| /dports/biology/ugene/ugene-40.1/src/libs_3rdparty/samtools/src/samtools/bcftools/ |
| H A D | index.c | 213 if ((strstr(fnidx, "ftp://") == fnidx || strstr(fnidx, "http://") == fnidx)) { in get_local_version()
215 int l = strlen(fnidx); in get_local_version()
216 for (p = fnidx + l - 1; p >= fnidx; --p) in get_local_version()
218 url = fnidx; fnidx = strdup(p + 1); in get_local_version()
221 return fnidx; in get_local_version()
227 if (stat(fnidx, &sbuf) == 0) return fnidx; in get_local_version()
228 free(fnidx); return 0; in get_local_version()
243 char *fnidx; in bcf_idx_build2() local
257 strcpy(fnidx, fn); strcat(fnidx, ".bci"); in bcf_idx_build2()
262 free(fnidx); in bcf_idx_build2()
[all …]
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| /dports/biology/seqan1/seqan-1.3.1/lib/samtools/bcftools/ |
| H A D | index.c | 212 if ((strstr(fnidx, "ftp://") == fnidx || strstr(fnidx, "http://") == fnidx)) { in get_local_version()
214 int l = strlen(fnidx); in get_local_version()
215 for (p = fnidx + l - 1; p >= fnidx; --p) in get_local_version()
217 url = fnidx; fnidx = strdup(p + 1); in get_local_version()
220 return fnidx; in get_local_version()
226 if (stat(fnidx, &sbuf) == 0) return fnidx; in get_local_version()
227 free(fnidx); return 0; in get_local_version()
242 char *fnidx; in bcf_idx_build2() local
256 strcpy(fnidx, fn); strcat(fnidx, ".bci"); in bcf_idx_build2()
261 free(fnidx); in bcf_idx_build2()
[all …]
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| /dports/biology/bcftools/bcftools-1.14/ |
| H A D | vcfindex.c | 76 char *fntemp = NULL, *fnidx = NULL; in vcf_index_stats() local
90 fntemp[fnidx-fname] = 0; in vcf_index_stats()
92 fnidx += strlen(HTS_IDX_DELIM); in vcf_index_stats()
96 fnidx = fname; in vcf_index_stats()
128 int len = strlen(fnidx); in vcf_index_stats()
135 tbx = tbx_index_load2(fname, fnidx); in vcf_index_stats()
140 idx = bcf_index_load2(fname, fnidx); in vcf_index_stats()
149 else if ( fnidx ) in vcf_index_stats()
151 char *ext = strrchr(fnidx, '.'); in vcf_index_stats()
153 tbx = tbx_index_load2(fname, fnidx); in vcf_index_stats()
[all …]
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| /dports/biology/bio-mocha/bcftools-1.14/ |
| H A D | vcfindex.c | 76 char *fntemp = NULL, *fnidx = NULL; in vcf_index_stats() local
90 fntemp[fnidx-fname] = 0; in vcf_index_stats()
92 fnidx += strlen(HTS_IDX_DELIM); in vcf_index_stats()
96 fnidx = fname; in vcf_index_stats()
128 int len = strlen(fnidx); in vcf_index_stats()
135 tbx = tbx_index_load2(fname, fnidx); in vcf_index_stats()
140 idx = bcf_index_load2(fname, fnidx); in vcf_index_stats()
149 else if ( fnidx ) in vcf_index_stats()
151 char *ext = strrchr(fnidx, '.'); in vcf_index_stats()
153 tbx = tbx_index_load2(fname, fnidx); in vcf_index_stats()
[all …]
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| /dports/biology/py-pysam/pysam-0.18.0/bcftools/ |
| H A D | vcfindex.c | 76 char *fntemp = NULL, *fnidx = NULL; in vcf_index_stats() local
90 fntemp[fnidx-fname] = 0; in vcf_index_stats()
92 fnidx += strlen(HTS_IDX_DELIM); in vcf_index_stats()
96 fnidx = fname; in vcf_index_stats()
128 int len = strlen(fnidx); in vcf_index_stats()
135 tbx = tbx_index_load2(fname, fnidx); in vcf_index_stats()
140 idx = bcf_index_load2(fname, fnidx); in vcf_index_stats()
149 else if ( fnidx ) in vcf_index_stats()
151 char *ext = strrchr(fnidx, '.'); in vcf_index_stats()
153 tbx = tbx_index_load2(fname, fnidx); in vcf_index_stats()
[all …]
