/**
* main function. Parses command-line arguments.
*/
int hisat2_build(int argc, const char **argv) {
string outfile;
try {
// Reset all global state, including getopt state
opterr = optind = 1;
resetOptions();
string infile;
EList<string> infiles(MISC_CAT);
parseOptions(argc, argv);
argv0 = argv[0];
if(showVersion) {
cout << argv0 << " version " << string(HISAT2_VERSION).c_str() << endl;
if(sizeof(void*) == 4) {
cout << "32-bit" << endl;
} else if(sizeof(void*) == 8) {
cout << "64-bit" << endl;
} else {
cout << "Neither 32- nor 64-bit: sizeof(void*) = " << sizeof(void*) << endl;
}
cout << "Built on " << BUILD_HOST << endl;
cout << BUILD_TIME << endl;
cout << "Compiler: " << COMPILER_VERSION << endl;
cout << "Options: " << COMPILER_OPTIONS << endl;
cout << "Sizeof {int, long, long long, void*, size_t, off_t}: {"
<< sizeof(int)
<< ", " << sizeof(long) << ", " << sizeof(long long)
<< ", " << sizeof(void *) << ", " << sizeof(size_t)
<< ", " << sizeof(off_t) << "}" << endl;
return 0;
}
// Get input filename
if(optind >= argc) {
cerr << "No input sequence or sequence file specified!" << endl;
printUsage(cerr);
return 1;
}
infile = argv[optind++];
// Get output filename
if(optind >= argc) {
cerr << "No output file specified!" << endl;
printUsage(cerr);
return 1;
}
outfile = argv[optind++];
tokenize(infile, ",", infiles);
if(infiles.size() < 1) {
cerr << "Tokenized input file list was empty!" << endl;
printUsage(cerr);
return 1;
}
if(!lineRate_provided) {
if(snp_fname == "" && ss_fname == "" && exon_fname == "") {
lineRate = GFM<TIndexOffU>::default_lineRate_fm;
} else {
lineRate = GFM<TIndexOffU>::default_lineRate_gfm;
}
}
// Optionally summarize
if(verbose) {
cerr << "Settings:" << endl
<< " Output files: \"" << outfile.c_str() << ".*." << gfm_ext << "\"" << endl
<< " Line rate: " << lineRate << " (line is " << (1<<lineRate) << " bytes)" << endl
<< " Lines per side: " << linesPerSide << " (side is " << ((1<<lineRate)*linesPerSide) << " bytes)" << endl
<< " Offset rate: " << offRate << " (one in " << (1<<offRate) << ")" << endl
<< " FTable chars: " << ftabChars << endl
<< " Strings: " << (packed? "packed" : "unpacked") << endl
<< " Local offset rate: " << localOffRate << " (one in " << (1<<localOffRate) << ")" << endl
<< " Local fTable chars: " << localFtabChars << endl
<< " Local sequence length: " << local_index_size << endl
<< " Local sequence overlap between two consecutive indexes: " << local_index_overlap << endl;
#if 0
if(bmax == OFF_MASK) {
cerr << " Max bucket size: default" << endl;
} else {
cerr << " Max bucket size: " << bmax << endl;
}
if(bmaxMultSqrt == OFF_MASK) {
cerr << " Max bucket size, sqrt multiplier: default" << endl;
} else {
cerr << " Max bucket size, sqrt multiplier: " << bmaxMultSqrt << endl;
}
if(bmaxDivN == 0xffffffff) {
cerr << " Max bucket size, len divisor: default" << endl;
} else {
cerr << " Max bucket size, len divisor: " << bmaxDivN << endl;
}
cerr << " Difference-cover sample period: " << dcv << endl;
#endif
cerr << " Endianness: " << (bigEndian? "big":"little") << endl
<< " Actual local endianness: " << (currentlyBigEndian()? "big":"little") << endl
<< " Sanity checking: " << (sanityCheck? "enabled":"disabled") << endl;
#ifdef NDEBUG
cerr << " Assertions: disabled" << endl;
#else
cerr << " Assertions: enabled" << endl;
#endif
cerr << " Random seed: " << seed << endl;
cerr << " Sizeofs: void*:" << sizeof(void*) << ", int:" << sizeof(int) << ", long:" << sizeof(long) << ", size_t:" << sizeof(size_t) << endl;
cerr << "Input files DNA, " << file_format_names[format].c_str() << ":" << endl;
for(size_t i = 0; i < infiles.size(); i++) {
cerr << " " << infiles[i].c_str() << endl;
}
}
// Seed random number generator
srand(seed);
{
Timer timer(cerr, "Total time for call to driver() for forward index: ", verbose);
try {
driver<SString<char> >(infile, infiles, snp_fname, ht_fname, ss_fname, exon_fname, sv_fname, outfile, false, REF_READ_FORWARD);
} catch(bad_alloc& e) {
if(autoMem) {
cerr << "Switching to a packed string representation." << endl;
packed = true;
} else {
throw e;
}
}
}
return 0;
} catch(std::exception& e) {
cerr << "Error: Encountered exception: '" << e.what() << "'" << endl;
cerr << "Command: ";
for(int i = 0; i < argc; i++) cerr << argv[i] << " ";
cerr << endl;
deleteIdxFiles(outfile, writeRef || justRef, justRef);
return 1;
} catch(int e) {
if(e != 0) {
cerr << "Error: Encountered internal HISAT2 exception (#" << e << ")" << endl;
cerr << "Command: ";
for(int i = 0; i < argc; i++) cerr << argv[i] << " ";
cerr << endl;
}
deleteIdxFiles(outfile, writeRef || justRef, justRef);
return e;
}
}
/**
* main function. Parses command-line arguments.
