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/******************************************************************************
* Copyright © 2009-2016 -- LIRMM/CNRS *
* (Laboratoire d'Informatique, de Robotique et de *
* Microélectronique de Montpellier / *
* Centre National de la Recherche Scientifique) *
* LIFL/INRIA *
* (Laboratoire d'Informatique Fondamentale de *
* Lille / Institut National de Recherche en *
* Informatique et Automatique) *
* LITIS *
* (Laboratoire d'Informatique, du Traitement de *
* l'Information et des Systèmes). *
* *
* Copyright © 2011-2016 -- IRB/INSERM *
* (Institut de Recherches en Biothérapie / *
* Institut National de la Santé et de la Recherche *
* Médicale). *
* *
* Copyright © 2015-2016 -- AxLR/SATT *
* (Lanquedoc Roussilon / *
* Societe d'Acceleration de Transfert de *
* Technologie). *
* *
* Programmeurs/Progammers: *
* Nicolas PHILIPPE <nphilippe.resear@gmail.com> *
* Mikaël SALSON <mikael.salson@lifl.fr> *
* Jérôme Audoux <jerome.audoux@gmail.com> *
* with additional contribution for the packaging of: *
* Alban MANCHERON <alban.mancheron@lirmm.fr> *
* *
* Contact: CRAC list <crac-bugs@lists.gforge.inria.fr> *
* Paper: CRAC: An integrated RNA-Seq read analysis *
* Philippe N., Salson M., Commes T., Rivals E. *
* Genome Biology 2013; 14:R30. *
* *
* ------------------------------------------------------------------------- *
* *
* This File is part of the CRAC program. *
* *
* This program is free software: you can redistribute it and/or modify *
* it under the terms of the GNU General Public License as published by *
* the Free Software Foundation, either version 3 of the License, or (at *
* your option) any later version. This program is distributed in the *
* hope that it will be useful, but WITHOUT ANY WARRANTY; without even *
* the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR *
* PURPOSE. See the GNU General Public License for more details. You *
* should have received a copy of the GNU General Public License along *
* with this program. If not, see <http://www.gnu.org/licenses/>. *
* *
******************************************************************************/
#include "Parameters.h"
#include "const.h"
using namespace std;
Parameters::Parameters(uint threshold,
uint max_nb_located_occs,
uint max_splice_length,
uint max_bio_ins_del,
uint max_localisation_duplication,
uint min_localisation_duplication,
float percent_min_unique_repetition,
float percent_min_duplicate,
uint min_occ_repetition,
float percent_support_variation_almost_normal,
float p_value_variation_biological,
float score_intra_ambiguous,
float score_inter_ambiguous,
uint max_bases_randomly_matched,
uint min_bases_before_break,
uint max_bases_retrieved,
int max_extension_length,
uint support_score_window_length,
uint nb_bases_substracted_low_average,
uint nb_positions_check_ones,
uint nb_tags_info_stored,
uint nb_threads,
float min_support_no_cover,
float max_support_out_no_cover,
float max_ambiguous_average_high,
float min_perc_ones_inside,
float min_ratio_support_fall,
float max_nb_overlapping_breaks,
float percent_min_single,
float percent_min_multiple,
bool deep_snp_search,
uint number_nucleotides_snp_comparison,
bool detailed_sam,
uint max_verynice_merge,
bool stringent_chimera,
uint stringent_chimera_max_number_of_merges,
float min_stringent_chimera_score,
bool no_ambiguity,
uint treat_multiple,
bool show_progressbar,
uint reads_length,
uint max_mapping_comparison,
float percent_max_loc_variation,
uint max_good_paired_reads,
float percent_very_good_paired,
bool use_x_in_cigar,
float percent_min_chunck,
paired_end_orientation_t paired_end_orientation,
float min_chimera_score
):
threshold(threshold)
,max_nb_located_occs(max_nb_located_occs)
,max_splice_length(max_splice_length)
,max_bio_ins_del(max_bio_ins_del)
,max_localisation_duplication(max_localisation_duplication)
,min_localisation_duplication(min_localisation_duplication)
,percent_min_unique_repetition(percent_min_unique_repetition)
,percent_min_duplicate(percent_min_duplicate)
,min_occ_repetition(min_occ_repetition)
,percent_support_variation_almost_normal(percent_support_variation_almost_normal)
,p_value_variation_biological(p_value_variation_biological)
,score_intra_ambiguous(score_intra_ambiguous)
,score_inter_ambiguous(score_inter_ambiguous)
,max_bases_randomly_matched(max_bases_randomly_matched)
,min_bases_before_break(min_bases_before_break)
,max_bases_retrieved(max_bases_retrieved)
,max_extension_length(max_extension_length)
,support_score_window_length(support_score_window_length)
,nb_bases_substracted_low_average(nb_bases_substracted_low_average)
,nb_positions_check_ones(nb_positions_check_ones)
,nb_tags_info_stored(nb_tags_info_stored)
,nb_threads(nb_threads)
,min_support_no_cover(min_support_no_cover)
,max_support_out_no_cover(max_support_out_no_cover)
,max_ambiguous_average_high(max_ambiguous_average_high)
,min_perc_ones_inside(min_perc_ones_inside)
,min_ratio_support_fall(min_ratio_support_fall)
,max_nb_overlapping_breaks(max_nb_overlapping_breaks)
,percent_min_single(percent_min_single)
,percent_min_multiple(percent_min_multiple)
,deep_snp_search(deep_snp_search)
,number_nucleotides_snp_comparison(number_nucleotides_snp_comparison)
,detailed_sam(detailed_sam)
,max_verynice_merge(max_verynice_merge)
,stringent_chimera(stringent_chimera)
,stringent_chimera_max_number_of_merges(stringent_chimera_max_number_of_merges)
,min_stringent_chimera_score(min_stringent_chimera_score)
,no_ambiguity(no_ambiguity)
,treat_multiple(treat_multiple)
,show_progressbar(show_progressbar)
,reads_length(reads_length)
,max_mapping_comparison(max_mapping_comparison)
,percent_max_loc_variation(percent_max_loc_variation)
,max_good_paired_reads(max_good_paired_reads)
,percent_very_good_paired(percent_very_good_paired)
,use_x_in_cigar(use_x_in_cigar)
,percent_min_chunck(percent_min_chunck)
,paired_end_orientation(paired_end_orientation)
,min_chimera_score(min_chimera_score)
{
if (max_nb_located_occs < min_occ_repetition){
cerr << "max_nb_located_occs must be greater than min_loc_repetition" << endl << endl;
exit(2);
}
if (reads_length > 0 && reads_length < threshold) {
cerr << "Minimum read length (-m option) should be greater than k length (-k option)." << endl << endl;
exit(2);
}
}
void Parameters::init() {
min_break_length = (uint) (MIN_BREAK_LENGTH*threshold);
}
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