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| H A D | vcfindex.c.pysam.c | 78 char *fntemp = NULL, *fnidx = NULL; in vcf_index_stats() local
92 fntemp[fnidx-fname] = 0; in vcf_index_stats()
94 fnidx += strlen(HTS_IDX_DELIM); in vcf_index_stats()
98 fnidx = fname; in vcf_index_stats()
130 int len = strlen(fnidx); in vcf_index_stats()
137 tbx = tbx_index_load2(fname, fnidx); in vcf_index_stats()
142 idx = bcf_index_load2(fname, fnidx); in vcf_index_stats()
151 else if ( fnidx ) in vcf_index_stats()
153 char *ext = strrchr(fnidx, '.'); in vcf_index_stats()
155 tbx = tbx_index_load2(fname, fnidx); in vcf_index_stats()
[all …]
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| /dports/misc/rump/buildrump.sh-b914579/src/sys/fs/cd9660/ |
| H A D | cd9660_util.c | 190 int fnidx = 0; in isofntrans() local
197 fnidx++; in isofntrans()
200 for(; infn != infnend; fnidx += sz) { in isofntrans()
206 if (fnidx > 0 && outfn[-1] == '.') in isofntrans()
207 fnidx--; in isofntrans()
211 sz = wput(outfn, ISO_MAXNAMLEN - fnidx, c, joliet_level); in isofntrans()
214 if (fnidx < ISO_MAXNAMLEN) { in isofntrans()
216 fnidx++; in isofntrans()
222 *outfnlen = fnidx; in isofntrans()
|
| /dports/biology/freebayes/freebayes-1.3.5/vcflib/tabixpp/ |
| H A D | tabix.cpp | 13 char *fnidx = (char*) calloc(strlen(cfilename) + 5, 1); in Tabix() local
14 strcat(strcpy(fnidx, cfilename), ".tbi"); in Tabix()
18 free(fnidx); in Tabix()
22 stat(fnidx, &stat_tbi); in Tabix()
27 free(fnidx); in Tabix()
30 free(fnidx); in Tabix()
|
| /dports/biology/tabixpp/tabixpp-1.0.0-10-g6bbe690/ |
| H A D | tabix.cpp | 13 char *fnidx = (char*) calloc(strlen(cfilename) + 5, 1); in Tabix() local
14 strcat(strcpy(fnidx, cfilename), ".tbi"); in Tabix()
18 free(fnidx); in Tabix()
22 stat(fnidx, &stat_tbi); in Tabix()
27 free(fnidx); in Tabix()
30 free(fnidx); in Tabix()
|
| /dports/biology/py-pysam/pysam-0.18.0/htslib/htslib/ |
| H A D | tbx.h | 86 int tbx_index_build2(const char *fn, const char *fnidx, int min_shift, const tbx_conf_t *conf);
89 …int tbx_index_build3(const char *fn, const char *fnidx, int min_shift, int n_threads, const tbx_co…
110 tbx_t *tbx_index_load2(const char *fn, const char *fnidx);
130 tbx_t *tbx_index_load3(const char *fn, const char *fnidx, int flags);
|
| /dports/biology/freebayes/freebayes-1.3.5/contrib/htslib/htslib/ |
| H A D | tbx.h | 86 int tbx_index_build2(const char *fn, const char *fnidx, int min_shift, const tbx_conf_t *conf);
89 …int tbx_index_build3(const char *fn, const char *fnidx, int min_shift, int n_threads, const tbx_co…
110 tbx_t *tbx_index_load2(const char *fn, const char *fnidx);
130 tbx_t *tbx_index_load3(const char *fn, const char *fnidx, int flags);
|
| /dports/biology/htslib/htslib-1.14/htslib/ |
| H A D | tbx.h | 86 int tbx_index_build2(const char *fn, const char *fnidx, int min_shift, const tbx_conf_t *conf);
89 …int tbx_index_build3(const char *fn, const char *fnidx, int min_shift, int n_threads, const tbx_co…
110 tbx_t *tbx_index_load2(const char *fn, const char *fnidx);
130 tbx_t *tbx_index_load3(const char *fn, const char *fnidx, int flags);
|
| /dports/biology/py-pysam/pysam-0.18.0/htslib/ |
| H A D | tbx.c | 365 int tbx_index_build3(const char *fn, const char *fnidx, int min_shift, int n_threads, const tbx_con… in tbx_index_build3() argument
376 ret = hts_idx_save_as(tbx->idx, fn, fnidx, min_shift > 0? HTS_FMT_CSI : HTS_FMT_TBI); in tbx_index_build3()
381 int tbx_index_build2(const char *fn, const char *fnidx, int min_shift, const tbx_conf_t *conf) in tbx_index_build2() argument
383 return tbx_index_build3(fn, fnidx, min_shift, 0, conf); in tbx_index_build2()
