int main ( int argc, char *argv[] )
{
/***********************************************************************
* Local variables
***********************************************************************/
int ierr = 0; // Flag errors
char *error = NULL; // Error message string
double t1, t2, t3, t4, t5; // Variables to track runtime
/* File in/out handling variables */
char *inputFile = NULL, *outputFile = NULL;
FILE *fp_in = NULL, *fp_out = NULL;
input_data input_vars; // Struct to store input variables
input_data_init ( &input_vars ); // Set variables to initial values
para_data para_vars; // Struct to store parallel variables
para_data_init ( ¶_vars ); // Set variables to initial values
time_data time_vars; // Struct to store time variables
time_data_init ( &time_vars ); // Set variables to initial values
geom_data geom_vars; // Struct to store geometry variables
geom_data_init ( &geom_vars ); // Set variables to initial values
sn_data sn_vars; // Struct to store sn variables
sn_data_init ( &sn_vars ); // Set variables to initial values
data_data data_vars; // Struct to store data variables
data_data_init ( &data_vars ); // Set variables to initial values
control_data control_vars; // Struct to store control variables
control_data_init ( &control_vars ); // Set variables to initial values
mms_data mms_vars; // Struct to store mms variables
mms_data_init ( &mms_vars ); // Set variables to initial values
solvar_data solvar_vars; // Struct to store solvar variables
solvar_data_init ( &solvar_vars ); // Set variables to initial values
sweep_data sweep_vars; // Struct to store sweep variables
sweep_data_init ( &sweep_vars ); // Set variables to initial values
dim_sweep_data dim_sweep_vars;
/***********************************************************************
* Perform calls that set up the parallel environment in MPI and
* OpenMP. Also starts the timer. Update parallel setup time.
***********************************************************************/
/* Initialize the parallel environment */
pinit ( argc, argv, ¶_vars, &t1, &ierr );
t2 = wtime(); // Get the MPI walltime
/* Calc parallel setup time */
time_vars.tparset = time_vars.tparset + t2 - t1;
/***********************************************************************
* Read the command line arguments to get i/o file names.
* Open the two files.
***********************************************************************/
ierr = cmdarg ( argc, argv, &inputFile, &outputFile, &error,
para_vars.iproc, para_vars.root );
bcast_i_scalar ( &ierr, para_vars.comm_snap, para_vars.root, para_vars.nproc );
/* Ensure arguments are valid */
if ( ierr != 0 )
{
print_error ( NULL, error, para_vars.iproc, para_vars.root );
FREE ( inputFile );
FREE ( outputFile );
FREE ( error );
stop_run ( 0, 0, 0, ¶_vars, &sn_vars, &data_vars, &mms_vars,
&geom_vars, &solvar_vars, &control_vars );
}
/* Open the input file to read in initial values */
ierr = open_file ( &fp_in, inputFile, "r", &error, para_vars.iproc, para_vars.root );
bcast_i_scalar ( &ierr, para_vars.comm_snap, para_vars.root, para_vars.nproc);
/* Ensure input file is found */
if ( ierr != 0 )
{
print_error ( NULL, error, para_vars.iproc, para_vars.root );
FREE ( inputFile );
FREE ( outputFile );
FREE ( error );
stop_run ( 0, 0, 0, ¶_vars, &sn_vars, &data_vars, &mms_vars,
&geom_vars, &solvar_vars, &control_vars );
}
/* Open the output file to write results and error messages */
ierr = open_file ( &fp_out, outputFile, "w", &error, para_vars.iproc, para_vars.root );
bcast_i_scalar ( &ierr, para_vars.comm_snap, para_vars.root, para_vars.nproc );
/* Ensure output file can be created */
if ( ierr != 0 )
{
print_error ( NULL, error, para_vars.iproc, para_vars.root );
FREE ( inputFile );
FREE ( outputFile );
FREE ( error );
stop_run ( 0, 0, 0, ¶_vars, &sn_vars, &data_vars, &mms_vars,
&geom_vars, &solvar_vars, &control_vars );
}
/***********************************************************************
* Write code version and execution time to output.
***********************************************************************/
if ( para_vars.iproc == para_vars.root ) version_print ( fp_out );
/***********************************************************************
* Read input
***********************************************************************/
ierr = read_input ( fp_in, fp_out, &input_vars, ¶_vars, &time_vars );
ierr = close_file ( fp_in, inputFile, &error, para_vars.iproc,
para_vars.root );
FREE ( inputFile );
bcast_i_scalar ( &ierr, para_vars.comm_snap, para_vars.root, para_vars.nproc );
if ( ierr != 0 )
{
print_error ( fp_out, error, para_vars.iproc, para_vars.root );
FREE ( outputFile );
FREE ( error );
stop_run ( 0, 0, 0, ¶_vars, &sn_vars, &data_vars, &mms_vars,
&geom_vars, &solvar_vars, &control_vars );
}
/***********************************************************************
* Get nthreads for each proc. Print the warning about resetting
* nthreads if necessary. Don't stop run. Set up the SDD MPI topology.
