf("\n");
if (!optset_w)
opt_w = 8;
float MinFractId = 0.95f;
if (optset_id)
MinFractId = (float) opt_id;
Log("%8.2f minh\n", opt_minh);
Log("%8.2f xn\n", opt_xn);
Log("%8.2f dn\n", opt_dn);
Log("%8.2f xa\n", opt_xa);
Log("%8.2f mindiv\n", opt_mindiv);
Log("%8u maxp\n", opt_maxp);
if (opt_input == "" && opt_uchime != "")
opt_input = opt_uchime;
if (opt_input == "")
Die("Missing --input");
g_UchimeDeNovo = (opt_db == "");
if (opt_uchimeout != "")
g_fUChime = CreateStdioFile(opt_uchimeout);
if (opt_uchimealns != "")
g_fUChimeAlns = CreateStdioFile(opt_uchimealns);
SeqDB Input;
SeqDB DB;
Input.FromFasta(opt_input);
if (!Input.IsNucleo())
Die("Input contains amino acid sequences");
const unsigned QuerySeqCount = Input.GetSeqCount();
vector<unsigned> Order;
for (unsigned i = 0; i < QuerySeqCount; ++i)
Order.push_back(i);
if (g_UchimeDeNovo)
{
vector<float> Abs;
for (unsigned i = 0; i < QuerySeqCount; ++i)
{
const char *Label = Input.GetLabel(i);
float Ab = GetAbFromLabel(Label);
Abs.push_back(Ab);
}
SortDescending(Abs, Order);
DB.m_IsNucleoSet = true;
DB.m_IsNucleo = true;
}
else
{
DB.FromFasta(opt_db);
if (!DB.IsNucleo())
Die("Database contains amino acid sequences");
}
vector<ChimeHit2> Hits;
unsigned HitCount = 0;
for (unsigned i = 0; i < QuerySeqCount; ++i)
{
unsigned QuerySeqIndex = Order[i];
SeqData QSD;
Input.GetSeqData(QuerySeqIndex, QSD);
float QAb = -1.0;
if (g_UchimeDeNovo)
QAb = GetAbFromLabel(QSD.Label);
ChimeHit2 Hit;
AlnParams &AP = *(AlnParams *) 0;
AlnHeuristics &AH = *(AlnHeuristics *) 0;
HSPFinder &HF = *(HSPFinder *) 0;
bool Found = SearchChime(DB, QSD, QAb, AP, AH, HF, MinFractId, Hit);
if (Found)
++HitCount;
else
{
if (g_UchimeDeNovo)
DB.AddSeq(QSD.Label, QSD.Seq, QSD.L);
}
WriteChimeHit(g_fUChime, Hit);
ProgressStep(i, QuerySeqCount, "%u/%u chimeras found (%.1f%%)", HitCount, i, Pct(HitCount, i+1));
}
Log("\n");
Log("%s: %u/%u chimeras found (%.1f%%)\n",
opt_input.c_str(), HitCount, QuerySeqCount, Pct(HitCount, QuerySeqCount));
CloseStdioFile(g_fUChime);
CloseStdioFile(g_fUChimeAlns);
ProgressExit();
return 0;
}
/*public virtual*/
morkStdioFile::~morkStdioFile() // assert CloseStdioFile() executed earlier
{
if (mStdioFile_File)
CloseStdioFile(mMorkEnv);
MORK_ASSERT(mStdioFile_File==0);
}