int main(int argc, char *argv[]) {
// First: Sort out the command line.
struct arg_file *files_to_verify = arg_filen(NULL, NULL, "<table file>", 0, 100000, "GRT parts to verify.");
struct arg_dbl *percent = arg_dbl0(NULL, "percent", "[0-100]", "Percent of chains to randomly verify.");
struct arg_int *sequential = arg_int0(NULL, "sequential", "<n>", "Check every nth chain");
/*
void *argtable[] = {table_files, output_directory, bits, move_source, end};
// Get arguments, collect data, check for basic errors.
if (arg_nullcheck(argtable) != 0) {
printf("error: insufficient memory\n");
}
// Look for errors
int nerrors = arg_parse(argc,argv,argtable);
if (nerrors > 0) {
// Print errors, exit.
arg_print_errors(stdout,end,argv[0]);
// Print help.
printf("\n\nOptions: \n");
arg_print_glossary(stdout,argtable," %-20s %s\n");
exit(1);
}
*/
}
int main(int argc, char **argv)
{
struct arg_dbl *a = arg_dbl1(NULL,NULL,"a","a is <double>");
struct arg_dbl *b = arg_dbl0(NULL,NULL,"b","b is <double>");
struct arg_dbl *c = arg_dbl0(NULL,NULL,"c","c is <double>");
struct arg_dbl *d = arg_dbln("dD","delta","<double>",0,3,"d can occur 0..3 times");
struct arg_dbl *e = arg_dbl0(NULL,"eps,eqn","<double>","eps is optional");
struct arg_lit *help = arg_lit0(NULL,"help","print this help and exit");
struct arg_end *end = arg_end(20);
void* argtable[] = {a,b,c,d,e,help,end};
int nerrors;
int exitcode=0;
int i;
double sum=0;
/*
printf("a=%p\n",a);
printf("b=%p\n",b);
printf("c=%p\n",c);
printf("d=%p\n",d);
printf("e=%p\n",e);
printf("help=%p\n",help);
printf("end=%p\n",end);
printf("argtable=%p\n",argtable);
*/
/* print the command line */
for (i=0; i<argc; i++)
printf("%s ",argv[i]);
printf("\n");
/* verify the argtable[] entries were allocated sucessfully */
if (arg_nullcheck(argtable) != 0)
{
/* NULL entries were detected, some allocations must have failed */
printf("%s: insufficient memory\n",argv[0]);
exitcode=1;
goto exit;
}
/* Parse the command line as defined by argtable[] */
nerrors = arg_parse(argc,argv,argtable);
/* special case: '--help' takes precedence over error reporting */
if (help->count > 0)
{
printf("Usage: %s ", argv[0]);
arg_print_syntax(stdout,argtable,"\n");
arg_print_glossary(stdout,argtable," %-25s %s\n");
exitcode=0;
goto exit;
}
/* If the parser returned any errors then display them and exit */
if (nerrors > 0)
{
/* Display the error details contained in the arg_end struct.*/
arg_print_errors(stdout,end,argv[0]);
exitcode=1;
goto exit;
}
/* parsing complete, verify all args sum to zero */
for (i=0; i<a->count; i++)
{
printf("a[%d]=%f\n",i,a->dval[i]);
sum += a->dval[i];
}
for (i=0; i<b->count; i++)
{
printf("b[%d]=%f\n",i,b->dval[i]);
sum += b->dval[i];
}
for (i=0; i<c->count; i++)
{
printf("c[%d]=%f\n",i,c->dval[i]);
sum += c->dval[i];
}
for (i=0; i<d->count; i++)
{
printf("d[%d]=%f\n",i,d->dval[i]);
sum += d->dval[i];
}
for (i=0; i<e->count; i++)
{
printf("e[%d]=%f\n",i,e->dval[i]);
sum += e->dval[i];
}
printf("sum=%f\n",sum);
if (sum<-1.0e-6 || sum>1.0e-6)
{
printf("%s: error - sum=%f is non-zero\n",argv[0],sum);
exitcode=1;
goto exit;
}
exit:
/* deallocate each non-null entry in argtable[] */
arg_freetable(argtable,sizeof(argtable)/sizeof(argtable[0]));
printf("%s: exitcode=%d\n\n",argv[0],exitcode);
/* close stdin and stdout to stop memcheck whining about their memory not being freed */
fclose(stdin);
fclose(stdout);
return exitcode;
}
int main(int argc, char *argv[]) {
struct arg_dbl *_dt = arg_dbl0("t",
"time-step",
NULL,
"time step for time history integration");
struct arg_dbl *_d = arg_dbl0("d",
"duration",
NULL,
"the duration of the analysis");
struct arg_dbl *_a = arg_dbl0("a",
"alpha",
NULL,
"Reynolds damping alpha");
struct arg_dbl *_b = arg_dbl0("b",
"beta",
NULL,
"Reynolds damping beta");
struct arg_dbl *_E = arg_dbl0("E",
"youngs-modulus",
NULL,
"the material stiffness");
struct arg_dbl *_A = arg_dbl0("A",
"area",
NULL,
"the member's cross-sectional stiffness");
struct arg_dbl *_I = arg_dbl0("I",
"moment-of-interia",
NULL,
"the member's moment of interia");
struct arg_dbl *_m = arg_dbl0("m",
"mass",
NULL,
"the mass at the top of the member");
struct arg_dbl *_F = arg_dbl0("F",
"force",
NULL,
"the force applied at the top of the member");
struct arg_dbl *_h = arg_dbl0("h",
"height",
NULL,
"the height of the member");
_dt->dval[0] = 0.1;
_d->dval[0] = 10;
_a->dval[0] = 0.0115;
_b->dval[0] = 0.0115;
_A->dval[0] = 0.0002;
_E->dval[0] = 200000000;
_I->dval[0] = 0.0000000133333;
_m->dval[0] = 10;
_F->dval[0] = 40;
_h->dval[0] = 2;
struct arg_end *end = arg_end(10);
void* argtable[] = {_dt,_d,_a,_b,_A,_E,_I,_m,_F,_h,end};
const char* progname = "sdof-step";
int exitcode = 0, returnvalue = 0;
int nerrors = arg_nullcheck(argtable);
if(nerrors != 0) {
cerr << "Not enough memory to proceed" << endl;
arg_print_errors(stderr,end,progname);
arg_freetable(argtable,sizeof(argtable)/sizeof(argtable[0]));
return nerrors;
}
nerrors = arg_parse(argc, argv, argtable);
if(nerrors != 0) {
arg_print_errors(stderr,end,progname);
cerr << "Usage: " << endl;
arg_print_syntaxv(stderr,argtable,"\n");
return(nerrors);
}
FILE* param = fopen("parameters.txt","w");
fprintf(param,"Input Parameters:\n");
fprintf(param,"Time step: %lf\n",_dt->dval[0]);
fprintf(param,"Duration: %lf\n",_d->dval[0]);
fprintf(param,"alpha: %lf\n",_a->dval[0]);
fprintf(param,"beta: %lf\n",_b->dval[0]);
fprintf(param,"area: %lf\n",_A->dval[0]);
fprintf(param,"I: %lf\n",_I->dval[0]);
fprintf(param,"E: %lf\n",_E->dval[0]);
fprintf(param,"mass: %lf\n",_m->dval[0]);
fprintf(param,"h: %lf\n",_h->dval[0]);
fprintf(param,"F: %lf\n",_F->dval[0]);
fclose(param);
double* x = new double[3];
double* v = new double[3];
double* a = new double[3];
bool* constrainType = new bool[3];
double* constrainValue = new double[3];
double* mass = new double[3];
Node** nodes = new Node*[2];
x[0] = x[1] = x[2] = 0.0;
v[0] = v[1] = v[2] = a[0] = a[1] = a[2] = 0.0;
constrainType[0] = Node::DISP;
constrainType[1] = Node::DISP;
constrainType[2] = Node::DISP;
constrainValue[0] = 0.0;
constrainValue[1] = 0.0;
constrainValue[2] = 0.0;
mass[0] = _m->dval[0];
mass[1] = _m->dval[0];
mass[2] = _m->dval[0]/4;
nodes[0] = new Node(x, v, a, 3, constrainType, constrainValue,
mass, 0);
// set y coord of second node
x[1] = _h->dval[0];
constrainType[0] = Node::FORCE;
constrainType[1] = Node::FORCE;
constrainType[2] = Node::FORCE;
cerr << "about to make the second node" << endl;
nodes[1] = new Node(x, v, a, 3, constrainType, constrainValue,
mass, 1);
cerr << "made 2nd node" << endl;
Element** elements = new Element*[1];
elements[0] = new LinearBeam(nodes,
2,
_A->dval[0],
_E->dval[0],
_I->dval[0]);
cerr << "generated elements" << endl;
double dt = _dt->dval[0];
double time = _d->dval[0];
int nSteps = (int) (time / dt);
cerr << "Number of Time Steps: " << nSteps << endl;
double wf = 2;
cerr << "bo" << endl;
double **loads;
cerr << "bi" << endl;
loads = new double*[6];
for(int i = 0; i < 6; i++) {
loads[i] = new double[nSteps];
}
cerr << "ba" << endl;
double E = _E->dval[0];
double I = _I->dval[0];
double L = _h->dval[0];
double k = 3*E*I/(L*L*L);
double w = sqrt(k/_m->dval[0]);
double T = 2*M_PI/w;
cerr << "Period is " << T << endl;
for(int i = 0; i < nSteps; i++) {
for(int j = 0; j < 6; j++)
loads[j][i] = 0.0;
}
loads[3][2] = _F->dval[0];
FILE* load = fopen("load.csv", "w");
for(int i = 0; i < nSteps; i++) {
for(int j = 0; j < 6; j++)
fprintf(load,"%lf,",loads[j][i]);
fprintf(load,"\n");;
}
Enoch* enoch = new Enoch(nodes,elements,loads,2,1,nSteps, dt,
_a->dval[0], _b->dval[0], 0.5, 0.25);
enoch->run();
}
int main(int argc, char *argv[]) {
int retcode = 1;
int nerrors = 0;
streamer_t streamer;
memset(&streamer, 0, sizeof(streamer_t));
// Signal handlers
signal(SIGINT, sig_fn);
signal(SIGTERM, sig_fn);
// Initialize SDL2
if (SDL_Init(SDL_INIT_AUDIO) != 0) {
fprintf(stderr, "%s\n", SDL_GetError());
return 1;
}
// Defaults
streamer.freq = 44100;
streamer.n_channels = 2;
streamer.bits = 16;
streamer.volume = 1.0f;
streamer.quality = DUMB_RQ_CUBIC;
// commandline argument parser options
struct arg_lit *arg_help =
arg_lit0("h", "help", "print this help and exits");
struct arg_dbl *arg_volume =
arg_dbl0("v", "volume", "<volume",
"sets the output volume (-8.0 to +8.0, default 1.0)");
struct arg_int *arg_samplerate = arg_int0(
"s", "samplerate", "<freq>", "sets the sampling rate (default 44100)");
struct arg_int *arg_quality = arg_int0(
"r", "quality", "<quality>", "specify the resampling quality to use");
struct arg_lit *arg_mono =
arg_lit0("m", "mono", "generate mono output instead of stereo");
struct arg_lit *arg_eight =
arg_lit0("8", "eight", "generate 8-bit instead of 16-bit");
struct arg_lit *arg_noprogress =
arg_lit0("n", "noprogress", "hide progress bar");
struct arg_file *arg_output =
arg_file0("o", "output", "<file>", "output file");
struct arg_file *arg_input =
arg_file1(NULL, NULL, "<file>", "input module file");
struct arg_end *arg_fend = arg_end(20);
void *argtable[] = {arg_help, arg_input, arg_volume,
arg_samplerate, arg_quality, arg_mono,
arg_eight, arg_noprogress, arg_fend};
const char *progname = "dumbplay";
// Make sure everything got allocated
if (arg_nullcheck(argtable) != 0) {
fprintf(stderr, "%s: insufficient memory\n", progname);
goto exit_0;
}
// Parse inputs
nerrors = arg_parse(argc, argv, argtable);
// Handle help
if (arg_help->count > 0) {
fprintf(stderr, "Usage: %s", progname);
arg_print_syntax(stderr, argtable, "\n");
fprintf(stderr, "\nArguments:\n");
arg_print_glossary(stderr, argtable, "%-25s %s\n");
goto exit_0;
}
// Handle libargtable errors
if (nerrors > 0) {
arg_print_errors(stderr, arg_fend, progname);
fprintf(stderr, "Try '%s --help' for more information.\n", progname);
goto exit_0;
}
// Handle the switch options
streamer.input = arg_input->filename[0];
if (arg_eight->count > 0) {
streamer.bits = 8;
}
if (arg_mono->count > 0) {
streamer.n_channels = 1;
}
if (arg_noprogress->count > 0) {
streamer.no_progress = true;
}
if (arg_volume->count > 0) {
streamer.volume = arg_volume->dval[0];
if (streamer.volume < -8.0f || streamer.volume > 8.0f) {
fprintf(stderr, "Volume must be between -8.0f and 8.0f.\n");
goto exit_0;
}
}
if (arg_samplerate->count > 0) {
streamer.freq = arg_samplerate->ival[0];
if (streamer.freq < 1 || streamer.freq > 96000) {
fprintf(stderr, "Sampling rate must be between 1 and 96000.\n");
goto exit_0;
}
}
if (arg_quality->count > 0) {
streamer.quality = arg_quality->ival[0];
if (streamer.quality < 0 || streamer.quality >= DUMB_RQ_N_LEVELS) {
fprintf(stderr, "Quality must be between %d and %d.\n", 0,
DUMB_RQ_N_LEVELS - 1);
goto exit_0;
}
}
// Load source file.
