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/******************************************************************************
* *
* Copyright © 2010-2013 -- IRB/INSERM *
* (Institut de Recherches en Biothérapie / *
* Institut National de la Santé et de la Recherche *
* Médicale) *
* LIFL/INRIA *
* (Laboratoire d'Informatique Fondamentale de *
* Lille / Institut National de Recherche en *
* Informatique et Automatique) *
* LIRMM/CNRS *
* (Laboratoire d'Informatique, de Robotique et de *
* Microélectronique de Montpellier / *
* Centre National de la Recherche Scientifique) *
* LITIS *
* (Laboratoire d'Informatique, du Traitement de *
* l'Information et des Systèmes). *
* *
* *
* Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe@lirmm.fr> *
* Mikaël SALSON <mikael.salson@lifl.fr> *
* Thierry LECROQ <thierry.lecroq@univ-rouen.fr> *
* Martine LÉONARD <Martine.Leonard@univ-rouen.fr> *
* Éric RIVALS <eric.rivals@lirmm.fr> *
* *
* Programmeurs *
* /Progammers: Nicolas PHILIPPE <nicolas.philippe@lirmm.fr> *
* Mikaël SALSON <mikael.salson@lifl.fr> *
* Alban MANCHERON <alban.mancheron@lirmm.fr> *
* *
* Contact: Gk-Arrays list <crac-gkarrays@lists.gforge.inria.fr> *
* *
* ------------------------------------------------------------------------- *
* *
* Ce fichier fait partie de la librairie Gk-arrays. *
* *
* La librairie Gk-arrays a pour objectif d'indexer de grands ensembles de *
* lectures de séquences issues du séquençage haut-débit. *
* *
* Ce logiciel est régi par la licence CeCILL-C soumise au droit français et *
* respectant les principes de diffusion des logiciels libres. Vous pouvez *
* utiliser, modifier et/ou redistribuer ce programme sous les conditions de *
* la licence CeCILL-C telle que diffusée par le CEA, le CNRS et l'INRIA sur *
* le site "http://www.cecill.info". *
* *
* En contrepartie de l'accessibilité au code source et des droits de copie, *
* de modification et de redistribution accordés par cette licence, il n'est *
* offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, *
* seule une responsabilité restreinte pèse sur l'auteur du programme, le *
* titulaire des droits patrimoniaux et les concédants successifs. *
* *
* À cet égard l'attention de l'utilisateur est attirée sur les risques *
* associés au chargement, à l'utilisation, à la modification et/ou au *
* développement et à la reproduction du logiciel par l'utilisateur étant *
* donné sa spécificité de logiciel libre, qui peut le rendre complexe à *
* manipuler et qui le réserve donc à des développeurs et des professionnels *
* avertis possédant des connaissances informatiques approfondies. Les *
* utilisateurs sont donc invités à charger et tester l'adéquation du *
* logiciel à leurs besoins dans des conditions permettant d'assurer la *
* sécurité de leurs systêmes et ou de leurs données et, plus généralement, *
* à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. *
* *
* Le fait que vous puissiez accéder à cet en-tête signifie que vous avez *
* pris connaissance de la licence CeCILL-C, et que vous en avez accepté les *
* termes. *
* *
* ------------------------------------------------------------------------- *
* *
* This File is part of the Gk-arrays library. *
* *
* The Gk-arrays library aims at indexing k-factors from a huge set of *
* sequencing reads. *
* *
* This software is governed by the CeCILL-C license under French law and *
