/dports/biology/gmap/gmap-2020-09-12/src/ |
H A D | datadir.c | 93 find_fileroot (char *genomesubdir, char *genomedir, char *dbroot) { in find_fileroot() argument 99 if ((dp = opendir(genomesubdir)) == NULL) { in find_fileroot() 129 fprintf(stderr,"Unable to close directory %s\n",genomesubdir); in find_fileroot() 142 fprintf(stderr,"Unable to close directory %s\n",genomesubdir); in find_fileroot() 219 char *genomesubdir, *genomedir, *filename, *p, *dbrootdir, *newgenomedir; in Datadir_find_genomesubdir() local 245 genomesubdir = genomedir; in Datadir_find_genomesubdir() 252 sprintf(genomesubdir,"%s/%s",genomedir,dbroot); in Datadir_find_genomesubdir() 269 sprintf(filename,"%s/%s.version",genomesubdir,*fileroot); in Datadir_find_genomesubdir() 278 return genomesubdir; in Datadir_find_genomesubdir() 292 sprintf(mapdir,"%s/%s.maps",genomesubdir,fileroot); in Datadir_find_mapdir() [all …]
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H A D | get-genome.c | 53 static char *genomesubdir = NULL; variable 1055 snpsdir = genomesubdir; in main() 1120 sprintf(iitfile,"%s/%s.iit",genomesubdir,map_iitfile); in main() 1170 FREE(genomesubdir); in main() 1191 FREE(genomesubdir); in main() 1251 FREE(genomesubdir); in main() 1290 FREE(genomesubdir); in main() 1442 sprintf(iitfile,"%s/%s.iit",genomesubdir,map_iitfile); in main() 1559 sprintf(iitfile,"%s/%s.iit",genomesubdir,map_iitfile); in main() 1722 sprintf(iitfile,"%s/%s.iit",genomesubdir,map_iitfile); in main() [all …]
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H A D | trindex.c | 88 static char *genomesubdir = NULL; variable 162 genomesubdir = Datadir_find_genomesubdir(&genome_fileroot,&dbversion,user_gmapdb, in main() 176 info_root = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+ in main() 179 sprintf(info_root,"%s/%s.transcripts/%s",genomesubdir,genome_fileroot,transcriptome_fileroot); in main() 216 iitfile = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+ in main() 218 sprintf(iitfile,"%s/%s.chromosome.iit",genomesubdir,genome_fileroot); in main() 311 genomesubdir,genome_fileroot,transcriptome_fileroot); in main() 314 FREE(genomesubdir); in main()
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H A D | indexdb.c | 472 if ((dp = opendir(genomesubdir)) == NULL) { in Indexdb_get_filenames_no_compression() 635 sprintf(positions_filename,"%s/",genomesubdir); in Indexdb_get_filenames_no_compression() 799 if ((dp = opendir(genomesubdir)) == NULL) { in Indexdb_get_filenames_bitpack() 1020 sprintf(offsetsmeta_filename,"%s/",genomesubdir); in Indexdb_get_filenames_bitpack() 1044 sprintf(offsetspages_filename,"%s/",genomesubdir); in Indexdb_get_filenames_bitpack() 1065 sprintf(positions_filename,"%s/",genomesubdir); in Indexdb_get_filenames_bitpack() 1078 sprintf(positions_filename,"%s/",genomesubdir); in Indexdb_get_filenames_bitpack() 1158 genomesubdir,fileroot,idx_filesuffix,snps_root, in Indexdb_get_filenames() 1169 genomesubdir,fileroot,idx_filesuffix,snps_root, in Indexdb_get_filenames() 1192 genomesubdir,fileroot,idx_filesuffix,snps_root, [all …]
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H A D | parserange.c | 254 filename = (char *) MALLOCA((strlen(genomesubdir)+strlen("/")+strlen(fileroot)+ in convert_to_chrpos() 256 sprintf(filename,"%s/%s.chromosome.iit",genomesubdir,fileroot); in convert_to_chrpos() 374 char *query, char *genomesubdir, char *fileroot) { in Parserange_universal() argument 405 filename = (char *) MALLOCA((strlen(genomesubdir)+strlen("/")+strlen(fileroot)+ in Parserange_universal() 407 sprintf(filename,"%s/%s.chromosome.iit",genomesubdir,fileroot); in Parserange_universal() 450 filename = (char *) MALLOCA((strlen(genomesubdir)+strlen("/")+strlen(fileroot)+ in Parserange_universal() 452 sprintf(filename,"%s/%s.contig.iit",genomesubdir,fileroot); in Parserange_universal() 507 sprintf(filename,"%s/%s.contig.iit",genomesubdir,fileroot); in Parserange_universal() 517 *div = convert_to_chrpos(&(*chrstart),genomesubdir,fileroot,*genomicstart); in Parserange_universal() 522 filename = (char *) MALLOCA((strlen(genomesubdir)+strlen("/")+strlen(fileroot)+ in Parserange_universal() [all …]