dumb_register_stdfiles();
streamer.src = dumb_load_any(streamer.input, 0, 0);
if (!streamer.src) {
fprintf(stderr, "Unable to load file %s for playback!\n",
streamer.input);
goto exit_0;
}
// Set up playback
streamer.renderer =
duh_start_sigrenderer(streamer.src, 0, streamer.n_channels, 0);
streamer.delta = 65536.0f / streamer.freq;
streamer.sbytes = (streamer.bits / 8) * streamer.n_channels;
streamer.ssize = duh_get_length(streamer.src);
// Stop producing samples on module end
DUMB_IT_SIGRENDERER *itsr = duh_get_it_sigrenderer(streamer.renderer);
dumb_it_set_loop_callback(itsr, &dumb_it_callback_terminate, NULL);
dumb_it_set_xm_speed_zero_callback(itsr, &dumb_it_callback_terminate, NULL);
dumb_it_set_resampling_quality(itsr, streamer.quality);
// Set up the SDL2 format we want for playback.
SDL_AudioSpec want;
SDL_zero(want);
want.freq = streamer.freq;
want.format = (streamer.bits == 16) ? AUDIO_S16 : AUDIO_S8;
want.channels = streamer.n_channels;
want.samples = SAMPLES;
want.callback = stream_audio;
want.userdata = &streamer;
// Find SDL2 audio device, and request the format we just set up.
// SDL2 will tell us what we got in the "have" struct.
SDL_AudioSpec have;
streamer.dev = SDL_OpenAudioDevice(NULL, 0, &want, &have, 0);
if (streamer.dev == 0) {
fprintf(stderr, "%s\n", SDL_GetError());
goto exit_1;
}
// Make sure we got the format we wanted. If not, stop here.
if (have.format != want.format) {
fprintf(stderr, "Could not get correct playback format.\n");
goto exit_2;
}
// Play file
SDL_PauseAudioDevice(streamer.dev, 0);
// Show initial state of the progress bar (if it is enabled)
int time_start = SDL_GetTicks();
float seek = 0.0f;
int ms_played = 0;
if (!streamer.no_progress) {
show_progress(PROGRESSBAR_LENGTH, seek, ms_played);
}
// Loop while dumb is still giving data. Update progressbar if enabled.
while (!stop_signal && !streamer.ended) {
if (!streamer.no_progress) {
seek = ((float)streamer.spos) / ((float)streamer.ssize);
ms_played = SDL_GetTicks() - time_start;
show_progress(PROGRESSBAR_LENGTH, seek, ms_played);
}
SDL_Delay(100);
}
// We made it this far without crashing, so let's just exit with no error :)
retcode = 0;
// Free up resources and exit.
if (streamer.sig_samples) {
destroy_sample_buffer(streamer.sig_samples);
}
exit_2:
SDL_CloseAudioDevice(streamer.dev);
exit_1:
if (streamer.renderer) {
duh_end_sigrenderer(streamer.renderer);
}
if (streamer.src) {
unload_duh(streamer.src);
}
exit_0:
arg_freetable(argtable, sizeof(argtable) / sizeof(argtable[0]));
SDL_Quit();
return retcode;
}
int main(int argc, char *argv[]) {
#ifndef _OPENMP
fprintf(stderr, "\nERROR: Program built with compiler lacking OpenMP support.\n");
fprintf(stderr, "See SEAStAR README file for information about suitable compilers.\n");
exit(EXIT_FAILURE);
#endif
///////////////////////////
// Variable declarations
///////////////////////////
// Input filenames
UT_string *in_read1_fq_fn, *in_read2_fq_fn, *in_single1_fq_fn, *in_single2_fq_fn;
utstring_new(in_read1_fq_fn);
utstring_new(in_read2_fq_fn);
utstring_new(in_single1_fq_fn);
utstring_new(in_single2_fq_fn);
// Output filenames
UT_string *out_read1_fn, *out_read2_fn, *out_single1_fn, *out_single2_fn, *out_mates_fn, *out_filetype;
utstring_new(out_filetype);
utstring_new(out_read1_fn);
utstring_new(out_read2_fn);
utstring_new(out_single1_fn);
utstring_new(out_single2_fn);
utstring_new(out_mates_fn);
// Read name prefix
UT_string *out_read_prefix;
utstring_new(out_read_prefix);
// Flags
int singles_flag = 0; // 1 when two output singles files being written
int num_input_singles_files = 0;
// Read counters
unsigned long int mp_org = 0, R1_org = 0, R2_org = 0, singlet1_org = 0, singlet2_org = 0;
unsigned long int mp_cnt = 0, R1_cnt = 0, R2_cnt = 0, singlet1_cnt = 0, singlet2_cnt = 0, s1_cnt = 0, s2_cnt = 0;
unsigned long int comp_r1 = 0, comp_r2 = 0, comp_s1 = 0, comp_s2 = 0;
unsigned long int read1_singlet_cnt = 0, read2_singlet_cnt = 0;
////////////////////////////////////////////////////////////////////////
// All done with variable declarations!!
///////////////////////////////////
// Command line argtable settings
///////////////////////////////////
struct arg_lit *gzip = arg_lit0("z", "gzip", "Output converted files in gzip compressed format. [NULL]");
struct arg_lit *inv_singles = arg_lit0("v", "invert_singles", "Causes singles output to be the inverse of the input. 2->1 or 1->2 [NULL]");
struct arg_lit *num_singles = arg_lit0("s", "singles", "Write two singlet files, one for each mate-paired input file. [NULL]");
struct arg_rem *sing_rem = arg_rem(NULL, "Note! -v is only valid when there are input singlet reads. -s is only valid when there are NO input singlet reads.");
struct arg_str *pre_read_id = arg_str0(NULL, "prefix", "<string>", "Prefix to add to read identifiers. [out_prefix]");
struct arg_lit *no_pre = arg_lit0(NULL, "no_prefix", "Do not change the read names in any way. [NULL]");
struct arg_lit *pre_read_len = arg_lit0(NULL, "add_len", "Add the final trimmed length value to the read id prefix. [length not added]");
struct arg_dbl *prob = arg_dbl0("p","correct_prob","<d>","Probability that output reads are correct. 0.0 disables quality trimming. [0.5]");
struct arg_int *fixed_len = arg_int0("f","fixed_len","<u>","Trim all reads to a fixed length, still filtering on quality [no fixed length]");
struct arg_int *len = arg_int0("l","min_read_len","<u>","Minimum length of a singlet or longest-mate in nucleotides [24]");
struct arg_int *mate_len = arg_int0("m","min_mate_len","<u>","Minimum length of the shortest mate in nucleotides [min_read_len]");
struct arg_dbl *entropy = arg_dbl0("e","entropy_filter","<d>","Remove reads with per position information below given value (in bits per dinucleotide) [No filter]");
struct arg_lit *entropy_strict = arg_lit0(NULL, "entropy_strict", "Reject reads for low entropy overall, not just the retained part after trimming [NULL]");
struct arg_lit *mates = arg_lit0(NULL, "mates_file", "Produce a Velvet compatible interleaved paired read output file (e.g. <out_prefix>_mates.fastq). [NULL]");
struct arg_lit *no_rev = arg_lit0(NULL, "no_rev", "By default, the second read in each pair is reversed for colorspace --mate-file output. --no_rev disables reversing. [rev]");
struct arg_lit *only_mates = arg_lit0(NULL, "only_mates", "Supress writing .read1 and .read2 outputs. Requires --mates_file. [NULL]");
struct arg_lit *fasta = arg_lit0(NULL, "fasta", "Write FASTA format files instead of FASTQ for all outputs (e.g. <out_prefix>.<read_type>.fasta). [FASTQ]");
struct arg_file *input = arg_file1(NULL, NULL, "<in_prefix>", "Input file prefix: (e.g. <in_prefix>_single.fastq [<in_prefix>_read1.fastq <in_prefix>_read2.fastq]) ");
struct arg_file *output = arg_file1(NULL, NULL, "<out_prefix>", "Output file prefix: (e.g. <out_prefix>_single.fastq [<out_prefix>_read1.fastq <out_prefix>_read2.fastq]) ");
struct arg_lit *version = arg_lit0(NULL,"version","Print the build version and exit.");
struct arg_lit *h = arg_lit0("h", "help", "Request help.");
struct arg_end *end = arg_end(20);
void *argtable[] = {h,version,gzip,inv_singles,num_singles,sing_rem,prob,len,mate_len,fixed_len,pre_read_id,pre_read_len,no_pre,entropy,entropy_strict,mates,no_rev,only_mates,fasta,input,output,end};
int arg_errors = 0;
////////////////////////////////////////////////////////////////////////
// Handle command line processing (via argtable2 library)
////////////////////////////////////////////////////////////////////////
arg_errors = arg_parse(argc, argv, argtable);
if (version->count) {
fprintf(stderr, "%s version: %s\n", argv[0], SS_BUILD_VERSION);
exit(EXIT_SUCCESS);
}
if (h->count) {
fprintf(stderr,"\ntrim_fastq is a utility for performing quality and information-based\n");
fprintf(stderr,"trimming on paired or unpaired, nucleotide or SOLiD colorspace reads. \n\n");
arg_print_syntaxv(stderr, argtable, "\n\n");
arg_print_glossary(stderr, argtable, "%-25s %s\n");
fprintf(stderr, "\nInput and output \"prefixes\" are the part of the filename before:\n");
fprintf(stderr, "_single.fastq [_read1.fastq _read2.fastq] A singlets (single) file\n");
fprintf(stderr, "is required. Mate-paired read files are automatically used if present.\n");
fprintf(stderr, "Multiple output files only produced for mate-paired inputs.\n");
fprintf(stderr, "\nNote! Input and output files may be gzipped, and outputs can be written\n");
fprintf(stderr, "as either FASTQ or FASTA format files.\n");
exit(EXIT_FAILURE);
}
if (arg_errors) {
arg_print_errors(stderr, end, "trimfastq");
arg_print_syntaxv(stderr, argtable, "\n");
exit(EXIT_FAILURE);
}
// Validate entropy
if (entropy->count) {
entropy_cutoff = entropy->dval[0];
if ((entropy_cutoff < 0.0) || (entropy_cutoff > 4.0)) {
fprintf(stderr, "entropy_filter must be [0.0 - 4.0] \n");
exit(EXIT_FAILURE);
}
strict_ent = entropy_strict->count;
} else {
if (entropy_strict->count) {
fprintf(stderr, "Error: --entropy_strict requires --entropy_filter.\n");
exit(EXIT_FAILURE);
}
entropy_cutoff = -1.0;
}
// Validate error_prob
if (prob->count) {
err_prob = prob->dval[0];
if ((err_prob < 0.0) || (err_prob > 1.0)) {
fprintf(stderr, "--correct_prob (-p) must be 0.0 - 1.0 inclusive\n");
exit(EXIT_FAILURE);
}
} else {
err_prob = 0.5;
}
// Validate min read len
if (len->count) {
min_len = len->ival[0];
if (min_len <= 0) {
fprintf(stderr, "min_read_len must be > 0\n");
exit(EXIT_FAILURE);
}
} else {
