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  • Committer: Package Import Robot
  • Author(s): Laszlo Kajan
  • Date: 2013-11-25 20:01:02 UTC
  • mfrom: (1.1.5)
  • Revision ID: package-import@ubuntu.com-20131125200102-quenacnokvrc76ij
Tags: 0.9.9.3-1
* New upstream release.
* Up-to-date standards-version.
* Vcs fields updated.

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src/ffindex_from_fasta.c
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/*
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 * FFindex
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 * written by Andy Hauser <hauser@genzentrum.lmu.de>.
 
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 * written by Andreas Hauser <andy@splashground.de>.
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 * Please add your name here if you distribute modified versions.
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 * 
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 * FFindex is provided under the Create Commons license "Attribution-ShareAlike
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                    "\t-s\tsort index file\n"
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                    "ENVIRONMENT\n"
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                    "\tFFINDEX_MAX_INDEX_ENTRIES - allocate memory for this number of entries\n"
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                    "\nDesigned and implemented by Andreas W. Hauser <hauser@genzentrum.lmu.de>.\n", basename(program_name));
 
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                    FFINDEX_COPYRIGHT,
 
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                    basename(program_name));
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}
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int main(int argn, char **argv)
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  char *index_filename = argv[optind++];
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  char *fasta_filename = argv[optind++];
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  FILE *data_file, *index_file, *fasta_file;
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  struct stat st;
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  if(stat(data_filename, &st) == 0) { errno = EEXIST; perror(data_filename); return EXIT_FAILURE; }
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  data_file  = fopen(data_filename, "w");
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  if( data_file == NULL) { perror(data_filename); return EXIT_FAILURE; }
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  if(stat(index_filename, &st) == 0) { errno = EEXIST; perror(index_filename); return EXIT_FAILURE; }
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  index_file = fopen(index_filename, "w+");
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  if(index_file == NULL) { perror(index_filename); return EXIT_FAILURE; }
 
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  size_t offset = 0;
 
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  /* open ffindex */
 
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  err = ffindex_index_open(data_filename, index_filename, "w", &data_file, &index_file, &offset);
 
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  if(err != EXIT_SUCCESS)
 
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    return err;
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  fasta_file = fopen(fasta_filename, "r");
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  if(fasta_file == NULL) { perror(fasta_filename); return EXIT_FAILURE; }
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  size_t fasta_size;
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  char *fasta_data = ffindex_mmap_data(fasta_file, &fasta_size);
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  size_t offset = 0;
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  size_t from_length = 0;
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  char name[FFINDEX_MAX_ENTRY_NAME_LENTH];
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  int seq_id = 1;