***********************************************************************/
t3 = wtime();
pinit_omp ( para_vars.comm_snap, &input_vars.nthreads, input_vars.nnested,
¶_vars.do_nested, &ierr, &error );
if ( ierr != 0 ) print_error ( NULL, error, para_vars.iproc,
para_vars.root );
pcomm_set ( input_vars.npey, input_vars.npez, ¶_vars, &ierr );
t4 = wtime();
time_vars.tparset = time_vars.tparset + t4 - t3;
/***********************************************************************
* Setup problem
***********************************************************************/
setup ( &input_vars, ¶_vars, &time_vars, &geom_vars, &sn_vars,
&data_vars, &solvar_vars, &control_vars, &mms_vars, fp_out,
&ierr, &error );
/***********************************************************************
* Call for the problem solution
***********************************************************************/
translv ( &input_vars, ¶_vars, &time_vars, &geom_vars, &sn_vars,
&data_vars, &control_vars, &solvar_vars, &mms_vars,
&sweep_vars, &dim_sweep_vars, fp_out, &ierr, &error );
/***********************************************************************
* Output the results. Print the timing summary
***********************************************************************/
output ( &input_vars, ¶_vars, &time_vars, &geom_vars, &data_vars,
&sn_vars, &control_vars, &mms_vars, &solvar_vars, &sweep_vars,
fp_out, &ierr, &error );
if ( para_vars.iproc == para_vars.root ) time_summ ( fp_out, &time_vars );
/***********************************************************************
* Final cleanup: deallocate, close output file, end the program
***********************************************************************/
dealloc_input ( 3, &sn_vars, &data_vars, &mms_vars );
dealloc_solve ( 3, &geom_vars, &solvar_vars, &control_vars );
t5 = wtime();
time_vars.tsnap = t5 - t1;
if ( para_vars.iproc == para_vars.root )
{
fprintf ( fp_out, " Total Execution time"
" %.4E\n\n", time_vars.tsnap );
fprintf ( fp_out, " Grind Time (nanoseconds)"
" %.4E\n\n", time_vars.tgrind );
fprintf ( fp_out,
"****************************************"
"****************************************\n" );
}
ierr = close_file ( fp_out, outputFile, &error, para_vars.iproc, para_vars.root );
FREE ( outputFile );
bcast_i_scalar ( &ierr, para_vars.comm_snap, para_vars.root, para_vars.nproc );
if ( ierr != 0 )
{
print_error ( 0, error, para_vars.iproc, para_vars.root );
FREE ( error );
stop_run ( 0, 0, 0, ¶_vars, &sn_vars, &data_vars, &mms_vars,
&geom_vars, &solvar_vars, &control_vars );
}
if ( control_vars.otrdone )
{
FREE ( error );
stop_run ( 0, 0, 1, ¶_vars, &sn_vars, &data_vars, &mms_vars,
&geom_vars, &solvar_vars, &control_vars );
}
else
{
FREE ( error );
stop_run ( 0, 0, 2, ¶_vars, &sn_vars, &data_vars, &mms_vars,
&geom_vars, &solvar_vars, &control_vars );
}
return 0;
}
/**
txt main
**/
void txt_main(int argc, char *argv[]) {
char c;
struct input_data *id = input_data_init();
struct output_data *od = output_data_init();
char ignoreLinesStartingWith = '#';
char secondInputFileName[1024] = "";
char str[1000000] = "";
char key[1024] = "";
double value = DBL_MIN;
int alsoPrintOtherColumns = 0;
int deleteColumns = 0;
int n = 0;
while ((c = getopt(argc, argv, "s:m:n:i:j:q:k:vAHD")) != -1) {
switch (c) {
case 'A':
alsoPrintOtherColumns = 1;
break;
case 'D':
deleteColumns = 1;
break;
case 'm':
id->mode = atoi(optarg);
break;
case 'n':
n = atoi(optarg);
break;
case 'q':
strcpy(id->inputFilePrefix, optarg);
break;
case 'i':
strcpy(id->inputFileName, optarg);
break;
case 'j':
strcpy(secondInputFileName, optarg);
break;
case 's':
strcpy(str, optarg);
value = atof(str);
break;
case 'k':
strcpy(key, optarg);
ignoreLinesStartingWith = key[0];
break;