min_len = 24;
}
// Validate min mate len
if (mate_len->count) {
min_mate_len = mate_len->ival[0];
if (min_mate_len <= 0) {
fprintf(stderr, "min_mate_len must be > 0\n");
exit(EXIT_FAILURE);
}
if (min_mate_len > min_len) {
fprintf(stderr, "min_mate_len must be <= min_len\n");
exit(EXIT_FAILURE);
}
} else {
min_mate_len = min_len;
}
if (fixed_len->count) {
fix_len = min_mate_len = min_len = fixed_len->ival[0];
if ((mate_len->count) || (len->count)) {
fprintf(stderr, "fixed_len cannot be used with min_read_len or min_mate_len\n");
exit(EXIT_FAILURE);
}
if (fix_len <= 0) {
fprintf(stderr, "fixed_len must be > 0\n");
exit(EXIT_FAILURE);
}
} else {
fix_len = 0;
}
if (pre_read_id->count) {
if (no_pre->count) {
fprintf(stderr, "Error: Both --prefix and --no_prefix were specified.\n");
exit(EXIT_FAILURE);
}
if (! strlen(pre_read_id->sval[0])) {
fprintf(stderr, "Read ID prefix may not be zero length.\n");
exit(EXIT_FAILURE);
}
if (strchr(pre_read_id->sval[0], ':') || strchr(pre_read_id->sval[0], '|') || strchr(pre_read_id->sval[0], '+') || strchr(pre_read_id->sval[0], '/')) {
fprintf(stderr, "Read ID prefix '%s' may not contain the characters ':', '|', '+' or '/'.\n", pre_read_id->sval[0]);
exit(EXIT_FAILURE);
}
// Build default read ID prefix
ss_strcat_utstring(out_read_prefix, pre_read_id->sval[0]);
} else {
if (!no_pre->count) {
if (strchr(output->filename[0], ':') || strchr(output->filename[0], '|') || strchr(output->filename[0], '+') || strchr(output->filename[0], '/')) {
fprintf(stderr, "Read ID prefix '%s' (from output prefix) may not contain the characters ':', '|', '+' or '/'.\n", output->filename[0]);
fprintf(stderr, "Hint: Use the --prefix parameter if the output file prefix contains path information.\n");
exit(EXIT_FAILURE);
}
// Build default read ID prefix
ss_strcat_utstring(out_read_prefix, output->filename[0]);
}
}
if ((only_mates->count) && (!mates->count)) {
fprintf(stderr, "--only_mates requires --mates.\n");
exit(EXIT_FAILURE);
}
if ((no_rev->count) && (!mates->count)) {
fprintf(stderr, "--no_rev requires --mates.\n");
exit(EXIT_FAILURE);
}
// Check for null string prefixes
if (!(strlen(input->filename[0]) && strlen(output->filename[0]))) {
fprintf(stderr, "Error: NULL prefix strings are not permitted.\n");
exit(EXIT_FAILURE);
}
// Construct input filenames
utstring_printf(in_read1_fq_fn, "%s.read1.fastq", input->filename[0]);
utstring_printf(in_read2_fq_fn, "%s.read2.fastq", input->filename[0]);
utstring_printf(in_single1_fq_fn, "%s.single.fastq", input->filename[0]);
FILE *in_read_file = NULL;
num_input_singles_files = 1;
// Try to open a singlet fastq file
// Check singlet output options -s and -v
// Set input singlet names to
// - *.single.fastq or
// - *.single1.fastq and *.single2.fastq
if (!(in_read_file = ss_get_gzFile(utstring_body(in_single1_fq_fn), "r"))) {
utstring_clear(in_single1_fq_fn);
utstring_printf(in_single1_fq_fn, "%s.single1.fastq", input->filename[0]);
utstring_printf(in_single2_fq_fn, "%s.single2.fastq", input->filename[0]);
num_input_singles_files = 2;
if ((in_read_file = ss_get_gzFile(utstring_body(in_single1_fq_fn), "r")) || (in_read_file = ss_get_gzFile(utstring_body(in_single2_fq_fn), "r"))) {
singles_flag = 1; // Two singlet outputs
} else {
singles_flag = num_singles->count; // Number of singlet outputs set by -s parm
if (inv_singles->count) {
fprintf(stderr, "Error: Invalid option -v, No input singlet file(s) found. Use -s to select multiple output singlet files.\n");
exit(EXIT_FAILURE);
}
}
}
if (in_read_file) {
gzclose(in_read_file);
if (num_singles->count) {
fprintf(stderr, "Error: Invalid option -s, Input singlet file(s) found, use -v to change the number of output singlet files.\n");
exit(EXIT_FAILURE);
}
}
// singles->count inverts the current singles file input scheme
singles_flag = (singles_flag ^ inv_singles->count);
// Check if input fastq is colorspace
// If some files are colorspace and some are basespace, throw an error
int fcount = 0;
int cscount = 0;
fcount += ss_is_fastq(utstring_body(in_read1_fq_fn));
fcount += ss_is_fastq(utstring_body(in_read2_fq_fn));
fcount += ss_is_fastq(utstring_body(in_single1_fq_fn));
fcount += ss_is_fastq(utstring_body(in_single2_fq_fn));
cscount += (ss_is_fastq(utstring_body(in_read1_fq_fn)) && ss_is_colorspace_fastq(utstring_body(in_read1_fq_fn)));
cscount += (ss_is_fastq(utstring_body(in_read2_fq_fn)) && ss_is_colorspace_fastq(utstring_body(in_read2_fq_fn)));
cscount += (ss_is_fastq(utstring_body(in_single1_fq_fn)) && ss_is_colorspace_fastq(utstring_body(in_single1_fq_fn)));
cscount += (ss_is_fastq(utstring_body(in_single2_fq_fn)) && ss_is_colorspace_fastq(utstring_body(in_single2_fq_fn)));
if (cscount && (cscount != fcount)) {
printf("Error: Mixed colorspace and basespace FASTQ files detected\n");
exit(EXIT_FAILURE);
}
colorspace_flag = cscount ? 1 : 0;
// Output filenames
if (fasta->count) {
ss_strcat_utstring(out_filetype, "fasta");
read_count_divisor = 2;
} else {
ss_strcat_utstring(out_filetype, "fastq");
read_count_divisor = 4;
}
if (!only_mates->count) {
utstring_printf(out_read1_fn, "%s.read1.%s", output->filename[0], utstring_body(out_filetype));
utstring_printf(out_read2_fn, "%s.read2.%s", output->filename[0], utstring_body(out_filetype));
}
if (singles_flag == 1) {
utstring_printf(out_single1_fn, "%s.single1.%s", output->filename[0], utstring_body(out_filetype));
utstring_printf(out_single2_fn, "%s.single2.%s", output->filename[0], utstring_body(out_filetype));
} else {
utstring_printf(out_single1_fn, "%s.single.%s", output->filename[0], utstring_body(out_filetype));
}
if (mates->count) {
utstring_printf(out_mates_fn, "%s.mates.%s", output->filename[0], utstring_body(out_filetype));
}
////////////////////////////////////////////////////////////////////////////////////////////////
// Begin processing!
#ifdef _OPENMP
omp_set_num_threads(10);
#endif
// This is the value of a non-valid pipe descriptor
#define NO_PIPE 0
int r1_pipe[2];
int r2_pipe[2];
int s1_pipe[2];
int s2_pipe[2];
pipe(r1_pipe);
pipe(r2_pipe);
pipe(s1_pipe);
pipe(s2_pipe);
int r1_out_pipe[2];
int r2_out_pipe[2];
int mates_out_pipe[2];
int s1_out_pipe[2];
int s2_out_pipe[2];
pipe(r1_out_pipe);
pipe(r2_out_pipe);
pipe(mates_out_pipe);
pipe(s1_out_pipe);
pipe(s2_out_pipe);
#pragma omp parallel sections default(shared)
{
#pragma omp section
{ // Read1 reader
fq_stream_trimmer(in_read1_fq_fn, r1_pipe[1], out_read_prefix, no_pre->count, pre_read_len->count, &comp_r1, &R1_org, '\0', fasta->count);
}
#pragma omp section
{ // Read1 writer
R1_cnt = ss_stream_writer(out_read1_fn, r1_out_pipe[0], gzip->count) / read_count_divisor;
}
#pragma omp section
{ // Read2 reader
fq_stream_trimmer(in_read2_fq_fn, r2_pipe[1], out_read_prefix, no_pre->count, pre_read_len->count, &comp_r2, &R2_org, '\0', fasta->count);
}
#pragma omp section
{ // Read2 writer
R2_cnt = ss_stream_writer(out_read2_fn, r2_out_pipe[0], gzip->count) / read_count_divisor;
}
#pragma omp section
{ // Single1 reader
// When there is only one input singles file, but two output singles files, then supply which mate to use for this stream in the split parameter
if ((singles_flag) && (num_input_singles_files == 1)) {
singlet1_cnt = fq_stream_trimmer(in_single1_fq_fn, s1_pipe[1], out_read_prefix, no_pre->count, pre_read_len->count, &comp_s1, &singlet1_org, '1', fasta->count);
} else {
singlet1_cnt = fq_stream_trimmer(in_single1_fq_fn, s1_pipe[1], out_read_prefix, no_pre->count, pre_read_len->count, &comp_s1, &singlet1_org, '\0', fasta->count);
}
}
#pragma omp section
{ // Single1 writer
s1_cnt = ss_stream_writer(out_single1_fn, s1_out_pipe[0], gzip->count) / read_count_divisor;
}
#pragma omp section
{ // Single2 reader
// When there is only one input singles file, but two output singles files, then supply which mate to use for this stream in the split parameter
if ((singles_flag) && (num_input_singles_files == 1)) {
singlet2_cnt = fq_stream_trimmer(in_single1_fq_fn, s2_pipe[1], out_read_prefix, no_pre->count, pre_read_len->count, &comp_s2, &singlet2_org, '2', fasta->count);
} else {
singlet2_cnt = fq_stream_trimmer(in_single2_fq_fn, s2_pipe[1], out_read_prefix, no_pre->count, pre_read_len->count, &comp_s2, &singlet2_org, '\0', fasta->count);
}
}
#pragma omp section
{ // Single2 writer
s2_cnt = ss_stream_writer(out_single2_fn, s2_out_pipe[0], gzip->count) / read_count_divisor;
}
#pragma omp section
{ // Velvet mates writer
// Divide count by 2 because both R1 and R2 reads go through this writer
mp_cnt = ss_stream_writer(out_mates_fn, mates_out_pipe[0], gzip->count) / 2 / read_count_divisor;
}
#pragma omp section
{ // Dispatcher
// Allocate data buffer strings
UT_string *r1_data;
utstring_new(r1_data);
UT_string *r2_data;
utstring_new(r2_data);
UT_string *s1_data;
utstring_new(s1_data);
UT_string *s2_data;
utstring_new(s2_data);
UT_string *rev_tmp;
utstring_new(rev_tmp);
UT_string *rev_data;
utstring_new(rev_data);
// Pipes
FILE *r1_in = fdopen(r1_pipe[0],"r");
FILE *r2_in = fdopen(r2_pipe[0],"r");
FILE *s1_in = fdopen(s1_pipe[0],"r");
FILE *s2_in = fdopen(s2_pipe[0],"r");
FILE *mates_out = fdopen(mates_out_pipe[1],"w");
FILE *r1_out = fdopen(r1_out_pipe[1],"w");
FILE *r2_out = fdopen(r2_out_pipe[1],"w");
FILE *s1_out = fdopen(s1_out_pipe[1],"w");
FILE *s2_out = fdopen(s2_out_pipe[1],"w");
if (!singles_flag) {
fclose(s2_out);
s2_out = s1_out;
}
// Flags for data left in single files
int single1_hungry = 1;
int single2_hungry = 1;