391 static tbx_t *index_load(const char *fn, const char *fnidx, int flags) in index_load() argument
400 tbx->idx = hts_idx_load3(fn, fnidx, HTS_FMT_TBI, flags); in index_load()
431 hts_log_error("Invalid index header for %s", fnidx ? fnidx : fn); in index_load()
438 tbx_t *tbx_index_load3(const char *fn, const char *fnidx, int flags) in tbx_index_load3() argument
440 return index_load(fn, fnidx, flags); in tbx_index_load3()
443 tbx_t *tbx_index_load2(const char *fn, const char *fnidx) in tbx_index_load2() argument
[all …]
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| /dports/biology/freebayes/freebayes-1.3.5/contrib/htslib/ |
| H A D | tbx.c | 365 int tbx_index_build3(const char *fn, const char *fnidx, int min_shift, int n_threads, const tbx_con… in tbx_index_build3() argument
376 ret = hts_idx_save_as(tbx->idx, fn, fnidx, min_shift > 0? HTS_FMT_CSI : HTS_FMT_TBI); in tbx_index_build3()
381 int tbx_index_build2(const char *fn, const char *fnidx, int min_shift, const tbx_conf_t *conf) in tbx_index_build2() argument
383 return tbx_index_build3(fn, fnidx, min_shift, 0, conf); in tbx_index_build2()
391 static tbx_t *index_load(const char *fn, const char *fnidx, int flags) in index_load() argument
400 tbx->idx = hts_idx_load3(fn, fnidx, HTS_FMT_TBI, flags); in index_load()
431 hts_log_error("Invalid index header for %s", fnidx ? fnidx : fn); in index_load()
438 tbx_t *tbx_index_load3(const char *fn, const char *fnidx, int flags) in tbx_index_load3() argument
440 return index_load(fn, fnidx, flags); in tbx_index_load3()
443 tbx_t *tbx_index_load2(const char *fn, const char *fnidx) in tbx_index_load2() argument
[all …]
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| /dports/biology/htslib/htslib-1.14/ |
| H A D | tbx.c | 365 int tbx_index_build3(const char *fn, const char *fnidx, int min_shift, int n_threads, const tbx_con… in tbx_index_build3() argument
376 ret = hts_idx_save_as(tbx->idx, fn, fnidx, min_shift > 0? HTS_FMT_CSI : HTS_FMT_TBI); in tbx_index_build3()
381 int tbx_index_build2(const char *fn, const char *fnidx, int min_shift, const tbx_conf_t *conf) in tbx_index_build2() argument
383 return tbx_index_build3(fn, fnidx, min_shift, 0, conf); in tbx_index_build2()
391 static tbx_t *index_load(const char *fn, const char *fnidx, int flags) in index_load() argument
400 tbx->idx = hts_idx_load3(fn, fnidx, HTS_FMT_TBI, flags); in index_load()
431 hts_log_error("Invalid index header for %s", fnidx ? fnidx : fn); in index_load()
438 tbx_t *tbx_index_load3(const char *fn, const char *fnidx, int flags) in tbx_index_load3() argument
440 return index_load(fn, fnidx, flags); in tbx_index_load3()
443 tbx_t *tbx_index_load2(const char *fn, const char *fnidx) in tbx_index_load2() argument
[all …]
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| /dports/biology/ugene/ugene-40.1/src/libs_3rdparty/samtools/src/samtools/ |
| H A D | bam_index.c | 388 char *fnidx, *fn; in bam_index_load_local() local
398 strcpy(fnidx, fn); strcat(fnidx, ".bai"); in bam_index_load_local()
402 strcpy(fnidx, fn); in bam_index_load_local()
403 fnidx[strlen(fn)-1] = 'i'; in bam_index_load_local()
407 free(fnidx); free(fn); in bam_index_load_local()
461 download_from_remote(fnidx); in bam_index_load()
470 char *fnidx; in bam_index_build2() local
486 strcpy(fnidx, fn); strcat(fnidx, ".bai"); in bam_index_build2()
487 } else fnidx = strdup(_fnidx); in bam_index_build2()
491 free(fnidx); in bam_index_build2()
[all …]
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| /dports/biology/stringtie/stringtie-2.1.1/samtools-0.1.18/ |
