1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51
|
/* BaitFisher (version 1.2.7) a program for designing DNA target enrichment baits
* Copyright 2013-2016 by Christoph Mayer
*
* This source file is part of the BaitFisher-package.
*
* 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 BaitFisher. If not, see <http://www.gnu.org/licenses/>.
*
*
* For any enquiries send an Email to Christoph Mayer
* c.mayer.zfmk@uni-bonn.de
*
* When publishing work that is based on the results please cite:
* Mayer et al. 2016: BaitFisher: A software package for multi-species target DNA enrichment probe design
*
*/
#include "faststring2.h"
#include "CSequences2.h"
#include "CSequence_Mol2_1.h"
faststring extract_taxon_name(faststring, char, unsigned short);
faststring extract_gene_name(faststring, char, unsigned short);
void read_alignment_sequence_of_species2(faststring, faststring,
CSequence_Mol*&, CSequences2*&,
unsigned&, char, unsigned short);
extern int DEBUG_COUNT_NEW_CALLS_FEATURE_ALIGNMENT;
extern int DEBUG_COUNT_NEW_CALLS_CBAIT_REGION_INFORMATION;
extern int DEBUG_COUNT_NEW_CALLS_CSEQUENCE_LOCI_CLUSTER_COLLECTION;
extern int DEBUG_COUNT_NEW_CALLS_MSA;
extern int DEBUG_COUNT_NEW_ALIGNMENT_FROM_FILE;
extern int DEBUG_COUNT_DELETE_CALLS_FEATURE_ALIGNMENT;
extern int DEBUG_COUNT_DELETE_CALLS_CBAIT_REGION_INFORMATION;
extern int DEBUG_COUNT_DELETE_CALLS_CSEQUENCE_LOCI_CLUSTER_COLLECTION;
extern int DEBUG_COUNT_DELETE_CALLS_MSA;
extern int DEBUG_COUNT_DELETE_ALIGNMENT_FROM_FILE;
|