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H A D | indexdb.h | 80 Width_T *index1part, Width_T *index1interval, char *genomesubdir, 113 Indexdb_shmem_remove (char *genomesubdir, char *fileroot, char *idx_filesuffix, char *snps_root, 122 char *genomesubdir, char *fileroot, char *idx_filesuffix, char *snps_root, 132 char *genomesubdir, char *fileroot, char *idx_filesuffix, char *snps_root,
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H A D | datadir.h | 13 Datadir_find_mapdir (char *user_mapdir, char *genomesubdir, char *fileroot); 22 Datadir_avail_maps (FILE *fp, char *user_mapdir, char *genomesubdir, char *fileroot);
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H A D | gsnap.c | 3077 char *genomesubdir, char *genome_fileroot) { in worker_setup() argument 3104 snpsdir = genomesubdir; in worker_setup() 3134 modedir = genomesubdir; in worker_setup() 3216 Datadir_list_directory(stderr,genomesubdir); in worker_setup() 3379 sprintf(iitfile,"%s/%s",genomesubdir,tally_root); in worker_setup() 3389 fprintf(stderr," or in %s\n",genomesubdir); in worker_setup() 3427 fprintf(stderr," or in %s\n",genomesubdir); in worker_setup() 3921 genomesubdir,genome_fileroot); in main() 3958 FREE(genomesubdir); in main() 3983 FREE(genomesubdir); in main() [all …]
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H A D | regiondb.h | 41 char *genomesubdir, char *fileroot, char *idx_filesuffix, char *snps_root, 47 char *genomesubdir, char *fileroot, char *idx_filesuffix, char *snps_root,
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H A D | genome-write.c | 784 Genome_write_comp32 (char *genomesubdir, char *fileroot, FILE *input, in Genome_write_comp32() argument 796 filename = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+ in Genome_write_comp32() 798 sprintf(filename,"%s/%s.genome",genomesubdir,fileroot); in Genome_write_comp32() 813 filename = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+ in Genome_write_comp32() 815 sprintf(filename,"%s/%s.genomecomp",genomesubdir,fileroot); in Genome_write_comp32() 828 filename = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+ in Genome_write_comp32() 830 sprintf(filename,"%s/%s.genomecomp",genomesubdir,fileroot); in Genome_write_comp32()
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H A D | gmapindex.c | 720 textfile = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+ in write_chromosome_file() 722 sprintf(textfile,"%s/%s.chromosome",genomesubdir,fileroot); in write_chromosome_file() 732 chrsubsetfile = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+ in write_chromosome_file() 734 sprintf(chrsubsetfile,"%s/%s.chrsubset",genomesubdir,fileroot); in write_chromosome_file() 820 iitfile = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+ in write_chromosome_file() 822 sprintf(iitfile,"%s/%s.chromosome.iit",genomesubdir,fileroot); in write_chromosome_file() 952 iitfile = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+ in write_alt_scaffold_file() 1057 textfile = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+ in write_contig_file() 1059 sprintf(textfile,"%s/%s.contig",genomesubdir,fileroot); in write_contig_file() 1149 iitfile = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+ in write_contig_file() [all …]
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H A D | genome.h | 33 Genome_shmem_remove (char *genomesubdir, char *fileroot, char *snps_root, Genometype_T genometype, 37 Genome_new (char *genomesubdir, char *fileroot, char *snps_root,
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H A D | transcriptome.c | 101 Transcriptome_new (char *genomesubdir, char *genome_fileroot, char *transcriptome_fileroot, in Transcriptome_new() argument 114 info_root = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+ in Transcriptome_new() 117 sprintf(info_root,"%s/%s.transcripts/%s",genomesubdir,genome_fileroot,transcriptome_fileroot); in Transcriptome_new()
