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/* Philip T.L.C. Clausen Jan 2017 plan@dtu.dk */
/*
* Copyright (c) 2017, Philip Clausen, Technical University of Denmark
* All rights reserved.
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*/
#include "compdna.h"
#include "qc.h"
#include "qseqs.h"
/* pointers determining how to deliver the input */
extern void (*printFsa_ptr)(Qseqs*, Qseqs*, Qseqs*, CompDNA*, FILE*);
extern void (*printFsa_pair_ptr)(Qseqs*, Qseqs*, Qseqs*, Qseqs*, Qseqs*, Qseqs*, CompDNA*, FILE*);
unsigned hardmask(unsigned char *seq, unsigned char *qual, int len, const int phredScale, int minQ);
int gcontent(unsigned char *seq, int len);
double qcstat(const unsigned char *seq, const unsigned char *qual, const int len, const double *prob, const int hardmaskQ, int *GC, int *NS, int *EQ);
int fsastat(unsigned char *seq, int len, const int minlen, const int maxlen, int *START, int *END, QCstat *qcreport);
int phredStat(unsigned char *seq, unsigned char *qual, int len, const double *prob, const int minPhred, const int minQ, const int hardmaskQ, const int fiveClip, const int threeClip, const int minlen, const int maxlen, int *START, int *END, QCstat *qcreport);
long unsigned run_input(char **inputfiles, int fileCount, int minPhred, int hardmaskQ, int minQ, int fiveClip, int threeClip, int minlen, int maxlen, char *trans, const double *prob, QCstat *qcreport, FILE *out);
long unsigned run_input_PE(char **inputfiles, int fileCount, int minPhred, int hardmaskQ, int minQ, int fiveClip, int threeClip, int minlen, int maxlen, char *trans, const double *prob, QCstat *qcreport, FILE *out);
long unsigned run_input_INT(char **inputfiles, int fileCount, int minPhred, int hardmaskQ, int minQ, int fiveClip, int threeClip, int minlen, int maxlen, char *trans, const double *prob, QCstat *qcreport, FILE *out);
void bootFsa(Qseqs *header, Qseqs *qseq, Qseqs *qual, CompDNA *compressor, FILE *out);
void printFsa(Qseqs *header, Qseqs *qseq, Qseqs *qual, CompDNA *compressor, FILE *out);
void printFsa_pair(Qseqs *header, Qseqs *qseq, Qseqs *qual, Qseqs *header_r, Qseqs *qseq_r, Qseqs *qual_r, CompDNA *compressor, FILE *out);
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