case 'H':
od->outputOrientation = OUTPUT_ORIENTATION_HORIZONTAL;
break;
case 'v':
id->verbose = 1;
break;
default:
//abort();
txt_main_Usage(argc, argv, id);
printf("\tInvalid option. Please see usage above.\n\n");
exit(0);
}
}
if (id->mode == 0) {
txt_main_Usage(argc,argv,id);
exit(1);
}
if (strlen(id->inputFileName)==0) {
txt_main_Usage(argc,argv,id);
printf ("\tMissing input file (-i). Please see usage above!\n\n");
exit(1);
}
if ((id->mode == MODE_TXT_COUNT_ENTRY)) {
int n,m;
n = txt_MODE_TXT_COUNT_ENTRY(id, id->inputFileName, ignoreLinesStartingWith);
if (strlen(secondInputFileName) > 0) {
m = txt_MODE_TXT_COUNT_ENTRY(id, secondInputFileName, ignoreLinesStartingWith);
printf ("\ndiff\tinput_file_name_1\tnumber_of_lines_1\tinput_file_name_2\tnumber_of_lines_2");
printf ("\n%d\t%s\t%d\t%s\t%d", m-n,id->inputFileName, n, secondInputFileName, m);
printf ("\n");
} else {
printf ("\ninput_file_name\tnumber_of_lines");
if (strstr(id->inputFileName,"/dev/stdin")) {
printf ("\n%s\t%d", id->inputFilePrefix, n);
} else {
printf ("\n%s\t%d", id->inputFileName, n);
}
printf ("\n");
}
} else if (id->mode == MODE_TXT_EXTRACT_COLUMN_FROM_FILE) {
if (strlen(key) == 0) {
txt_main_Usage(argc,argv,id);
printf ("\tMissing columns to be extracted (-k). Please see usage above!\n\n");
exit(1);
}
if (deleteColumns == 0)
txt_MODE_TXT_EXTRACT_COLUMN_FROM_FILE(id, id->inputFileName, key,value, alsoPrintOtherColumns);
else
txt_MODE_TXT_DELETE_COLUMN_FROM_FILE(id, id->inputFileName, key);
} else if (id->mode == MODE_TXT_EXTRACT_ROW_FROM_FILE) {
txt_MODE_TXT_DELETE_ROW_FROM_FILE(id, id->inputFileName, secondInputFileName, n, deleteColumns);
}
}
/**
tabix main
**/
void tabix_main(int argc, char *argv[]) {
char c;
struct input_data *id = input_data_init();
struct output_data *od = output_data_init();
struct my_tabix *tabix = tabix_init();
tabix->considerMisMatchedALT = 0;
int chrColumn = -1, posColumn = -1;
// assume input file will be in VCF format
vcf_setInputFileToVCFformat(id);
while ((c = getopt(argc, argv, "F:m:i:d:q:n:s:b:vNR")) != -1) {
switch (c) {
case 'F':
tabix->inputFileFormat = atoi(optarg);
break;
case 'R':
tabix->considerMisMatchedALT = 1;
break;
case 'm':
id->mode = atoi(optarg);
break;
case 'd':
strcpy(tabix->inputFileName, optarg);
break;
case 'q':
strcpy(tabix->inputFilePrefix, optarg);
break;
case 'N':
tabix->includeDataFromDatabase = 1;
break;
case 'i':
strcpy(id->inputFileName, optarg);
break;
case 'n':
id->columnOffSet = atoi(optarg);
break;
case 's':
chrColumn = atoi(optarg);
break;
case 'b':
posColumn = atoi(optarg);
break;
case 'v':
id->verbose = 1;
break;
default:
//abort();
tabix_main_Usage(argc, argv, id);
printf("\tInvalid option. Please see usage above\n\n");
exit(0);
}
}
if (id->mode == 0) {
tabix_main_Usage(argc,argv,id);
exit(1);
}
if (strlen(id->inputFileName)==0) {
tabix_main_Usage(argc,argv,id);
printf ("\tMissing input file (-i). Please see usage above!\n\n");
exit(1);
} else if ((strlen(tabix->inputFileName)==0) || (strlen(tabix->inputFilePrefix)==0)) {
tabix_main_Usage(argc,argv,id);
printf ("\tMissing database file (-d) or database file prefix (-q). Please see usage above!\n\n");
exit(1);
}
if (id->mode == MODE_TABIX_ANNOTATE_VCF_WITH_BED) {
tabix_MODE_TABIX_ANNOTATE_VCF_WITH_BED(id,od,tabix);
} else if (id->mode == MODE_TABIX_ANNOTATE_VCF_WITH_PILEUP) {
tabix_MODE_TABIX_ANNOTATE_VCF_WITH_PILEUP(id,od,tabix);
} else if (id->mode == MODE_TABIX_ANNOTATE_VCF_WITH_VCF) {
tabix_MODE_TABIX_ANNOTATE_VCF_WITH_VCF(id,od,tabix);
} else if (id->mode == MODE_TABIX_ANNOTATE_TXT_WITH_BED) {
id->chrColumnNumber = 1;
id->startColumnNumber = 2;
id->endColumnNumber = 3;
tabix_MODE_TABIX_ANNOTATE_TXT_WITH_BED(id,od,tabix,chrColumn,posColumn);
}
}