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H A D | genome.c | 168 filename = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+strlen(fileroot)+ 170 sprintf(filename,"%s/%s.genomecomp.%s",genomesubdir,fileroot,snps_root); 174 sprintf(filename,"%s/%s.genomecomp",genomesubdir,fileroot); 181 sprintf(filename,"%s/%s.genomebits128.%s",genomesubdir,fileroot,snps_root); 185 sprintf(filename,"%s/%s.genomebits128",genomesubdir,fileroot); 203 sprintf(filename,"%s/%s.genome",genomesubdir,fileroot); 232 sprintf(filename,"%s/%s.genomecomp.%s",genomesubdir,fileroot,snps_root); in Genome_new() 236 sprintf(filename,"%s/%s.genomecomp",genomesubdir,fileroot); in Genome_new() 243 sprintf(filename,"%s/%s.genomebits128.%s",genomesubdir,fileroot,snps_root); in Genome_new() 247 sprintf(filename,"%s/%s.genomebits128",genomesubdir,fileroot); in Genome_new() [all …]
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H A D | genome-write.h | 13 Genome_write_comp32 (char *genomesubdir, char *fileroot, FILE *input,
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H A D | transcriptome.h | 14 Transcriptome_new (char *genomesubdir, char *genome_fileroot, char *transcriptome_fileroot,
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H A D | regiondb.c | 1489 char *genomesubdir, char *fileroot, char *idx_filesuffix, char *snps_root, in Regiondb_get_filenames() argument 1527 if ((dp = opendir(genomesubdir)) == NULL) { in Regiondb_get_filenames() 1528 fprintf(stderr,"Unable to open directory %s\n",genomesubdir); in Regiondb_get_filenames() 1676 fprintf(stderr,"Unable to close directory %s\n",genomesubdir); in Regiondb_get_filenames() 1692 …regiondb_filename = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+strlen(base_filename)+1,sizeo… in Regiondb_get_filenames() 1693 regiondb_basename_ptr = &(regiondb_filename[strlen(genomesubdir)+strlen("/")]); in Regiondb_get_filenames() 1696 sprintf(regiondb_filename,"%s/%s",genomesubdir,base_filename); in Regiondb_get_filenames() 1709 fprintf(stderr,"Looking for region files in directory %s\n",genomesubdir); in Regiondb_get_filenames() 1735 char *genomesubdir, char *fileroot, char *idx_filesuffix, char *snps_root, in Regiondb_new_genome() argument 1753 genomesubdir,fileroot,idx_filesuffix,snps_root, in Regiondb_new_genome()
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H A D | parserange.h | 28 char *query, char *genomesubdir, char *fileroot);
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H A D | sam_sort.c | 120 static char *genomesubdir = NULL; variable 1448 genomesubdir = Datadir_find_genomesubdir(&fileroot,&dbversion,user_genomedir,dbroot); in main() 1449 iitfile = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+ in main() 1451 sprintf(iitfile,"%s/%s.chromosome.iit",genomesubdir,fileroot); in main() 1456 FREE(genomesubdir); in main()
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H A D | gmap.c | 6655 genomesubdir = Datadir_find_genomesubdir(&fileroot,&dbversion,user_genomedir,dbroot); in main() 6657 iitfile = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+ in main() 6659 sprintf(iitfile,"%s/%s.chromosome.iit",genomesubdir,fileroot); in main() 6674 iitfile = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+ in main() 6676 sprintf(iitfile,"%s/%s.altscaffold.iit",genomesubdir,fileroot); in main() 6701 Datadir_avail_maps(stdout,user_mapdir,genomesubdir,fileroot); in main() 6704 mapdir = Datadir_find_mapdir(user_mapdir,genomesubdir,fileroot); in main() 6743 mapdir = Datadir_find_mapdir(/*user_mapdir*/NULL,genomesubdir,fileroot); in main() 6810 snpsdir = genomesubdir; in main() 6825 modedir = genomesubdir; in main() [all …]
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/dports/biology/gmap/gmap-2020-09-12/ |
H A D | ChangeLog | 2584 * get-genome.c: If map file is not in mapdir, then look in genomesubdir 12746 * indexdb.c: Printing genomesubdir and then individual index file names in 25111 variable names to genomesubdir, fileroot, and dbversion. 25113 * gmap.c: Added -g flag. Changing variable names to genomesubdir, fileroot, 25119 genomesubdir and fileroot.
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