// Handle read1 and read2 files
while (ss_get_utstring(r1_in, r1_data)) {
if (!ss_get_utstring(r2_in, r2_data)) {
fprintf(stderr, "Error: Input read1 and read2 files are not synced\n");
exit(EXIT_FAILURE);
}
if (keep_read(r1_data)) {
if (keep_read(r2_data)) {
// Output both read1 and read2
if (mates->count) {
if (only_mates->count) {
// Interleaved velvet output only
output_read(r1_data, NULL, NULL, r1_in, NULL, mates_out, fasta->count);
if (no_rev->count || !colorspace_flag) {
output_read(r2_data, NULL, NULL, r2_in, NULL, mates_out, fasta->count);
} else {
output_read(r2_data, rev_data, rev_tmp, r2_in, NULL, mates_out, fasta->count);
}
} else {
// Interleaved velvet output and normal read file output
output_read(r1_data, NULL, NULL, r1_in, r1_out, mates_out, fasta->count);
if (no_rev->count || !colorspace_flag) {
output_read(r2_data, NULL, NULL, r2_in, r2_out, mates_out, fasta->count);
} else {
output_read(r2_data, rev_data, rev_tmp, r2_in, r2_out, mates_out, fasta->count);
}
}
} else {
// No interleaved velvet output
output_read(r1_data, NULL, NULL, r1_in, r1_out, NULL, fasta->count);
output_read(r2_data, NULL, NULL, r2_in, r2_out, NULL, fasta->count);
}
} else {
// Discard read2, output read1 as singlet
output_read(r1_data, NULL, NULL, r1_in, s1_out, NULL, fasta->count);
read1_singlet_cnt++;
}
} else {
if (keep_read(r2_data)) {
// Discard read1, output read2 as singlet
output_read(r2_data, NULL, NULL, r2_in, s2_out, NULL, fasta->count);
read2_singlet_cnt++;
}
}
// Process reads from singles here to take advantage of
// parallelism
if (single1_hungry || single2_hungry) {
if (single1_hungry) {
if (ss_get_utstring(s1_in, s1_data)) {
if (keep_read(s1_data)) {
output_read(s1_data, NULL, NULL, s1_in, s1_out, NULL, fasta->count);
}
} else {
single1_hungry = 0;
}
}
if (single2_hungry) {
if (ss_get_utstring(s2_in, s2_data)) {
if (keep_read(s2_data)) {
output_read(s2_data, NULL, NULL, s2_in, s2_out, NULL, fasta->count);
}
} else {
single2_hungry = 0;
}
}
}
}
while (single1_hungry || single2_hungry) {
if (single1_hungry) {
if (ss_get_utstring(s1_in, s1_data)) {
if (keep_read(s1_data)) {
output_read(s1_data, NULL, NULL, s1_in, s1_out, NULL, fasta->count);
}
} else {
single1_hungry = 0;
}
}
if (single2_hungry) {
if (ss_get_utstring(s2_in, s2_data)) {
if (keep_read(s2_data)) {
output_read(s2_data, NULL, NULL, s2_in, s2_out, NULL, fasta->count);
}
} else {
single2_hungry = 0;
}
}
}
fclose(r1_in);
fclose(r2_in);
fclose(s1_in);
fclose(s2_in);
fclose(mates_out);
fclose(r1_out);
fclose(r2_out);
fclose(s1_out);
if (singles_flag) {
fclose(s2_out);
}
// Free buffers
utstring_free(r1_data);
utstring_free(r2_data);
utstring_free(s1_data);
utstring_free(s2_data);
utstring_free(rev_tmp);
utstring_free(rev_data);
}
}
if (!(R1_org+singlet1_org+singlet2_org)) {
fprintf(stderr, "ERROR! No reads found in input files, or input(s) not found.\n");
exit(EXIT_FAILURE);
}
if (R1_org != R2_org) {
fprintf(stderr, "\nWarning! read1 and read2 fastq files did not contain an equal number of reads. %lu %lu\n", R1_org, R2_org);
}
if ((R1_org + R2_org) && !(singlet1_cnt + singlet2_cnt)) {
fprintf(stderr, "\nWarning! read1/read2 files were processed, but no corresponding input singlets were found.\n");
}
if (entropy->count) {
printf("\nLow complexity reads discarded: Read1: %lu, Read2: %lu, Singlets: %lu %lu\n", comp_r1, comp_r2, comp_s1, comp_s2);
}
mp_org = R1_org;
if (!only_mates->count) {
mp_cnt = R1_cnt;
}
printf("\nMatepairs: Before: %lu, After: %lu\n", mp_org, mp_cnt);
printf("Singlets: Before: %lu %lu After: %lu %lu\n", singlet1_org, singlet2_org, s1_cnt, s2_cnt);
printf("Read1 singlets: %lu, Read2 singlets: %lu, Original singlets: %lu %lu\n", read1_singlet_cnt, read2_singlet_cnt, singlet1_cnt, singlet2_cnt);
printf("Total Reads Processed: %lu, Reads retained: %lu\n", 2*mp_org+singlet1_org+singlet2_org, 2*mp_cnt+s1_cnt+s2_cnt);
utstring_free(in_read1_fq_fn);
utstring_free(in_read2_fq_fn);
utstring_free(in_single1_fq_fn);
utstring_free(in_single2_fq_fn);
utstring_free(out_read1_fn);
utstring_free(out_read2_fn);
utstring_free(out_single1_fn);
utstring_free(out_single2_fn);
utstring_free(out_mates_fn);
utstring_free(out_filetype);
utstring_free(out_read_prefix);
exit(EXIT_SUCCESS);
}
int main(int argc, char* argv[])
{
struct arg_lit *help, *strip;
struct arg_file *input, *output;
struct arg_str *translation, *rotation;
struct arg_dbl *scale;
struct arg_end *end;
/* command line parsing through argtable package */
void* argtable[] = {
help = arg_lit0("h", "help", "display this help and exit"),
input = arg_file0("i", "input", "input", "name of the input file (default stdin"),
output = arg_file0("o", "output", "file", "name of the output file (default stdout)"),
strip = arg_lit0(NULL, "strip", "remove numbers from the atom labels"),
scale = arg_dbl0(NULL, "scale", "scalar", "scale with a factor s"),
translate = arg_str0(NULL, "translate", "\"x y z\"", "translate along vector x y z"),
rotate = arg_str0(NULL, "rotate", "\"x y z w\"", "rotate w degrees around axis x y z"),
end = arg_end(20) };
const char* progname = "xyztk-rotate";
int rc = 0;
int nerrors;
/* verify the argtable[] entries were allocated sucessfully */
if (arg_nullcheck(argtable) != 0)
{
/* NULL entries were detected, some allocations must have failed */
printf("%s: insufficient memory\n", progname);
rc=1;
goto exit;
}
/* set default values */
scale->dval[0] = 1.0;
/* parse the command line flags, overriding default values */
nerrors = arg_parse(argc,argv,argtable);
/* special case: '--help' takes precedence over error reporting */
if (help->count > 0)
{
printf("Usage: %s", progname);
arg_print_syntax(stdout,argtable,"\n");
printf("\n");
arg_print_glossary(stdout,argtable," %-40s %s\n");
printf("\n");
rc=0;
goto exit;
}
/* special case: no command line options induces brief help */
if (argc==1) {
printf("Try '%s --help' for more information.\n",progname);
rc=0;
goto exit;
}
/* If the parser returned any errors then display them and exit */
if (nerrors > 0)
{
/* Display the error details contained in the arg_end struct.*/
arg_print_errors(stdout,end,progname);
printf("Try '%s --help' for more information.\n",progname);
rc=1;
goto exit;
}
/* set global structures */
/* initialize I/O pointers */
FILE* in;
if (input->count) {
in = fopen(input->filename[0], "r");
} else {
in = stdin;
}
FILE* out;
if (output->count) {
out = fopen(output->filename[0], "w");
} else {
out = stdout;
}
/* initialize molecule structure */
xyztk_molecule_t molecule;
xyztk_molecule_load (&molecule, in);
/* read rotation from string */
xyztk_quat_t r;
sscanf (rotation->sval[0], "%lf%lf%lf%lf", &r.x, &r.y, &r.z, &r.w);
xyztk_molecule_rotate (&molecule, &r);
/* print output */
int i;
fprintf(out, "%d\n", molecule.n_atoms);
fprintf(out, "%s", molecule.name);
for (i = 0; i < molecule.n_atoms; ++i)
{
fprintf(out, "%-8s %20.14lf %20.14lf %20.14lf \n",
molecule.label[i].s, molecule.coord[i].x, molecule.coord[i].y, molecule.coord[i].z);
}
exit:
/* deallocate each non-null entry in argtable[] */
arg_freetable(argtable,sizeof(argtable)/sizeof(argtable[0]));
return rc;
}
int main(int argc, char** argv)
{
// force routine can appear at most once --> arg_str0
struct arg_str* arg_force_routine
= arg_str0("f", "force", "<string>",
"Specify the force subroutine.\n"
" - N2 N2 refrence\n"
" - cell_ref Cell-list refrence\n"
" - cell_v1 Cell-list improvement 1\n"
" - cell_v2 Cell-list improvement 2\n"
" - knuth Cell-list (Knuth)\n"
" - q Quadrant\n"
" - q_g Quadrant (ghost)\n"
" - q_g_u Quadrant (ghost unrolled)\n"
" - q_g_avx Quadrant (ghost-avx)\n"
" - q_g_fma Quadrant (ghost-fma)");
// integrator routine can appear at most once --> arg_str0
struct arg_str* arg_integrator_routine
= arg_str0("i", "integrator", "<string>",
"Specify the integrator subroutine.\n"
" - lf Leap-frog (refrence)\n"
" - lf2 Leap-frog (unroll x2)\n"
" - lf4 Leap-frog (unroll x4)\n"
" - lf8 Leap-frog (unroll x8)\n"
" - lf_avx Leap-frog (avx)");
// periodic routine
struct arg_str* arg_periodic_routine
= arg_str0("p", "periodic", "<string>",
"Specify the periodic subroutine.\n"
" - ref Refrence implementation\n"
" - c With assumption\n"
" - c4 With assumption (unroll x4)");
// parameter can appear at most once --> arg_file0
struct arg_file* arg_parameters
= arg_file0("c", "config", "<file>", "Path to to the configuration file.");
// contains the number of desired particles
struct arg_int* arg_desired_particles
= arg_int0("n", "N", "<int>", "Set the number of particles.");
// contains the number of desired timesteps
struct arg_int* arg_desired_steps
= arg_int0("s", "step", "<int>", "Set the number of timesteps.");
// contains the number of desired timesteps
struct arg_dbl* arg_desired_density
= arg_dbl0("r", "rho", "<flaot>", "Set the particle density.");
// help
struct arg_lit* arg_help = arg_lit0("h", "help", "Print this help statement and exit.");
// verbosity
struct arg_int* arg_verb
= arg_int0("v", "verbose", "<int>",
"Set verbosity level.\n"
" - 0: Only print timers in the end\n"
" - 1: Print settings (default)\n"
" - 2: Full output (print energies every step)");
// maximal number of errors = 20
struct arg_end* end_struct = arg_end(20);
void* argtable[] = {arg_force_routine,
arg_integrator_routine,
arg_periodic_routine,
arg_parameters,
arg_desired_particles,
arg_desired_steps,
arg_desired_density,
arg_help,
arg_verb,
end_struct};
char* progname = "molec";
// verify the argtable[] entries were allocated sucessfully
