static int gthsplit_process_files(Gthsplitinfo *gthsplitinfo,
const GthPlugins *plugins, GtError *err)
{
Store_in_subset_file_data store_in_subset_file_data;
GthInput *inputinfo;
unsigned long i;
int had_err;
gt_error_check(err);
/* initialization */
inputinfo = gth_input_new(plugins->file_preprocessor, plugins->seq_con_new);
store_in_subset_file_data.gthsplitinfo = gthsplitinfo;
store_in_subset_file_data.num_of_subset_files = 100 / gthsplitinfo->range;
store_in_subset_file_data.sa_filter = gthsplitinfo->sa_filter;
store_in_subset_file_data.current_outputfilename = NULL;
store_in_subset_file_data.subset_files =
gt_malloc(sizeof (GtFile*) *
store_in_subset_file_data.num_of_subset_files);
store_in_subset_file_data.subset_filenames =
gt_malloc(sizeof (GtStr*) *
store_in_subset_file_data.num_of_subset_files);
store_in_subset_file_data.subset_file_sa_counter =
gt_malloc(sizeof (unsigned long) *
store_in_subset_file_data.num_of_subset_files);
for (i = 0; i < store_in_subset_file_data.num_of_subset_files; i++) {
store_in_subset_file_data.subset_files[i] = NULL;
store_in_subset_file_data.subset_filenames[i] = NULL;
store_in_subset_file_data.subset_file_sa_counter[i] = 0;
}
store_in_subset_file_data.sa_visitor = gth_xml_inter_sa_visitor_new(inputinfo,
0, NULL);
if (gthsplitinfo->showverbose)
gthsplitinfo->showverbose("process all intermediate output files");
/* split up intermediate files */
had_err = gth_process_intermediate_files(inputinfo,
gthsplitinfo->consensusfiles,
store_in_subset_file,
&store_in_subset_file_data,
gthsplitinfo->showverbose, err);
/* close the split files */
close_output_files(&store_in_subset_file_data);
/* free */
gth_sa_visitor_delete(store_in_subset_file_data.sa_visitor);
gth_input_delete_complete(inputinfo);
gt_free(store_in_subset_file_data.current_outputfilename);
gt_free(store_in_subset_file_data.subset_files);
gt_free(store_in_subset_file_data.subset_filenames);
gt_free(store_in_subset_file_data.subset_file_sa_counter);
return had_err;
}
static int gthfilestat_process_files(GthFileStatInfo *file_stat_info,
const GthPlugins *plugins, GtError *err)
{
GthSACollection *sa_collection;
GthStat *stat;
GthInput *input;
GthPGLCollection *pgl_collection = NULL;
int had_err = 0;
gt_error_check(err);
/* initialization */
sa_collection = gth_sa_collection_new(GTH_DC_NONE);
input = gth_input_new(plugins->file_preprocessor, plugins->seq_con_new);
stat = gth_stat_new();
gth_stat_enable_sa_stats(stat);
gth_stat_enable_gthfilestat_mode(stat);
if (file_stat_info->showverbose)
file_stat_info->showverbose("process all intermediate output files");
/* build tree of alignments from intermediate files */
had_err = gth_build_sa_collection(sa_collection, input,
file_stat_info->consensusfiles,
file_stat_info->sa_filter, stat,
file_stat_info->showverbose, err);
if (!had_err && gth_sa_collection_contains_sa(sa_collection)) {
/* compute PGLs */
pgl_collection = gth_pgl_collection_new(sa_collection, false);
/* save statistics for PGLs */
gth_stat_increase_numofPGLs_stored(stat,
gth_pgl_collection_size(pgl_collection));
}
/* output statistics */
gth_stat_show(stat, false, false, NULL);
/* free */
gth_sa_collection_delete(sa_collection);
gth_input_delete_complete(input);
gth_stat_delete(stat);
gth_pgl_collection_delete(pgl_collection);
return had_err;
}
