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#include <stdio.h>
#include <unistd.h>
#include <fstream>
#define ulong4 uint32_t
#include "mummergpu.h"
char * OPT_reffilename = NULL;
char * OPT_qryfilename = NULL;
char * OPT_dotfilename = NULL;
char * OPT_texfilename = NULL;
int OPT_num_reference_pages = 1;
char * OPT_stats_file = NULL;
// MUMmer options
int OPT_match_length = 20;
bool OPT_reverse = false;
bool OPT_forwardreverse = false;
bool OPT_forwardcoordinates = false;
bool OPT_showQueryLength = false;
bool OPT_maxmatch = false;
MUMMERGPU_OPTIONS options = DEFAULT;
void printHelp()
{
fprintf(stderr,
"Align a set of query strings to a reference sequence using the GPU.\n"
"\n"
"Usage: mummergpu [options] reference.fa query.fa\n"
"\n"
"Options\n"
" -h Print this help\n"
// " -d file.dot Output suffix tree in dot format\n"
// " -t file.tex Output suffix tree texture\n"
" -C Compute the matches using the CPU instead of the GPU\n"
" -s <file> write timing and memory stats to <file> \n"
"\n"
" -l <matchlen> minimal match length to report [Default: 20]\n"
" -b compute forward and reverse complement matches\n"
" -r only compute reverse complement matches\n"
" -c report the query-position of a reverse complement match\n"
" relative to the original query sequence\n"
" -L show the length of the query sequences on the header line\n"
);
exit(0);
}
void printUsage()
{
fprintf(stderr, "Usage: mummergpu [options] reference.fa query.fa\n");
exit(0);
}
void ParseCommandLine(int argc, char ** argv)
{
bool errflg = false;
int ch;
optarg = NULL;
while(!errflg && ((ch = getopt (argc, argv, "aCchql:d:t:s:brcLM")) != EOF))
{
switch (ch)
{
case 'h': printHelp(); break;
case '?': fprintf(stderr, "Unknown option %c\n", optopt); errflg = true; break;
case 'd': OPT_dotfilename = optarg; break;
case 't': OPT_texfilename = optarg; break;
case 'C': options |= ON_CPU; break;
case 'l': OPT_match_length = atoi(optarg); break;
case 'b': OPT_forwardreverse = true; break;
case 'r': OPT_reverse = true; break;
case 's': OPT_stats_file = optarg; break;
case 'c': OPT_forwardcoordinates = true; break;
case 'L': OPT_showQueryLength = true; break;
case 'M': OPT_maxmatch = true; break;
default: errflg = true; break;
};
}
if ((optind != argc-2) || errflg) { printUsage(); }
if (!OPT_maxmatch)
{
OPT_maxmatch = true;
}
if (OPT_reverse && OPT_forwardreverse)
{
fprintf(stderr, "ERROR: Reverse (-r) and Forward & Reverse (-b) specified\n");
exit(1);
}
OPT_reffilename = argv[optind++];
OPT_qryfilename = argv[optind++];
}
int main(int argc, char* argv[])
{
ParseCommandLine(argc, argv);
int err = 0;
Reference ref;
if ((err = createReference(OPT_reffilename, &ref)))
{
printStringForError(err);
exit(err);
}
QuerySet queries;
if ((err = createQuerySet(OPT_qryfilename, &queries)))
{
printStringForError(err);
exit(err);
}
MatchContext ctx;
if ((err = createMatchContext(&ref,
&queries,
0,
options,
OPT_match_length,
OPT_stats_file,
OPT_reverse,
OPT_forwardreverse,
OPT_forwardcoordinates,
OPT_showQueryLength,
&ctx)))
{
printStringForError(err);
exit(err);
}
if ((err = matchQueries(&ctx)))
{
printStringForError(err);
exit(err);
}
if ((err = destroyMatchContext(&ctx)))
{
printStringForError(err);
exit(err);
}
}
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