if(arg_nullcheck(argtable) != 0)
{
// NULL entries were detected, some allocations must have failed
printf("%s: insufficient memory\n", progname);
exit(1);
}
// set any command line default values prior to parsing
arg_force_routine->sval[0] = "cell_ref";
arg_integrator_routine->sval[0] = "lf";
arg_periodic_routine->sval[0] = "ref";
arg_parameters->filename[0] = "";
arg_desired_particles->ival[0] = 1000;
arg_desired_steps->ival[0] = 100;
arg_desired_density->dval[0] = 1.25f;
arg_verb->ival[0] = 1;
// parse argtable
int nerrors = arg_parse(argc, argv, argtable);
// special case: '--help | -h' takes precedence over error reporting
if(arg_help->count > 0)
{
printf("Usage: %s", progname);
arg_print_syntax(stdout, argtable, "\n");
arg_print_glossary(stdout, argtable, " %-25s %s\n");
exit(0);
}
if(nerrors > 0)
{
// Display the error details contained in the arg_end struct
arg_print_errors(stdout, end_struct, progname);
printf("Try '%s --help' for more information.\n", progname);
exit(1);
}
// normal case: take the command line options at face value
molec_force_calculation force_calculation = arg_get_force_routine(arg_force_routine->sval[0]);
molec_force_integration force_integration
= arg_get_integration_routine(arg_integrator_routine->sval[0]);
molec_periodic periodic = arg_get_periodic_routine(arg_periodic_routine->sval[0]);
const char* config_file_name = arg_parameters->filename[0];
const int desired_N = arg_desired_particles->ival[0];
const float desired_rho = arg_desired_density->dval[0];
molec_verbose = arg_verb->ival[0];
srand(42);
molec_load_parameters(config_file_name, 1, desired_N, desired_rho);
// set the number of steps
molec_parameter->Nstep = arg_desired_steps->ival[0];
// print the used routines passed as argument
if(molec_verbose)
{
printf("\n ================ MOLEC - Settings ================\n\n");
printf(" %-20s %10s\n", "Force routine:", arg_force_routine->sval[0]);
printf(" %-20s %10s\n", "Integrator routine:", arg_integrator_routine->sval[0]);
printf(" %-20s %10s\n", "Periodic routine:", arg_periodic_routine->sval[0]);
}
MOLEC_MEASUREMENT_INIT;
MOLEC_MEASUREMENT_SIMULATION_START();
molec_run_simulation(force_calculation, force_integration, periodic);
MOLEC_MEASUREMENT_SIMULATION_STOP();
printf("\n");
MOLEC_MEASUREMENT_PRINT;
// free memory
MOLEC_FREE(molec_parameter);
MOLEC_MEASUREMENT_FINISH;
arg_freetable(argtable, sizeof(argtable) / sizeof(argtable[0]));
}
int main(int argc, char * argv[])
{
struct arg_file * train_file = arg_file1("f", "features", "<filename>", "Training dataset");
struct arg_file * index_file = arg_file0("x", "index", "<filename>", "Training dataset index");
struct arg_file * output_index = arg_file0(NULL, "output-index", "<filename>", "Save used index to file");
struct arg_file * input = arg_file0("i", "input", "<filename>", "Input dataset in libsvm format");
struct arg_file * output = arg_file0("o", "output", "<filename>", "");
struct arg_lit * hist = arg_lit0(NULL, "hist", "");
struct arg_lit * help = arg_lit0("h", "help", "Print this help and exit");
struct arg_int * verbosity = arg_int0 ("v", "verbosity", "{0..4}", "Log verbosity"
"\nIndex parameters :");
struct arg_int * distance = arg_int0("d", "distance", "{1..9}", "Distance metric"
"\n\t1=L2 (default), 2=L1, 3=MINKOWSKI,\n\t4=MAX, 5=HIST_INTERSECT, 6=HELLLINGER,"
"\n\t7=CS, 8=KULLBACK_LEIBLER, 9=HAMMING");
struct arg_int * index_type = arg_int0("t", "index-type", "{0..5}", "Constructed index type"
"\n t=0 - linear brute force search"
"\n t=1 - kd-tree :");
struct arg_int * kd_tree_count = arg_int0(NULL, "kd-tree-count", "{1..16+}", "Number of parallel trees (default 4)"
"\n t=2 - k-means :");
struct arg_int * km_branching = arg_int0(NULL, "km-branching", "n", "Branching factor (default 32)");
struct arg_int * km_iterations = arg_int0(NULL, "km-iterations", "n", "Maximum iterations (default 11)");
struct arg_int * km_centers = arg_int0(NULL, "km-centers", "{0..2}", "Initial cluster centers"
"\n\t0=CENTERS_RANDOM (default)\n\t1=CENTERS_GONZALES\n\t2=CENTERS_KMEANSPP");
struct arg_dbl * km_index = arg_dbl0(NULL, "km-index", "", "Cluster boundary index (default 0.2)"
"\n t=3 (default) - kd-tree + k-means"
"\n t=4 - LSH :");
struct arg_int * lsh_table_count = arg_int0(NULL, "lsh-table-count", "{0..}", "Number of hash tables");
struct arg_int * lsh_key_size = arg_int0(NULL, "lsh-key-size", "{0..}", "Hash key bits");
struct arg_int * lsh_probe_level = arg_int0(NULL, "lsh-probe-level", "{0..}", "Bit shift for neighboring bucket check"
"\n t=5 - automatically tuned index :");
struct arg_dbl * auto_precision = arg_dbl0(NULL, "auto-precision", "[0,1]", "Expected percentage of exact hits");
struct arg_dbl * auto_build_weight = arg_dbl0(NULL, "auto-build-weight", "", "");
struct arg_dbl * auto_memory_weight = arg_dbl0(NULL, "auto-memory-weight", "", "");
struct arg_dbl * auto_sample_fraction = arg_dbl0(NULL, "auto-sample-fraction", "[0,1]", ""
"\nSearch parameters :");
struct arg_int * neighbors = arg_int0("n", "neighbors", "n", "Neighbor count (default 1)");
struct arg_dbl * radius = arg_dbl0("r", "radius", "r", "Search radius, requests radius search");
struct arg_int * checks = arg_int0("c", "checks", "...", "Search checks (default 32)");
struct arg_end * end = arg_end(20);
void * argtable[] = {
train_file, index_file, output_index, input, output, hist, help, verbosity,
distance, index_type, kd_tree_count,
km_branching, km_iterations, km_centers, km_index,
lsh_table_count, lsh_key_size, lsh_probe_level,
auto_precision, auto_build_weight, auto_memory_weight, auto_sample_fraction,
neighbors, radius, checks, end };
if(arg_nullcheck(argtable) != 0)
{
fprintf(stderr, "%s: insufficient memory\n", argv[0]);
return EXIT_FAILURE;
}
// -- Defaults --
verbosity->ival[0] = 0;
distance->ival[0] = 1;//L2
index_type->ival[0] = 3;//kd + km
// kd-tree
kd_tree_count->ival[0] = 4;
// k-means
km_branching ->ival[0] = 32;
km_iterations->ival[0] = 11;
km_centers ->ival[0] = 0;//CENTERS_RANDOM
km_index ->dval[0] = 0.2;
// auto
auto_precision ->dval[0] = 0.9;
auto_build_weight ->dval[0] = 0.01;
auto_memory_weight ->dval[0] = 0;
auto_sample_fraction->dval[0] = 0.1;
// search
neighbors->ival[0] = 1;
checks->ival[0] = 32;
// -- Parse --
int arg_errors = arg_parse(argc, argv, argtable);
if(help->count > 0)
{
printf("Usage: %s", argv[0]);
arg_print_syntax(stdout, argtable, "\n");
arg_print_glossary(stdout, argtable," %-25s %s\n");
return EXIT_SUCCESS;
}
if(arg_errors > 0)
{
arg_print_errors(stderr, end, argv[0]);
fprintf(stderr, "Try '%s --help' for more information.\n", argv[0]);
return EXIT_FAILURE;
}
cvflann::log_verbosity(verbosity->ival[0]);
std::cout << "Loading features '" << train_file->filename[0] << "' ..." << std::flush;
auto train = load(train_file->filename[0]);
cv::Mat_<float> mat = cv::Mat_<float>::zeros(train.data.size(), train.dim);
boost::dynamic_bitset<> train_class_set;
std::vector<size_t> train_class_hist;
for(size_t i = 0; i < train.data.size(); ++i)
{
size_t const c = train.data[i].first;
if(c >= train_class_set.size())
{
train_class_set.resize(c+1);
train_class_hist.resize(c+1, 0);
}
train_class_set.set(c);
train_class_hist[c] += 1;
for(auto p : train.data[i].second)
mat(i, p.first-1) = p.second;
}
std::cout << " OK\n"
"\tdata : " << train.data.size() << 'x' << train.dim << ", " << train_class_set.count() << " classes\n";
if(hist->count > 0)
{
std::cout << "\thistogram :\n";
for(size_t i = 0; i < train_class_set.size(); ++i)
std::cout << '\t' << i << " : " << train_class_hist[i] << " (" << (100.*train_class_hist[i]/train.data.size()) << "%)\n";
}
// -- Index --
cv::flann::Index index;
if(index_file->count > 0)
{
std::cout << "Loading index '" << index_file->filename[0] << "' ..." << std::flush;
if(!index.load(mat, index_file->filename[0]))
{
fprintf(stderr, "Can't load index '%s'.\n", index_file->filename[0]);
return EXIT_SUCCESS;
}
}
else
{
std::cout << "Building index ..." << std::flush;
// Parameters
std::unique_ptr<cv::flann::IndexParams> params;
switch(index_type->ival[0])
{
case 0 : // linear brute force search
params = std::make_unique<cv::flann::LinearIndexParams>();
break;
case 1 : // k-d tree
params = std::make_unique<cv::flann::KDTreeIndexParams>(
kd_tree_count->ival[0]);
break;
case 2 : // k-means
params = std::make_unique<cv::flann::KMeansIndexParams>(
km_branching ->ival[0],
km_iterations->ival[0],
static_cast<cvflann::flann_centers_init_t>(km_centers->ival[0]),
km_index->dval[0]);
break;
case 3 : // k-d tree + k-means
params = std::make_unique<cv::flann::CompositeIndexParams>(
kd_tree_count->ival[0],
km_branching ->ival[0],
km_iterations->ival[0],
static_cast<cvflann::flann_centers_init_t>(km_centers->ival[0]),
km_index->dval[0]);
break;
case 4 : // lsh
if((lsh_table_count->count == 0) || (lsh_key_size == 0) || (lsh_probe_level == 0))
{
std::cerr << "For t=4, lsh-table-count, lsh-key-size and lsh-probe-level must be set.\n";
return EXIT_FAILURE;
}
params = std::make_unique<cv::flann::LshIndexParams>(
lsh_table_count->ival[0],
lsh_key_size ->ival[0],
lsh_probe_level->ival[0]);
break;
case 5 : // autotuned index
params = std::make_unique<cv::flann::AutotunedIndexParams>(
auto_precision ->dval[0],
auto_build_weight ->dval[0],
auto_memory_weight ->dval[0],
auto_sample_fraction->dval[0]);
break;
default :
std::cerr << "Unknown index type " << index_type->ival[0] << std::endl;
return EXIT_FAILURE;
}
