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/** Testing handling of compressed alignment strings
*/
/*****************************************************************************
*****************************************************************************
* *
* Copyright (C) 2013 - 2014 Genome Research Ltd. *
* *
* Author: Hannes Ponstingl (hp3@sanger.ac.uk) *
* *
* This file is part of SMALT. *
* *
* SMALT 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 <stdio.h>
#include <stdlib.h>
#include "elib.h"
#include "diffstr.h"
enum {
DIFFSTR_BLKSZ = 64,
CIGAR_MAXLEN = 256,
};
int main(int argc, char *argv[])
{
int errcode = ERRCODE_SUCCESS;
char *cigstr;
char cigarout[CIGAR_MAXLEN];
const unsigned char isSAMCIGAR = 1;
const char isSoftClipped = 1;
int clip_start, clip_end, nchar=0;
DiffStr *dfsp, *dfsbfp;
ErrMsg *errmsgp = 0;
if (argc != 2) {
printf("usage: %s <GIGAR string>\n", argv[0]);
exit(1);
}
cigstr = argv[1];
ERRMSG_CREATE(errmsgp);
dfsp = diffStrCreate(DIFFSTR_BLKSZ);
if (dfsp == NULL)
ERRMSGNO(errmsgp, ERRCODE_NOMEM);
dfsbfp = diffStrCreate(DIFFSTR_BLKSZ);
if (dfsbfp == NULL)
ERRMSGNO(errmsgp, ERRCODE_NOMEM);
if ((errcode = diffStrParseSimul(dfsp, &clip_start, &clip_end, isSAMCIGAR, cigstr)))
ERRMSGNO(errmsgp, errcode);
printf("CIGAR_RAW ");
if ((errcode = diffStrPrintf(stdout, dfsp->dstrp, DIFFSTRFORM_RAW,
clip_start, clip_end, isSoftClipped)))
ERRMSGNO(errmsgp, errcode);
printf("CIGAR_SSAHA ");
if ((errcode = diffStrPrintf(stdout, dfsp->dstrp, DIFFSTRFORM_CIGNORM,
clip_start, clip_end, isSoftClipped)))
ERRMSGNO(errmsgp, errcode);
printf("\nCIGAR_EXT ");
if ((errcode = diffStrPrintf(stdout, dfsp->dstrp, DIFFSTRFORM_CIGEXT,
clip_start, clip_end, isSoftClipped)))
ERRMSGNO(errmsgp, errcode);
printf("\nCIGAR_SAM ");
if ((errcode = diffStrPrintfStr(cigarout, &nchar, dfsp->dstrp, DIFFSTRFORM_CIGEXT,
clip_start, clip_end, isSoftClipped)))
ERRMSGNO(errmsgp, errcode);
printf("%s\nCIGAR_SAMX ", cigarout);
if ((errcode = diffStrPrintfStr(cigarout, &nchar, dfsp->dstrp, DIFFSTRFORM_CIGEXT_XMISMATCH,
clip_start, clip_end, isSoftClipped)))
ERRMSGNO(errmsgp, errcode);
printf("%s\n", cigarout);
diffStrDelete(dfsp);
ERRMSG_END(errmsgp);
exit(errcode);
}
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