* abiding by the rules of distribution of free software. You can use, *
* modify and/ or redistribute the software under the terms of the CeCILL-C *
* license as circulated by CEA, CNRS and INRIA at the following URL *
* "http://www.cecill.info". *
* *
* As a counterpart to the access to the source code and rights to copy, *
* modify and redistribute granted by the license, users are provided only *
* with a limited warranty and the software's author, the holder of the *
* economic rights, and the successive licensors have only limited *
* liability. *
* *
* In this respect, the user's attention is drawn to the risks associated *
* with loading, using, modifying and/or developing or reproducing the *
* software by the user in light of its specific status of free software, *
* that may mean that it is complicated to manipulate, and that also *
* therefore means that it is reserved for developers and experienced *
* professionals having in-depth computer knowledge. Users are therefore *
* encouraged to load and test the software's suitability as regards their *
* requirements in conditions enabling the security of their systems and/or *
* data to be ensured and, more generally, to use and operate it in the same *
* conditions as regards security. *
* *
* The fact that you are presently reading this means that you have had *
* knowledge of the CeCILL-C license and that you accept its terms. *
* *
******************************************************************************/
#undef NDEBUG
#include "checkConsistency.h"
#include <gkArrays.h>
#include <utils.h>
#include <cstring>
#include <iostream>
#include "testing.h"
using namespace std;
using namespace gkarrays;
void checkConsistency(const char *file, uint k, uint read_length, bool use_bitvector,
bool stranded, uint nb_threads) {
#undef TAP_ADDITIONAL_INFOS
#define TAP_ADDITIONAL_INFOS "file = " << file << ", read_length = " << read_length <<", k = " << k <<", stranded = " << stranded << ", bit_vector = " << use_bitvector <<", nb_threads = " << nb_threads
RECORD_TAP_TEST(TEST_SORTED_STRING, "Check that strings are sorted in gkSA");
RECORD_TAP_TEST(TEST_GKCFA, "Check GkCFA values");
RECORD_TAP_TEST(TEST_GKISA, "Check GkIFA values");
RECORD_TAP_TEST(TEST_GKCFALENGTH, "Check GkCFA length");
RECORD_TAP_TEST(TEST_READING_READS, "Compare reading sequences from file and retrieving them from the structure");
RECORD_TAP_TEST(TEST_READ_LENGTH, "Check read length");
RECORD_TAP_TEST(TEST_EPOTN, "Check endPosOfTagNum");
RECORD_TAP_TEST(TEST_SPOTN, "Check startPosOfTagNum");
RECORD_TAP_TEST(TEST_SQPOTN, "Check startQPosOfTagNum");
RECORD_TAP_TEST(TEST_SUPPORT_LENGTH, "Check support length");
RECORD_TAP_TEST(TEST_TAGNUM, "Check read number");
RECORD_TAP_TEST(TEST_TAGPOS, "Check tag position computation");
RECORD_TAP_TEST(TEST_NBOCCS_TAGS, "Check number of occurrences among reads");
RECORD_TAP_TEST(TEST_SUPPORT, "Check support");
RECORD_TAP_TEST(TEST_KMER, "Check k-mer extraction from the structure");
RECORD_TAP_TEST(TEST_FIND_MYSELF, "Check I find myself among the occurrences");
RECORD_TAP_TEST(TEST_NBTAGS_FOUND, "Check number of occurrences among reads (with multiplicity");
RECORD_TAP_TEST(TEST_PPOSITION, "Check isPposition is true when needed");
RECORD_TAP_TEST(TEST_PPOS_TO_QPOS, "Check conversion of Pposition in Qposition");
RECORD_TAP_TEST(TEST_NOT_PPOSITION, "Check isPposition is false when needed");