index.build(mat, *params, static_cast<cvflann::flann_distance_t>(distance->ival[0]));
}
std::cout << " OK\n";
if(output_index->count > 0)
{
std::cout << "Saving index '" << output_index->filename[0] << "' ..." << std::flush;
index.save(output_index->filename[0]);
std::cout << " OK\n";
}
// -- Query --
if(input->count > 0)
{
std::cout << "Loading query '" << input->filename[0] << "' ..." << std::flush;
auto test = load(input->filename[0]);
boost::dynamic_bitset<> test_class_set(train_class_set.size());
std::vector<size_t> test_class_hist(train_class_set.size());
for(size_t i = 0; i < test.data.size(); ++i)
{
size_t const c = test.data[i].first;
if(c >= test_class_set.size())
{
test_class_set.resize(c+1);
test_class_hist.resize(c+1, 0);
}
test_class_set.set(c);
test_class_hist[c] += 1;
}
std::cout << " OK\n"
"\tdata : " << test.data.size() << 'x' << test.dim << ", " << test_class_set.count() << " classes\n";
if(!test_class_set.is_subset_of(train_class_set))
std::cout << "\t!!! " << (test_class_set-train_class_set).count() << " test classes not in training data\n";
//std::cout << "\thistogram :\n";
//for(size_t i = 0; i < test_class_set.size(); ++i)
// std::cout << '\t' << i << " : " << test_class_hist[i] << " (" << (100.*test_class_hist[i]/test.data.size()) << "%)\n";
std::cout << "Searching ..." << std::flush;
cv::flann::SearchParams const params{checks->ival[0]};
std::ofstream file;
if(output->count > 0)
{
file.open(output->filename[0]);
if(!file)
{
fprintf(stderr, "Can't open output file '%s'\n", output->filename[0]);
return EXIT_FAILURE;
}
}
auto const n = neighbors->ival[0];
std::vector<size_t> match_counts(n, 0);
std::vector<size_t> cumulative_match_counts(n, 0);
std::vector<size_t> match_hist(n+1, 0);
namespace acc = boost::accumulators;
std::vector<acc::accumulator_set<double, acc::stats<
acc::tag::mean, acc::tag::min, acc::tag::max>>> class_matches(test_class_set.size());
for(size_t i = 0; i < test.data.size(); ++i)
{
std::vector<float> query(test.dim, 0);
std::vector<int > indices(n);
std::vector<float> dists(n);
for(auto p : test.data[i].second)
query[p.first-1] = p.second;
if(radius->count > 0)
index.radiusSearch(query, indices, dists, radius->dval[0], n, params);
else
index.knnSearch(query, indices, dists, n, params);
unsigned matching_neighbors = 0;
bool found = false;
file << test.data[i].first;
for(int j = 0; j < n; ++j)
{
file << ' ' << indices[j] << ':' << train.data[indices[j]].first;
bool ok = abs(test.data[i].first - train.data[indices[j]].first) < 0.1;
if(ok)
{
++matching_neighbors;
++match_counts[j];
}
found = found || ok;
if(found)
++cumulative_match_counts[j];
}
file << ' ' << matching_neighbors << std::endl;
++match_hist[matching_neighbors];
class_matches[test.data[i].first](matching_neighbors);
}
std::cout << " OK\n";
auto const count = test.data.size();
for(int i = 0; i < n; ++i)
{
std::cout << i << " : " << match_counts[i] << ", total " << cumulative_match_counts[i]
<< " (" << (100.*match_counts[i]/count) << "%, " << (100.*cumulative_match_counts[i]/count) << "%)\n";
}
for(int i = 0; i < (n+1); ++i)
{
std::cout << i << " : " << match_hist[i] << " (" << (100.*match_hist[i]/count) << "%)\n";
}
std::cout << "Class matches :\n";
for(size_t i = 0; i < class_matches.size(); ++i)
{
auto const cnt = acc::count(class_matches[i]);
if(cnt > 0)
{
auto const mean = acc::mean(class_matches[i]);
std::cout << i << " : " << cnt << " (" << (100.*cnt/count) << "%) - "
<< mean << " (" << (100.*mean/n)
<< "%) in [" << acc::min(class_matches[i]) << ',' << acc::max(class_matches[i]) << "]\n";
}
}
}
return EXIT_SUCCESS;
}
int _tmain(int argc, char* argv[])
{
// determine my process name
_splitpath(argv[0],NULL,NULL,gszProcName,NULL);
#else
int
main(int argc, const char** argv)
{
// determine my process name
CUtility::splitpath((char *)argv[0],NULL,gszProcName);
#endif
int iFileLogLevel; // level of file diagnostics
int iScreenLogLevel; // level of file diagnostics
char szLogFile[_MAX_PATH]; // write diagnostics to this file
int Rslt = 0; // function result code >= 0 represents success, < 0 on failure
int Idx;
etPMode PMode; // processing mode
int MinCovBases; // accept SNPs with at least this number covering bases
double MaxPValue; // accept SNPs with at most this P-value
int MinSpeciesTotCntThres; // individual species must have at least this number of total bases at SNP loci to count as SNP - 0 if no threshold
int AltSpeciesMaxCnt; // only report markers if no other species has more than this number of counts at the putative SNP loci
int MinSpeciesWithCnts; // only report markers where at least this number of species has SNP at the SNP loci
char szRefGenome[cMaxLenName+1]; // reference genome against which other relative genomes were aligned
int NumRelGenomes; // number of relative genome names
char *pszRelGenomes[cRRMaxInFileSpecs]; // names of relative genome names
int NumSNPFiles; // number of input SNP files
char *pszSNPFiles[cRRMaxInFileSpecs]; // input SNP files
int NumAlignFiles; // number of input alignment files
char *pszAlignFiles[cRRMaxInFileSpecs]; // input alignment files
char szMarkerFile[_MAX_PATH]; // write markers to this file
int NumberOfProcessors; // number of installed CPUs
int NumThreads; // number of threads (0 defaults to number of CPUs)
// command line args
struct arg_lit *help = arg_lit0("hH","help", "print this help and exit");
struct arg_lit *version = arg_lit0("v","version,ver", "print version information and exit");
struct arg_int *FileLogLevel=arg_int0("f", "FileLogLevel", "<int>","Level of diagnostics written to logfile 0=fatal,1=errors,2=info,3=diagnostics,4=debug");
struct arg_file *LogFile = arg_file0("F","log","<file>", "diagnostics log file");
struct arg_int *pmode = arg_int0("m","mode","<int>", "Marker processing mode: 0 - default");
struct arg_int *mincovbases=arg_int0("b", "MinCovBases","<int>","Filter out SNPs with less than this number of covering bases (default 5)");
struct arg_dbl *maxpvalue=arg_dbl0("p", "MaxPValue","<dbl>", "Filter out SNPs with P-Value higher (default 0.05)");
struct arg_int *mintotcntthres = arg_int0("z","mintotcntthres","<int>", "Species must have at least this number of total bases covering marker loci");
struct arg_int *mincovspecies=arg_int0("Z", "mincovspecies","<int>","Do not report markers unless this minimum number of species have SNP at same loci");
struct arg_int *altspeciesmaxcnt = arg_int0("a","altspeciesmaxcnt","<int>", "Only report markers if no other species has more than this number of counts at the putative SNP loci (defaults to 1)");
struct arg_str *refgenome=arg_str1("r", "refgenome","<str>", "alignments and SNPs of relative genomes were against this genome assembly (default 'RefGenome')");
struct arg_str *relgenomes = arg_strn("R","relgenomes","<relgenomes>",1,cRRMaxInFileSpecs,"alignments and SNPs from these genomes");
struct arg_file *snpfiles = arg_filen("i","insnps","<file>",1,cRRMaxInFileSpecs,"Load SNPs from file(s)");
struct arg_file *alignfiles = arg_filen("I","inaligns","<file>",1,cRRMaxInFileSpecs,"Load alignments from file(s)");
struct arg_file *markerfile = arg_file1("o","out","<file>", "Output markers to this file");
struct arg_int *threads = arg_int0("T","threads","<int>", "number of processing threads 0..128 (defaults to 0 which sets threads to number of CPU cores)");
struct arg_end *end = arg_end(100);
void *argtable[] = {help,version,FileLogLevel,LogFile,
pmode,mincovbases,maxpvalue,mintotcntthres,altspeciesmaxcnt,mincovspecies,refgenome,relgenomes,snpfiles,alignfiles,markerfile,threads,
end};
char **pAllArgs;
int argerrors;
argerrors = CUtility::arg_parsefromfile(argc,(char **)argv,&pAllArgs);
if(argerrors >= 0)
argerrors = arg_parse(argerrors,pAllArgs,argtable);
/* special case: '--help' takes precedence over error reporting */
if (help->count > 0)
{
printf("\n%s Generate Markers, Version %s\nOptions ---\n", gszProcName,cpszProgVer);
arg_print_syntax(stdout,argtable,"\n");
arg_print_glossary(stdout,argtable," %-25s %s\n");
printf("\nNote: Parameters can be entered into a parameter file, one parameter per line.");
printf("\n To invoke this parameter file then precede its name with '@'");
printf("\n e.g. %s @myparams.txt\n",gszProcName);
printf("\nPlease report any issues regarding usage of %s at https://github.com/csiro-crop-informatics/biokanga/issues\n\n",gszProcName);
exit(1);
}
/* special case: '--version' takes precedence error reporting */
if (version->count > 0)
{
printf("\n%s Version %s\n",gszProcName,cpszProgVer);
exit(1);
}
if (!argerrors)
{
if(FileLogLevel->count && !LogFile->count)
{
printf("\nError: FileLogLevel '-f%d' specified but no logfile '-F<logfile>\n'",FileLogLevel->ival[0]);
exit(1);
}
iScreenLogLevel = iFileLogLevel = FileLogLevel->count ? FileLogLevel->ival[0] : eDLInfo;
if(iFileLogLevel < eDLNone || iFileLogLevel > eDLDebug)
{
printf("\nError: FileLogLevel '-l%d' specified outside of range %d..%d\n",iFileLogLevel,eDLNone,eDLDebug);
exit(1);
}
if(LogFile->count)
{
strncpy(szLogFile,LogFile->filename[0],_MAX_PATH);
szLogFile[_MAX_PATH-1] = '\0';
}
else
{
iFileLogLevel = eDLNone;
szLogFile[0] = '\0';
}
// now that log parameters have been parsed then initialise diagnostics log system
if(!gDiagnostics.Open(szLogFile,(etDiagLevel)iScreenLogLevel,(etDiagLevel)iFileLogLevel,true))
{
printf("\nError: Unable to start diagnostics subsystem\n");
if(szLogFile[0] != '\0')
printf(" Most likely cause is that logfile '%s' can't be opened/created\n",szLogFile);
