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Searched refs:genomesubdir (Results 1 – 21 of 21) sorted by relevance

/dports/biology/gmap/gmap-2020-09-12/src/
H A Ddatadir.c93 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()
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H A Dget-genome.c53 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()
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H A Dtrindex.c88 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()
H A Dindexdb.c472 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,
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H A Dparserange.c254 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()
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H A Dindexdb.h80 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,
H A Ddatadir.h13 Datadir_find_mapdir (char *user_mapdir, char *genomesubdir, char *fileroot);
22 Datadir_avail_maps (FILE *fp, char *user_mapdir, char *genomesubdir, char *fileroot);
H A Dgsnap.c3077 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()
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H A Dregiondb.h41 char *genomesubdir, char *fileroot, char *idx_filesuffix, char *snps_root,
47 char *genomesubdir, char *fileroot, char *idx_filesuffix, char *snps_root,
H A Dgenome-write.c784 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()
H A Dgmapindex.c720 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()
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H A Dgenome.h33 Genome_shmem_remove (char *genomesubdir, char *fileroot, char *snps_root, Genometype_T genometype,
37 Genome_new (char *genomesubdir, char *fileroot, char *snps_root,
H A Dtranscriptome.c101 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()
H A Dgenome.c168 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()
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H A Dgenome-write.h13 Genome_write_comp32 (char *genomesubdir, char *fileroot, FILE *input,
H A Dtranscriptome.h14 Transcriptome_new (char *genomesubdir, char *genome_fileroot, char *transcriptome_fileroot,
H A Dregiondb.c1489 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()
H A Dparserange.h28 char *query, char *genomesubdir, char *fileroot);
H A Dsam_sort.c120 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()
H A Dgmap.c6655 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()
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/dports/biology/gmap/gmap-2020-09-12/
H A DChangeLog2584 * 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.