*/
int bowtie_build(int argc, const char **argv) {
try {
// Reset all global state, including getopt state
opterr = optind = 1;
resetOptions();
string infile;
vector<string> infiles;
string outfile;
parseOptions(argc, argv);
argv0 = argv[0];
if(showVersion) {
cout << argv0 << " version " << BOWTIE_VERSION << endl;
if(sizeof(void*) == 4) {
cout << "32-bit" << endl;
} else if(sizeof(void*) == 8) {
cout << "64-bit" << endl;
} else {
cout << "Neither 32- nor 64-bit: sizeof(void*) = " << sizeof(void*) << endl;
}
cout << "Built on " << BUILD_HOST << endl;
cout << BUILD_TIME << endl;
cout << "Compiler: " << COMPILER_VERSION << endl;
cout << "Options: " << COMPILER_OPTIONS << endl;
cout << "Sizeof {int, long, long long, void*, size_t, off_t}: {"
<< sizeof(int)
<< ", " << sizeof(long) << ", " << sizeof(long long)
<< ", " << sizeof(void *) << ", " << sizeof(size_t)
<< ", " << sizeof(off_t) << "}" << endl;
return 0;
}
// Get input filename
if(optind >= argc) {
cerr << "No input sequence or sequence file specified!" << endl;
printUsage(cerr);
return 1;
}
infile = argv[optind++];
// Get output filename
if(optind >= argc) {
cerr << "No output file specified!" << endl;
printUsage(cerr);
return 1;
}
outfile = argv[optind++];
tokenize(infile, ",", infiles);
if(infiles.size() < 1) {
cerr << "Tokenized input file list was empty!" << endl;
printUsage(cerr);
return 1;
}
// Optionally summarize
if(verbose) {
cout << "Settings:" << endl
<< " Output files: \"" << outfile << ".*." + gEbwt_ext + "\"" << endl
<< " Line rate: " << lineRate << " (line is " << (1<<lineRate) << " bytes)" << endl
<< " Lines per side: " << linesPerSide << " (side is " << ((1<<lineRate)*linesPerSide) << " bytes)" << endl
<< " Offset rate: " << offRate << " (one in " << (1<<offRate) << ")" << endl
<< " FTable chars: " << ftabChars << endl
<< " Strings: " << (packed? "packed" : "unpacked") << endl
;
if(bmax == OFF_MASK) {
cout << " Max bucket size: default" << endl;
} else {
cout << " Max bucket size: " << bmax << endl;
}
if(bmaxMultSqrt == OFF_MASK) {
cout << " Max bucket size, sqrt multiplier: default" << endl;
} else {
cout << " Max bucket size, sqrt multiplier: " << bmaxMultSqrt << endl;
}
if(bmaxDivN == 0xffffffff) {
cout << " Max bucket size, len divisor: default" << endl;
} else {
cout << " Max bucket size, len divisor: " << bmaxDivN << endl;
}
cout << " Difference-cover sample period: " << dcv << endl;
cout << " Endianness: " << (bigEndian? "big":"little") << endl
<< " Actual local endianness: " << (currentlyBigEndian()? "big":"little") << endl
<< " Sanity checking: " << (sanityCheck? "enabled":"disabled") << endl;
#ifdef NDEBUG
cout << " Assertions: disabled" << endl;
#else
cout << " Assertions: enabled" << endl;
#endif
cout << " Random seed: " << seed << endl;
cout << " Sizeofs: void*:" << sizeof(void*) << ", int:" << sizeof(int) << ", long:" << sizeof(long) << ", size_t:" << sizeof(size_t) << endl;
cout << "Input files DNA, " << file_format_names[format] << ":" << endl;
for(size_t i = 0; i < infiles.size(); i++) {
cout << " " << infiles[i] << endl;
}
}
// Seed random number generator
srand(seed);
{
Timer timer(cout, "Total time for call to driver() for forward index: ", verbose);
if(!packed) {
try {
driver<String<Dna, Alloc<> > >(infile, infiles, outfile);
} catch(bad_alloc& e) {
if(autoMem) {
cerr << "Switching to a packed string representation." << endl;
packed = true;
} else {
throw e;
}
}
}
if(packed) {
driver<String<Dna, Packed<Alloc<> > > >(infile, infiles, outfile);
}
}
if(doubleEbwt) {
srand(seed);
Timer timer(cout, "Total time for backward call to driver() for mirror index: ", verbose);
if(!packed) {
try {
driver<String<Dna, Alloc<> > >(infile, infiles, outfile + ".rev", true);
} catch(bad_alloc& e) {
if(autoMem) {
cerr << "Switching to a packed string representation." << endl;
packed = true;
} else {
throw e;
}
}
}
if(packed) {
driver<String<Dna, Packed<Alloc<> > > >(infile, infiles, outfile + ".rev", true);
}
}
return 0;
} catch(std::exception& e) {
cerr << "Command: ";
for(int i = 0; i < argc; i++) cerr << argv[i] << " ";
cerr << endl;
return 1;
} catch(int e) {
if(e != 0) {
cerr << "Command: ";
for(int i = 0; i < argc; i++) cerr << argv[i] << " ";
cerr << endl;
}
return e;
}
}