exit(1);
}
gDiagnostics.DiagOut(eDLInfo,gszProcName,"Version: %s",cpszProgVer);
PMode = (etPMode)(pmode->count ? pmode->ival[0] : ePMdefault);
if(PMode < ePMdefault || PMode >= ePMplaceholder)
{
gDiagnostics.DiagOut(eDLFatal,gszProcName,"Error: Processing mode '-m%d' specified outside of range %d..%d\n",PMode,ePMdefault,(int)ePMplaceholder-1);
exit(1);
}
#ifdef _WIN32
SYSTEM_INFO SystemInfo;
GetSystemInfo(&SystemInfo);
NumberOfProcessors = SystemInfo.dwNumberOfProcessors;
#else
NumberOfProcessors = sysconf(_SC_NPROCESSORS_CONF);
#endif
int MaxAllowedThreads = min(cMaxWorkerThreads,NumberOfProcessors); // limit to be at most cMaxWorkerThreads
if((NumThreads = threads->count ? threads->ival[0] : MaxAllowedThreads)==0)
NumThreads = MaxAllowedThreads;
if(NumThreads < 0 || NumThreads > MaxAllowedThreads)
{
gDiagnostics.DiagOut(eDLWarn,gszProcName,"Warning: Number of threads '-T%d' specified was outside of range %d..%d",NumThreads,1,MaxAllowedThreads);
gDiagnostics.DiagOut(eDLWarn,gszProcName,"Warning: Defaulting number of threads to %d",MaxAllowedThreads);
NumThreads = MaxAllowedThreads;
}
MinCovBases = mincovbases->count ? mincovbases->ival[0] : 5;
if(MinCovBases < 1 || MinCovBases > 10000)
{
gDiagnostics.DiagOut(eDLFatal,gszProcName,"Error: Minimum covering bases '-b%d' must be in range 1..1000",MinCovBases);
exit(1);
}
AltSpeciesMaxCnt = altspeciesmaxcnt->count ? altspeciesmaxcnt->ival[0] : 1;
if(AltSpeciesMaxCnt < 1 || AltSpeciesMaxCnt > 10000)
{
gDiagnostics.DiagOut(eDLFatal,gszProcName,"Error: Max alternative species coverage '-a%d' at putative marker loci must be in range 1..1000",AltSpeciesMaxCnt);
exit(1);
}
MaxPValue = maxpvalue->count ? maxpvalue->dval[0] : 0.05;
if(MaxPValue < 0.0 || MaxPValue > 0.25)
{
gDiagnostics.DiagOut(eDLFatal,gszProcName,"Error: Maximum P-Value '-p%1.4f' must be in range 0.0..0.25",MaxPValue);
exit(1);
}
if(refgenome->count)
{
strncpy(szRefGenome,refgenome->sval[0],cMaxLenName);
szRefGenome[cMaxLenName-1]= '\0';
}
else
strcpy(szRefGenome,"RefGenome");
if(!relgenomes->count)
{
gDiagnostics.DiagOut(eDLFatal,gszProcName,"Error: No alignment from genome name(s) specified with with '-R<relgenomes>' option)");
exit(1);
}
for(NumRelGenomes=Idx=0;NumRelGenomes < cRRMaxInFileSpecs && Idx < relgenomes->count; Idx++)
{
pszRelGenomes[Idx] = NULL;
if(pszRelGenomes[NumRelGenomes] == NULL)
pszRelGenomes[NumRelGenomes] = new char [_MAX_PATH];
strncpy(pszRelGenomes[NumRelGenomes],relgenomes->sval[Idx],_MAX_PATH);
pszRelGenomes[NumRelGenomes][_MAX_PATH-1] = '\0';
CUtility::TrimQuotedWhitespcExtd(pszRelGenomes[NumRelGenomes]);
if(pszRelGenomes[NumRelGenomes][0] != '\0')
NumRelGenomes++;
}
strncpy(szMarkerFile,markerfile->filename[0],_MAX_PATH);
szMarkerFile[_MAX_PATH-1] = '\0';
if(!snpfiles->count)
{
gDiagnostics.DiagOut(eDLFatal,gszProcName,"Error: No input SNP file(s) specified with with '-i<filespec>' option)");
exit(1);
}
for(NumSNPFiles=Idx=0;NumSNPFiles < cRRMaxInFileSpecs && Idx < snpfiles->count; Idx++)
{
pszSNPFiles[Idx] = NULL;
if(pszSNPFiles[NumSNPFiles] == NULL)
pszSNPFiles[NumSNPFiles] = new char [_MAX_PATH];
strncpy(pszSNPFiles[NumSNPFiles],snpfiles->filename[Idx],_MAX_PATH);
pszSNPFiles[NumSNPFiles][_MAX_PATH-1] = '\0';
CUtility::TrimQuotedWhitespcExtd(pszSNPFiles[NumSNPFiles]);
if(pszSNPFiles[NumSNPFiles][0] != '\0')
NumSNPFiles++;
}
if(!NumSNPFiles)
{
gDiagnostics.DiagOut(eDLFatal,gszProcName,"Error: After removal of whitespace, no input SNP file(s) specified with '-i<filespec>' option");
exit(1);
}
if(!alignfiles->count)
{
gDiagnostics.DiagOut(eDLFatal,gszProcName,"Error: No input alignment file(s) specified with with '-I<filespec>' option)");
exit(1);
}
for(NumAlignFiles=Idx=0;NumAlignFiles < cRRMaxInFileSpecs && Idx < alignfiles->count; Idx++)
{
pszAlignFiles[Idx] = NULL;
if(pszAlignFiles[NumAlignFiles] == NULL)
pszAlignFiles[NumAlignFiles] = new char [_MAX_PATH];
strncpy(pszAlignFiles[NumAlignFiles],alignfiles->filename[Idx],_MAX_PATH);
pszAlignFiles[NumAlignFiles][_MAX_PATH-1] = '\0';
CUtility::TrimQuotedWhitespcExtd(pszAlignFiles[NumAlignFiles]);
if(pszAlignFiles[NumAlignFiles][0] != '\0')
NumAlignFiles++;
}
if(!NumAlignFiles)
{
gDiagnostics.DiagOut(eDLFatal,gszProcName,"Error: After removal of whitespace, no input alignment file(s) specified with '-I<filespec>' option");
exit(1);
}
// number of alignment files must be same as the number of SNP files and genome names!
if(NumAlignFiles != NumSNPFiles && NumAlignFiles != NumRelGenomes)
{
gDiagnostics.DiagOut(eDLFatal,gszProcName,"Error: Expected same number of genome names, alignment files and SNP files, %d genome names, %d alignment files, %d SNP files",NumRelGenomes,NumAlignFiles,NumSNPFiles);
exit(1);
}
MinSpeciesTotCntThres = mincovspecies->count ? mincovspecies->ival[0] : 1;
if(MinSpeciesTotCntThres < 1 || MinSpeciesTotCntThres > 10000)
{
gDiagnostics.DiagOut(eDLFatal,gszProcName,"Error: Minimum species total bases '-z%d' must be in range 1..10000",MinSpeciesTotCntThres);
exit(1);
}
MinSpeciesWithCnts = mincovspecies->count ? mincovspecies->ival[0] : 1;
if(MinSpeciesWithCnts < 1 || MinSpeciesWithCnts > NumAlignFiles)
{
gDiagnostics.DiagOut(eDLFatal,gszProcName,"Error: Minimum species to call marker '-Z%d' must be in range 1..%d",NumAlignFiles);
exit(1);
}
// show user current resource limits
#ifndef _WIN32
gDiagnostics.DiagOut(eDLInfo, gszProcName, "Resources: %s",CUtility::ReportResourceLimits());
#endif
gDiagnostics.DiagOut(eDLInfo,gszProcName,"Processing parameters:");
const char *pszDescr;
switch(PMode) {
case ePMdefault:
pszDescr = "Default marker processing";
break;
}
gDiagnostics.DiagOutMsgOnly(eDLInfo,"Processing mode is : '%s'",pszDescr);
gDiagnostics.DiagOutMsgOnly(eDLInfo,"Minimum coverage : %d",MinCovBases);
gDiagnostics.DiagOutMsgOnly(eDLInfo,"Maximum P-Value : %1.4f'",MaxPValue);
gDiagnostics.DiagOutMsgOnly(eDLInfo,"Reference genome assembly name : '%s'",szRefGenome);
gDiagnostics.DiagOutMsgOnly(eDLInfo,"Minimum total bases for species at SNP call loci : %d",MinSpeciesTotCntThres);
gDiagnostics.DiagOutMsgOnly(eDLInfo,"Maximum alternative species coverage at SNP call loci : %d",AltSpeciesMaxCnt);
gDiagnostics.DiagOutMsgOnly(eDLInfo,"Minimum number of species with SNP call at same loci : %d",MinSpeciesWithCnts);
for(Idx=0; Idx < NumRelGenomes; Idx++)
gDiagnostics.DiagOutMsgOnly(eDLInfo,"Alignments and SNPs from this genome (%d) : '%s'",Idx+1,pszRelGenomes[Idx]);
for(Idx=0; Idx < NumSNPFiles; Idx++)
gDiagnostics.DiagOutMsgOnly(eDLInfo,"Input SNP file (%d) : '%s'",Idx+1,pszSNPFiles[Idx]);
for(Idx=0; Idx < NumAlignFiles; Idx++)
gDiagnostics.DiagOutMsgOnly(eDLInfo,"Input alignment file (%d) : '%s'",Idx+1,pszAlignFiles[Idx]);
gDiagnostics.DiagOutMsgOnly(eDLInfo,"Output markers to file : '%s'",szMarkerFile);
gDiagnostics.DiagOutMsgOnly(eDLInfo,"number of threads : %d",NumThreads);
#ifdef _WIN32
SetPriorityClass(GetCurrentProcess(), BELOW_NORMAL_PRIORITY_CLASS);
#endif
gStopWatch.Start();
Rslt = Process(PMode,MinCovBases,MaxPValue,MinSpeciesTotCntThres,MinSpeciesWithCnts,AltSpeciesMaxCnt,szRefGenome,NumRelGenomes,pszRelGenomes,NumThreads,NumSNPFiles,pszSNPFiles,NumAlignFiles,pszAlignFiles,szMarkerFile);
gStopWatch.Stop();
Rslt = Rslt >=0 ? 0 : 1;
gDiagnostics.DiagOut(eDLInfo,gszProcName,"Exit code: %d Total processing time: %s",Rslt,gStopWatch.Read());
exit(Rslt);
}
else
{
printf("\n%s Generate Markers, Version %s\n",gszProcName,cpszProgVer);
arg_print_errors(stdout,end,gszProcName);
arg_print_syntax(stdout,argtable,"\nUse '-h' to view option and parameter usage\n");
exit(1);
}
return 0;
}
int _tmain(int argc, char* argv[])
{
// determine my process name
_splitpath(argv[0],NULL,NULL,gszProcName,NULL);
#else
int
main(int argc, const char** argv)
{
// determine my process name
CUtility::splitpath((char *)argv[0],NULL,gszProcName);
#endif
int iScreenLogLevel; // level of screen diagnostics
int iFileLogLevel; // level of file diagnostics
char szLogFile[_MAX_PATH]; // write diagnostics to this file
int Rslt = 0; // function result code >= 0 represents success, < 0 on failure
etPMode PMode; // processing mode
etFMode FMode; // format output mode
int TruncLength; // truncate regions to be no longer than this length
int OfsLoci; // offset region loci by this many bases
int DeltaLen; // change region lengths by this many bases
int MovAvgFilter; // apply this moving average window size filter
int BaselineFilter; // use this window size when normalising for baseline
char szTrackTitle[cMaxDatasetSpeciesChrom]; // title to identify predicted nucleosome track
double Dyadratio;
double Dyad2ratio;
double Dyad3ratio;
char szRsltsFile[_MAX_PATH];
char szInConfFile[_MAX_PATH];
char szInGenomeFile[_MAX_PATH];
char szInclRegionFile[_MAX_PATH]; // only report predicted nucleosomes if intersecting with regions in this file
// command line args
struct arg_lit *help = arg_lit0("hH","help", "print this help and exit");
struct arg_lit *version = arg_lit0("v","version,ver", "print version information and exit");
struct arg_int *FileLogLevel=arg_int0("f", "FileLogLevel", "<int>","Level of diagnostics written to logfile 0=fatal,1=errors,2=info,3=diagnostics,4=debug");
struct arg_file *LogFile = arg_file0("F","log","<file>", "diagnostics log file");
struct arg_int *pmode = arg_int0("m","mode","<int>", "processing mode: 0 - predict from minor groove (default = 0)");
struct arg_file *inGenomefile = arg_file1("i","in","<file>", "input from this bioseq genome file");
