/usr/include/io_lib/translate.h is in libstaden-read-dev 1.14.6-2.
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* Copyright (c) 2007 Genome Research Ltd.
* Author(s): James Bonfield
*
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
* 1. Redistributions of source code must retain the above copyright notice,
* this list of conditions and the following disclaimer.
*
* 2. Redistributions in binary form must reproduce the above
* copyright notice, this list of conditions and the following
* disclaimer in the documentation and/or other materials provided
* with the distribution.
*
* 3. Neither the names Genome Research Ltd and Wellcome Trust Sanger
* Institute nor the names of its contributors may be used to endorse
* or promote products derived from this software without specific
* prior written permission.
*
* THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS
* IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED
* TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
* PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH
* LTD OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
* SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
* LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
* DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
* THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
* (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
* OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
*/
/*
* Author(s): James Bonfield, Mark Jordan
*
* Copyright (c) 1995-1996, 1998, 2002-2003 MEDICAL RESEARCH COUNCIL
* All rights reserved
*
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
* 1 Redistributions of source code must retain the above copyright notice,
* this list of conditions and the following disclaimer.
*
* 2 Redistributions in binary form must reproduce the above copyright
* notice, this list of conditions and the following disclaimer in
* the documentation and/or other materials provided with the
* distribution.
*
* 3 Neither the name of the MEDICAL RESEARCH COUNCIL, THE LABORATORY OF
* MOLECULAR BIOLOGY nor the names of its contributors may be used
* to endorse or promote products derived from this software without
* specific prior written permission.
*
* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
* AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
* IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
* ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
* LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
* CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
* SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
* INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
* CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
* ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
* POSSIBILITY OF SUCH DAMAGE.
*/
/*
* Copyright (c) Medical Research Council 1994. All rights reserved.
*
* Permission to use, copy, modify and distribute this software and its
* documentation for any purpose is hereby granted without fee, provided that
* this copyright and notice appears in all copies.
*
* This file was written by James Bonfield, Simon Dear, Rodger Staden,
* as part of the Staden Package at the MRC Laboratory of Molecular
* Biology, Hills Road, Cambridge, CB2 2QH, United Kingdom.
*
* MRC disclaims all warranties with regard to this software.
*/
#ifndef _TRANSLATE_H_
#define _TRANSLATE_H_
#include "io_lib/scf.h"
#include "io_lib/Read.h"
#include "io_lib/expFileIO.h"
#ifdef __cplusplus
extern "C" {
#endif
/*
* Translates an Scf structure into a Read structure.
* The Scf structure is left unchanged.
*
* Returns:
* A pointer to an allocated Read structure upon success.
* NULLRead upon failure.
*/
Read *scf2read(Scf *scf);
/*
* Translates a Read structure into a Scf structure.
* The Read structure is left unchanged.
*
* Returns:
* A pointer to an allocated Scf structure upon success.
* NULL upon failure.
*/
Scf *read2scf(Read *read);
/*
* Translates a Read structure and an Experiment file.
* The Read structure is left unchanged.
*
* Returns:
* A pointer to an allocated Exp_info structure upon success.
* NULL upon failure (FIXME: need to free memory here)
*/
Exp_info *read2exp(Read *read, char *EN);
/*
* Controls the use of the SQ and ON lines when loading an experiment file.
* The default (value&1 == 1) is to load these into the Read structure.
* With value&1 == 0 we load the sequence directly from the trace file
* (LT line).
* value&2 controls whether to use the SL/SR fields when setting the cutoff.
* value&2 == 0 implies to do so, and value&2 == 2 implies to not.
*
* Returns:
* The old value.
*/
int read_experiment_redirect(int value);
/*
* Takes an original read structure and a set of edit change arrays and
* produces a new base position array incorporating all the edits. For
* insertions, interpolation is used to derive a suitable sample position.
*
* INPUTS:
*
* Read *r = The original unedited read structure
* int Comp = 0=Normal sequence, 1=Complemented sequence
* int Ned = Length of edited arrays to follow
* char *edBases = Sequence of base characters incorporating ins/del edits
* uint_2 *edPos = Corresponding original base numbers, 0 indicates an
* insertion. Base numbers start at 1.
*
* OUTPUTS:
*
* This array is assumed to be empty with an allocated length of Ned elements.
*
* uint_2* basePos = Base positions in samples
*/
void read_update_base_positions( Read *r, int Comp, int Ned, char *edBases,
int_2 *edPos, uint_2 *basePos );
/*
* Takes a set of edit change arrays and produces a new set of confidence
* arrays incorporating all the edits.
*
* INPUTS:
*
* int Ned = Length of edited arrays to follow
* char* edBases = Sequence of base characters incorporating ins/del edits
* int1* edConf = Corresponding confidence values, 100 for insertions
*
*
* OUTPUTS:
*
* These output arrays are assumed to be empty with an allocated length
* of Ned elements each. The names and types are identical to the same
* elements in the Read structure.
*
* char* prob_A = Base confidence A
* char* prob_C = Base confidence C
* char* prob_G = Base confidence G
* char* prob_T = Base confidence T
*
*/
void read_update_confidence_values( int Ned, char* edBases, int1* edConf,
char* prob_A, char* prob_C, char* prob_G, char* prob_T );
/*
* Translates an experiment file to a Read structure.
* The Exp_Info structure is left unchanged.
*
* Returns:
* A pointer to an allocated Read structure upon success.
* NULLRead upon failure.
*/
Read *exp2read(Exp_info *e, char *fn);
#ifdef __cplusplus
}
#endif
#endif
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