RECORD_TAP_TEST(TEST_NB_READS, "Check number of reads");
gkArrays *gk = new gkArrays((char *)file, k, use_bitvector, read_length, stranded,
nb_threads);
readIterator *it = gk->getReads()->begin();
uint nb_reads = 0;
uint current_length;
uintSA cumulative_length = 0;
uintSA cumulativePpos = 0;
// Testing GkISA, GkSA and GkCFPS
char *previous_factor = gk->getTextFactor(gk->getGkSA(0), k);
uintSA nb_distinct_factors = 0;
uintSA nb_factors_current_bucket = 1;
for (uintSA i = 1; i < gk->getGkSALength(); i++) {
char *current_factor = gk->getTextFactor(gk->getGkSA(i), k);
int compar = strcmp(previous_factor, current_factor);
TAP_TEST(compar <= 0, TEST_SORTED_STRING,
"i = " << i << ", gkSA[i] = " << gk->getGkSA(i) << ", we should have "
<< previous_factor << "<=" << current_factor);
if (compar < 0) {
TAP_TEST(gk->getGkCFA(nb_distinct_factors) == nb_factors_current_bucket,
TEST_GKCFA,
"i = " << i << ", gkSA[i] = " << gk->getGkSA(i) << ", we should have "
<< gk->getGkCFA(nb_distinct_factors) << "=="
<< nb_factors_current_bucket);
nb_distinct_factors++;
nb_factors_current_bucket = 1;
} else
nb_factors_current_bucket++;
TAP_TEST(gk->getGkISA(gk->convertPposToQpos(gk->getGkSA(i))) == nb_distinct_factors,
TEST_GKISA,
"gk->getGkISA(gk->convertPposToQpos(gk->getGkSA(i))) = " << gk->getGkISA(gk->convertPposToQpos(gk->getGkSA(i))) << ", nb_distinct_factors = " << nb_distinct_factors);
delete [] previous_factor;
previous_factor = current_factor;
}
TAP_TEST(gk->getGkCFALength() == nb_distinct_factors+1,
TEST_GKCFALENGTH,
"|GkCFA| = " << gk->getGkCFALength() << ", nb_distinct_factors = " << nb_distinct_factors);
while (!it->isFinished()) {
char *current_read = gk->getTag(nb_reads);
char *it_read = it->getSequence();
current_length = gk->getTagLength(nb_reads);
if (read_length) {
dnaFiltration(it_read, read_length);
TAP_TEST(strncmp(current_read, it_read, read_length) == 0,
TEST_READING_READS,
"Read n°" << nb_reads << " read " << it_read
<< ", in GkArrays: " << current_read);
TAP_TEST(current_length == read_length,
TEST_READ_LENGTH,
"read_length (parameter) = " << read_length
<< " current_length (given by gkA) = "
<< current_length);
} else {
dnaFiltration(it_read, strlen(it_read));
TAP_TEST(strcmp(current_read, it_read) == 0,
TEST_READING_READS,
"current_read = " << current_read <<", it->getSequence() = " << it_read);
TAP_TEST(strlen(current_read) == current_length,
TEST_READ_LENGTH,
"length of read is " << strlen(current_read) <<", should have been "
<< current_length << " (according to gkA)");
}
TAP_TEST(gk->getEndPosOfTagNum(nb_reads) == cumulative_length + current_length - 1,
TEST_EPOTN,
"nb_reads = " << nb_reads
<< ", gk->getEndPosOfTagNum(nb_reads) = "
<< gk->getEndPosOfTagNum(nb_reads)
<< "cumulative_length + current_length - 1 = "
<< cumulative_length + current_length - 1);
TAP_TEST(gk->getStartPosOfTagNum(nb_reads) == cumulative_length,
TEST_SPOTN,
"nb_reads = " << nb_reads
<< ", gk->getStartPosOfTagNum(nb_reads) = "
<< gk->getStartPosOfTagNum(nb_reads)
<< "cumulative_length = " << cumulative_length);
TAP_TEST(gk->getStartQPosOfTagNum(nb_reads) == cumulativePpos,
TEST_SQPOTN,
"nb_reads = " << nb_reads
<< ", gk->getStartQPosOfTagNum(nb_reads) = "
<< gk->getStartQPosOfTagNum(nb_reads)
<< "cumulativePpos = " << cumulativePpos);
TAP_TEST(gk->getSupportLength(nb_reads) == current_length - k + 1,
TEST_SUPPORT_LENGTH,