struct arg_file *inConfFile = arg_file1("I","conf","<file>", "input conformation characteristics from this file");
struct arg_file *inclRegionFile = arg_file0("r","inclregions","<file>", "only report predicted nucleosomes if intersecting with regions in this file");
struct arg_int *trunclength = arg_int0("T","trunclength","<int>","truncate regions to be no longer than this length (default 147)");
struct arg_int *ofsloci = arg_int0("u","offset","<int>", "offset region loci by this many bases, -2048 to +2048 (default 0)");
struct arg_int *deltalen = arg_int0("U","deltalen","<int>", "delta region lengths by this many bases, -2048 to +2048 (default 0)");
struct arg_dbl *dyadratio=arg_dbl0("d", "dyadratio", "<double>","dyad minor grooves must be at least this ratio to background (default 1.020");
struct arg_dbl *dyad2ratio=arg_dbl0("D", "dyad2ratio", "<double>","immediately flanking minor grooves must be at least this ratio to background (default 1.015");
struct arg_dbl *dyad3ratio=arg_dbl0("e", "dyad3ratio", "<double>","remainder flanking minor grooves must be at least this ratio to background (default 1.010");
struct arg_int *movavgfilter = arg_int0("a","avgwindow","<int>","apply lowpass filter as a moving average window of this size, 0 if none else 5..100 (default: 10)");
struct arg_int *baselinefilter = arg_int0("A","basewindow","<int>","baseline normalisation window size, 0 if none else 25..5000 (default: 250)");
struct arg_file *outfile = arg_file1("o","out","<file>", "output nucleosome predictions to this file");
struct arg_int *format = arg_int0("M","format","<int>", "output format: 0 - UCSC bedGraph dyads, 1 - UCSC BED dyads, 2 - CSV dyads, 3 - UCSC bedGraph nucleosomes, 4 - UCSC BED nucleosomes, 5 - CSV nucleosomes, 6 - CSV scores (default: 0)");
struct arg_str *title = arg_str0("t","title","<string>", "track title");
struct arg_end *end = arg_end(20);
void *argtable[] = {help,version,FileLogLevel,LogFile,
pmode,format,movavgfilter,baselinefilter,title,dyadratio,dyad2ratio,dyad3ratio,inGenomefile,inConfFile,outfile,
inclRegionFile,trunclength,ofsloci,deltalen,
end};
char **pAllArgs;
int argerrors;
argerrors = CUtility::arg_parsefromfile(argc,(char **)argv,&pAllArgs);
if(argerrors >= 0)
argerrors = arg_parse(argerrors,pAllArgs,argtable);
/* special case: '--help' takes precedence over error reporting */
if (help->count > 0)
{
printf("\n%s ", gszProcName);
arg_print_syntax(stdout,argtable,"\n");
arg_print_glossary(stdout,argtable," %-25s %s\n");
printf("\nNote: Parameters can be entered into a parameter file, one parameter per line.");
printf("\n To invoke this parameter file then precede its name with '@'");
printf("\n e.g. %s @myparams.txt\n\n",gszProcName);
exit(1);
}
/* special case: '--version' takes precedence error reporting */
if (version->count > 0)
{
printf("\n%s Version %d.%2.2d",gszProcName,cProgVer/100,cProgVer%100);
exit(1);
}
if (!argerrors)
{
if(FileLogLevel->count && !LogFile->count)
{
printf("\nError: FileLogLevel '-f%d' specified but no logfile '-F<logfile>'",FileLogLevel->ival[0]);
exit(1);
}
iScreenLogLevel = iFileLogLevel = FileLogLevel->count ? FileLogLevel->ival[0] : eDLInfo;
if(iFileLogLevel < eDLNone || iFileLogLevel > eDLDebug)
{
printf("\nError: FileLogLevel '-l%d' specified outside of range %d..%d",iFileLogLevel,eDLNone,eDLDebug);
exit(1);
}
if(LogFile->count)
{
strncpy(szLogFile,LogFile->filename[0],_MAX_PATH);
szLogFile[_MAX_PATH-1] = '\0';
}
else
{
iFileLogLevel = eDLNone;
szLogFile[0] = '\0';
}
PMode = (etPMode)(pmode->count ? pmode->ival[0] : 0);
if(PMode < 0 || PMode >= ePMplaceholder)
{
printf("\nError: Processing mode '-m%d' specified outside of range %d..%d",PMode,0,(int)ePMplaceholder-1);
exit(1);
}
FMode = (etFMode)(format->count ? format->ival[0] : eFMbedGraphDyads);
if(FMode < eFMbedGraphDyads || FMode >= eFMplaceholder)
{
printf("\nError: Output format mode '-m%d' specified outside of range %d..%d",FMode,eFMbedGraphDyads,(int)eFMplaceholder-1);
exit(1);
}
MovAvgFilter = movavgfilter->count ? movavgfilter->ival[0] : 10;
if(MovAvgFilter != 0 && (MovAvgFilter < 5 || MovAvgFilter > 100))
{
printf("\nError: Moving average filter width '-a%d' specified outside of range 0 or 5..100",MovAvgFilter);
exit(1);
}
BaselineFilter = baselinefilter->count ? baselinefilter->ival[0] : 250;
if(BaselineFilter != 0 && (BaselineFilter < 25 || MovAvgFilter > 5000))
{
printf("\nError: Baseline normalisation window width '-A%d' specified outside of range 0 or 25..5000",BaselineFilter);
exit(1);
}
Dyadratio = dyadratio->count ? dyadratio->dval[0] : cDfltDyadratio;
Dyad2ratio = dyad2ratio->count ? dyad2ratio->dval[0] : cDfltDyad2ratio;
Dyad3ratio = dyad3ratio->count ? dyad3ratio->dval[0] : cDfltDyad3ratio;
if(Dyadratio < 1.0f || Dyad2ratio < 1.0f || Dyad3ratio < 1.0f)
{
printf("\nError: All dyad and flanking threshold ratios must be at least 1.0");
exit(1);
}
if(!title->count)
{
printf("\nError: no track title has been specified with '-t<title>' option");
exit(1);
}
if(strlen(title->sval[0]) >= cMaxDatasetSpeciesChrom)
{
printf("\nError: track title '%s' is too long, must be shorter than %d chars",title->sval[0],cMaxDatasetSpeciesChrom-1);
exit(1);
}
strncpy(szTrackTitle,title->sval[0],sizeof(szTrackTitle));
szTrackTitle[sizeof(szTrackTitle)-1] = '\0';
CUtility::TrimQuotedWhitespcExtd(szTrackTitle);
CUtility::ReduceWhitespace(szTrackTitle);
if(szTrackTitle[0] == '\0')
{
printf("\nError: specified track title is empty or whitespace only");
exit(1);
}
strcpy(szInGenomeFile,inGenomefile->filename[0]);
strcpy(szInConfFile,inConfFile->filename[0]);
strcpy(szRsltsFile,outfile->filename[0]);
if(inclRegionFile->count)
{
strncpy(szInclRegionFile,inclRegionFile->filename[0],_MAX_PATH);
szInclRegionFile[_MAX_PATH-1] = '\0';
OfsLoci = ofsloci->count ? ofsloci->ival[0] : 0;
if(abs(OfsLoci) > 1024)
{
printf("Error: loci offset '-u%d' must be in the range -2048 to +2048",OfsLoci);
exit(1);
}
DeltaLen = deltalen->count ? deltalen->ival[0] : 0;
if(abs(DeltaLen) > 1024)
{
printf("Error: delta length '-U%d' must be in the range -2048 to +2048",DeltaLen);
exit(1);
}
TruncLength = trunclength->count ? trunclength->ival[0] : 147;
if(TruncLength < 147)
{
printf("Error: regions truncation length '-T%d' must be at least 147",TruncLength);
exit(1);
}
}
else
{
szInclRegionFile[0] = '\0';
OfsLoci = 0;
DeltaLen = 0;
TruncLength = 0;
}
// now that command parameters have been parsed then initialise diagnostics log system
if(!gDiagnostics.Open(szLogFile,(etDiagLevel)iScreenLogLevel,(etDiagLevel)iFileLogLevel,true))
{
printf("\nError: Unable to start diagnostics subsystem.");
if(szLogFile[0] != '\0')
printf(" Most likely cause is that logfile '%s' can't be opened/created",szLogFile);
exit(1);
}
// show user current resource limits
#ifndef _WIN32
gDiagnostics.DiagOut(eDLInfo, gszProcName, "Resources: %s",CUtility::ReportResourceLimits());
#endif
gDiagnostics.DiagOut(eDLInfo,gszProcName,"Version: %d.%2.2d Processing parameters:",cProgVer/100,cProgVer%100);
const char *pszDescr;
switch(PMode) {
case ePMdefault:
pszDescr = "Default - predict from minor groove";
break;
}
gDiagnostics.DiagOutMsgOnly(eDLInfo,"processing mode is : '%s'",pszDescr);
switch(FMode) {
case eFMbedGraphDyads:
pszDescr = "UCSC bedGraph dyads";
break;
case eFMbedDyads:
pszDescr = "UCSC BED dyads";
break;
case eFMcsvDyads:
pszDescr = "CSV dyads";
break;
case eFMbedGraphNucs:
pszDescr = "UCSC bedGraph nucleosomes";
break;
case eFMbedNucs:
pszDescr = "UCSC BED nucleosomes";
break;
case eFMcsvNucs:
pszDescr = "CSV nucleosomes";
break;
case eFMMcsvScores:
pszDescr = "CSV dyad scores along genome";
break;
}
gDiagnostics.DiagOutMsgOnly(eDLInfo,"output format is : '%s'",pszDescr);
gDiagnostics.DiagOutMsgOnly(eDLInfo,"moving average filter width : %d",MovAvgFilter);
gDiagnostics.DiagOutMsgOnly(eDLInfo,"baseline noramlisation width : %d",BaselineFilter);
gDiagnostics.DiagOutMsgOnly(eDLInfo,"dyad name: '%s'",szTrackTitle);
gDiagnostics.DiagOutMsgOnly(eDLInfo,"dyad minor groove threshold: %1.4f",Dyadratio);
gDiagnostics.DiagOutMsgOnly(eDLInfo,"dyad immediately flanking minor groove threshold: %1.4f",Dyad2ratio);
gDiagnostics.DiagOutMsgOnly(eDLInfo,"dyad remainder flanking minor groove threshold: %1.4f",Dyad3ratio);
gDiagnostics.DiagOutMsgOnly(eDLInfo,"input genome file: '%s'",szInGenomeFile);
gDiagnostics.DiagOutMsgOnly(eDLInfo,"input conformation file: '%s'",szInConfFile);
gDiagnostics.DiagOutMsgOnly(eDLInfo,"output predicted nucleosomes file: '%s'",szRsltsFile);
if(szInclRegionFile[0] != '0')
{
gDiagnostics.DiagOutMsgOnly(eDLInfo,"Offset region start loci by : %d",OfsLoci);
gDiagnostics.DiagOutMsgOnly(eDLInfo,"Delta region length by : %d",DeltaLen);
gDiagnostics.DiagOutMsgOnly(eDLInfo,"Truncate region length: %d",TruncLength);
gDiagnostics.DiagOutMsgOnly(eDLInfo,"include regions file: '%s'",szInclRegionFile);
}
#ifdef _WIN32
SetPriorityClass(GetCurrentProcess(), BELOW_NORMAL_PRIORITY_CLASS);
#endif
gStopWatch.Start();
Rslt = Process(PMode,FMode,MovAvgFilter,BaselineFilter,szTrackTitle,Dyadratio,Dyad2ratio,Dyad3ratio,szInGenomeFile,szInConfFile,szRsltsFile,
szInclRegionFile,OfsLoci,DeltaLen,TruncLength);
gStopWatch.Stop();
Rslt = Rslt >=0 ? 0 : 1;
gDiagnostics.DiagOut(eDLInfo,gszProcName,"Exit code: %d Total processing time: %s",Rslt,gStopWatch.Read());
exit(Rslt);
}
else
{
arg_print_errors(stdout,end,gszProcName);
arg_print_syntax(stdout,argtable,"\nend of help\n");
exit(1);
}
return 0;
}
