/*
* CORE functions
*/
void gt_stats_parallel_generate_stats() {
// Stats info
gt_stats_analysis stats_analysis = GT_STATS_ANALYSIS_DEFAULT();
gt_stats** stats = malloc(parameters.num_threads*sizeof(gt_stats*));
// Select analysis
stats_analysis.best_map = parameters.best_map;
stats_analysis.maps_profile = parameters.maps_profile|parameters.mismatch_quality|parameters.mismatch_transitions;
stats_analysis.nucleotide_stats = true;
stats_analysis.split_map_stats = parameters.splitmaps_profile;
stats_analysis.indel_profile = parameters.indel_profile;
// Open file
gt_input_file* input_file = (parameters.name_input_file==NULL) ?
gt_input_stream_open(stdin) : gt_input_file_open(parameters.name_input_file,parameters.mmap_input);
gt_sequence_archive* sequence_archive = NULL;
if (stats_analysis.indel_profile) {
sequence_archive = gt_sequence_archive_new();
register gt_input_file* const reference_file = gt_input_file_open(parameters.name_reference_file,false);
fprintf(stderr,"Loading reference file ...");
if (gt_input_multifasta_parser_get_archive(reference_file,sequence_archive)!=GT_IFP_OK) {
fprintf(stderr,"\n");
gt_fatal_error_msg("Error parsing reference file '%s'\n",parameters.name_reference_file);
}
gt_input_file_close(reference_file);
fprintf(stderr," done! \n");
}
// Parallel reading+process
#pragma omp parallel num_threads(parameters.num_threads)
{
uint64_t tid = omp_get_thread_num();
gt_buffered_input_file* buffered_input = gt_buffered_input_file_new(input_file);
gt_status error_code;
gt_template *template = gt_template_new();
gt_status parse_arguments(int argc,char** argv) {
gt_status err=GT_STATUS_OK;
struct option* gt_coverage_getopt = gt_options_adaptor_getopt(gt_coverage_options);
gt_string* const gt_coverage_short_getopt = gt_options_adaptor_getopt_short(gt_coverage_options);
int option, option_index;
while (true) {
if ((option=getopt_long(argc,argv,
gt_string_get_string(gt_coverage_short_getopt),gt_coverage_getopt,&option_index))==-1) break;
switch (option) {
case 'c':
parameters.combine=true;
break;
case 'd':
parameters.detailed_output=true;
break;
case 'b':
parameters.block_size = atol(optarg);
break;
case 'o':
parameters.output_file = optarg;
break;
case 'p':
parameters.prefix = optarg;
break;
case 'r':
parameters.ranges_file = optarg;
break;
case 't':
parameters.target_file = optarg;
break;
case 'x':
parameters.extend = atol(optarg);
break;
case 'P':
parameters.paired = true;
break;
case 'U':
if(!strcasecmp("first",optarg)) parameters.unique=GT_UNIQUE_FIRST;
else if(!strcasecmp("gem",optarg)) parameters.unique=GT_UNIQUE_GEM;
else if(!strcasecmp("xt",optarg)) parameters.unique=GT_UNIQUE_XT;
else if(!strncasecmp("mq:",optarg,3)) {
parameters.unique=GT_UNIQUE_MQ;
parameters.MQ_limit=atol(optarg+3);
} else {
gt_fatal_error_msg("Unique mode not recognized: '%s'",optarg);
}
break;
case 'D':
if(!strcasecmp("ignore",optarg)) parameters.duplicate=GT_DUPLICATE_IGNORE;
else if(!strcasecmp("remove",optarg)) parameters.duplicate=GT_DUPLICATE_REMOVE;
else {
gt_fatal_error_msg("Duplicate mode not recognized: '%s'",optarg);
}
break;
case 'q':
parameters.min_quality = atol(optarg);
break;
case 'v':
parameters.verbose=true;
break;
case 'T':
#ifdef HAVE_OPENMP
parameters.num_threads = atol(optarg);
#endif
break;
case 'h':
usage(gt_coverage_options,gt_coverage_groups,false);
exit(1);
break;
case 'H':
usage(gt_coverage_options,gt_coverage_groups,true);
exit(1);
case 'J':
gt_options_fprint_json_menu(stderr,gt_coverage_options,gt_coverage_groups,true,false);
exit(1);
break;
case '?':
default:
usage(gt_coverage_options,gt_coverage_groups,false);
gt_fatal_error_msg("Option '%c' %d not recognized",option,option);
break;
}
}
if(!parameters.ranges_file) {
fputs("No ranges file specified. Use -r or --ranges_file option\n",stderr);
}
return err;
}