"nb_reads = " << nb_reads << " support length: "
<< gk->getSupportLength(nb_reads) << ", current_length - k + 1 = "
<< current_length - k + 1);
for (uint i = 0; i < current_length; i++) {
for (uint j = 1; j < current_length - i; j++) {
char *factor = gk->getTagFactor(nb_reads, i, j);
assert(strncmp(factor, ¤t_read[i], j) == 0);
delete [] factor;
}
}
for (uint i = 0; i < current_length; i++) {
std::pair<uint, uint> tagNumPos = gk->getTagNumAndPosFromAbsolutePos(cumulative_length + i);
TAP_TEST(gk->getTagNum(cumulative_length + i) == nb_reads,
TEST_TAGNUM,
"cumulative_length = " << cumulative_length << ", i = " << i <<", nb_reads = " << nb_reads <<", gk->getTagNum(cumulative_length + i) = " << gk->getTagNum(cumulative_length + i));
TAP_TEST(i == tagNumPos.second,
TEST_TAGPOS,
"i = " << i <<", tagNumPos.second = " << tagNumPos.second);
TAP_TEST(nb_reads == tagNumPos.first, TEST_TAGNUM,
"nb_reads = " << nb_reads <<", tagNumPos.first = " << tagNumPos.first);
}
uint *support = gk->getSupport(nb_reads);
for (uint i = 0; i < current_length - k + 1; i++) {
uint nb_tags = gk->getNbTagsWithFactor(nb_reads, i, false);
char *kmer = gk->getTagFactor(nb_reads, i, k);
uint *tags_num = gk->getTagNumWithFactor(nb_reads, i);
uint nb_occs = gk->getNbTagsWithFactor(nb_reads, i, true);
pair<uint, uint> *tags = gk->getTagsWithFactor(nb_reads, i);
bool found_me = false;
uint nb_found = 0;
TAP_TEST(nb_occs >= nb_tags, TEST_NBOCCS_TAGS,
"i = " << i << "nb_occs = " << nb_occs <<", nb_tags = " << nb_tags);
TAP_TEST(support[i] == nb_occs, TEST_SUPPORT,
"i = " << i << ", support[i] = " << support[i]
<< ", nb_occs = " << nb_occs);
for (uint j = 0; j < nb_occs; j++) {
if (tags[j].first == nb_reads)
found_me = true;
// Search this tag in tags_num
uint p;
for (p = 0; p < nb_tags && tags_num[p] != tags[j].first ; p++) {}
if (p < nb_tags) {
// Count the read found
nb_found++;
// And change it in the array so that we don't count it twice.
tags_num[p] = ~0;
}
char *current_kmer = gk->getTagFactor(tags[j].first, tags[j].second, k);
TAP_TEST(strcmp(current_kmer, kmer) == 0,
TEST_KMER,
"current_kmer = " << current_kmer << ", kmer = " << kmer << ", j = " << j << ", nb_occs = " << nb_occs);
delete [] current_kmer;
}
TAP_TEST(found_me, TEST_FIND_MYSELF,
"i = " << i);
TAP_TEST(nb_found == nb_tags,
TEST_NBTAGS_FOUND,
"nb_found = " << nb_found <<", nb_tags = " << nb_tags );
TAP_TEST(gk->isPposition(cumulative_length + i),
TEST_PPOSITION,
"i = " << i <<", cumulative_length = " << cumulative_length);
TAP_TEST(gk->convertPposToQpos(cumulative_length + i) == cumulativePpos + i,
TEST_PPOS_TO_QPOS,
"i = " << i <<", cumulative_length = " << cumulative_length
<<", cumulativePpos = " << cumulativePpos <<
"gk->convertPposToQpos(cumulative_length + i) = "
<< gk->convertPposToQpos(cumulative_length + i));
delete [] kmer;
free(tags_num);
delete [] tags;
}
delete [] support;
for (uint i = current_length - k + 1; i < current_length; i++) {
TAP_TEST(! gk->isPposition(cumulative_length+i), TEST_NOT_PPOSITION,
"cumulative_length = " << cumulative_length << ", i = " << i);
}
cumulative_length += current_length;
cumulativePpos += current_length - k + 1;
nb_reads++;
++(*it);
delete [] current_read;
}
delete it;
TAP_TEST(nb_reads == gk->getNbTags(),
TEST_NB_READS,
"nb_reads = " << nb_reads <<", gk->getNbTags() = "
<< gk->getNbTags());
delete gk;
}
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