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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 "bamUtils.h"
int bam_reg2bin(int beg, int end)
{
--end;
if (beg>>14 == end>>14) return ((1<<15)-1)/7 + (beg>>14);
if (beg>>17 == end>>17) return ((1<<12)-1)/7 + (beg>>17);
if (beg>>20 == end>>20) return ((1<<9)-1)/7 + (beg>>20);
if (beg>>23 == end>>23) return ((1<<6)-1)/7 + (beg>>23);
if (beg>>26 == end>>26) return ((1<<3)-1)/7 + (beg>>26);
return 0;
}
int cigarop2int(char op) {
int cigar_op_mask = 0;
switch ( op ) {
case 'M':
cigar_op_mask = BAM_CMATCH;
break;
case 'I':
cigar_op_mask = BAM_CINS;
break;
case 'D':
cigar_op_mask = BAM_CDEL;
break;
case 'N':
cigar_op_mask = BAM_CREF_SKIP;
break;
case 'S':
cigar_op_mask = BAM_CSOFT_CLIP;
break;
case 'H':
cigar_op_mask = BAM_CHARD_CLIP;
break;
case 'P':
cigar_op_mask = BAM_CPAD;
break;
case '=':
cigar_op_mask = BAM_CEQUAL;
break;
case 'X':
cigar_op_mask = BAM_CDIFF;
break;
case 'B':
cigar_op_mask = BAM_CBACK;
break;
default:
std::cerr << "Wrong cigar operator" << std::endl;
}
return cigar_op_mask;
}
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