/* PANDAseq -- Assemble paired FASTQ Illumina reads and strip the region between amplification primers.

Copyright (C) 2014 Andre Masella

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 "config.h"

#include "pandaseq.h"

#include "misc.h"

int main(

int argc,

char **argv) {

MANAGED_STACK(PandaNextSeq,

next);

PandaAssembler control_assembler;

PandaAssembler experimental_assembler;

PandaArgsFastq data = panda_args_fastq_new();

bool result;

bool suppress_quality_diffs;

if (!panda_diff_parse_args(argv, argc, panda_stdargs, panda_stdargs_length, panda_args_fastq_args, panda_args_fastq_args_length, (PandaTweakGeneral) panda_args_fastq_tweak, (PandaOpener) panda_args_fastq_opener, (PandaSetup) panda_args_fastq_setup, data, &control_assembler, &experimental_assembler, &next, &next_data, &next_destroy, &suppress_quality_diffs)) {

panda_args_fastq_free(data);

DESTROY_STACK(next);

return 1;

}

result = panda_diff(next, next_data, (PandaAssemble) panda_assembler_assemble, control_assembler, (PandaAssemble) panda_assembler_assemble, experimental_assembler, suppress_quality_diffs);

DESTROY_STACK(next);

panda_assembler_unref(control_assembler);

panda_assembler_unref(experimental_assembler);

panda_args_fastq_free(data);

return result ? 0 : 1;

}