| H A D | bam_index.c | 387 char *fnidx, *fn; in bam_index_load_local() local
397 strcpy(fnidx, fn); strcat(fnidx, ".bai"); in bam_index_load_local()
398 fp = fopen(fnidx, "rb"); in bam_index_load_local()
402 strcpy(fnidx, fn); in bam_index_load_local()
404 fp = fopen(fnidx, "rb"); in bam_index_load_local()
407 free(fnidx); free(fn); in bam_index_load_local()
470 char *fnidx; in bam_index_build2() local
486 strcpy(fnidx, fn); strcat(fnidx, ".bai"); in bam_index_build2()
488 fpidx = fopen(fnidx, "wb"); in bam_index_build2()
491 free(fnidx); in bam_index_build2()
[all …]
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| /dports/biology/seqan1/seqan-1.3.1/lib/samtools/ |
| H A D | bam_index.c | 376 char *fnidx, *fn; in bam_index_load_local() local
386 strcpy(fnidx, fn); strcat(fnidx, ".bai"); in bam_index_load_local()
387 fp = fopen(fnidx, "rb"); in bam_index_load_local()
391 strcpy(fnidx, fn); in bam_index_load_local()
393 fp = fopen(fnidx, "rb"); in bam_index_load_local()
396 free(fnidx); free(fn); in bam_index_load_local()
459 char *fnidx; in bam_index_build2() local
471 strcpy(fnidx, fn); strcat(fnidx, ".bai"); in bam_index_build2()
473 fpidx = fopen(fnidx, "wb"); in bam_index_build2()
476 free(fnidx); in bam_index_build2()
[all …]
|
| /dports/net-mgmt/aircrack-ng/aircrack-ng-1.5.2/src/aircrack-osdep/radiotap/ |
| H A D | parse.c | 100 int fd, err, fnidx = 1, i; in main() local
111 fnidx++; in main()
114 fd = open(argv[fnidx], O_RDONLY); in main()
116 fprintf(stderr, "cannot open file %s\n", argv[fnidx]); in main()
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| /dports/biology/vt/vt-0.57721/lib/htslib/ |
| H A D | tbx.c | 266 int tbx_index_build3(const char *fn, const char *fnidx, int min_shift, int n_threads, const tbx_con… in tbx_index_build3() argument
277 ret = hts_idx_save_as(tbx->idx, fn, fnidx, min_shift > 0? HTS_FMT_CSI : HTS_FMT_TBI); in tbx_index_build3()
282 int tbx_index_build2(const char *fn, const char *fnidx, int min_shift, const tbx_conf_t *conf) in tbx_index_build2() argument
284 return tbx_index_build3(fn, fnidx, min_shift, 0, conf); in tbx_index_build2()
292 tbx_t *tbx_index_load2(const char *fn, const char *fnidx) in tbx_index_load2() argument
299 tbx->idx = fnidx? hts_idx_load2(fn, fnidx) : hts_idx_load(fn, HTS_FMT_TBI); in tbx_index_load2()
330 hts_log_error("Invalid index header for %s", fnidx ? fnidx : fn); in tbx_index_load2()
|
| /dports/biology/bedtools/bedtools2-2.30.0/src/utils/htslib/ |
| H A D | tbx.c | 266 int tbx_index_build3(const char *fn, const char *fnidx, int min_shift, int n_threads, const tbx_con… in tbx_index_build3() argument
277 ret = hts_idx_save_as(tbx->idx, fn, fnidx, min_shift > 0? HTS_FMT_CSI : HTS_FMT_TBI); in tbx_index_build3()
282 int tbx_index_build2(const char *fn, const char *fnidx, int min_shift, const tbx_conf_t *conf) in tbx_index_build2() argument
284 return tbx_index_build3(fn, fnidx, min_shift, 0, conf); in tbx_index_build2()
292 tbx_t *tbx_index_load2(const char *fn, const char *fnidx) in tbx_index_load2() argument
299 tbx->idx = fnidx? hts_idx_load2(fn, fnidx) : hts_idx_load(fn, HTS_FMT_TBI); in tbx_index_load2()
330 hts_log_error("Invalid index header for %s", fnidx ? fnidx : fn); in tbx_index_load2()
|
| /dports/biology/stacks/stacks-2.4/htslib/ |
| H A D | tbx.c | 266 int tbx_index_build3(const char *fn, const char *fnidx, int min_shift, int n_threads, const tbx_con… in tbx_index_build3() argument
277 ret = hts_idx_save_as(tbx->idx, fn, fnidx, min_shift > 0? HTS_FMT_CSI : HTS_FMT_TBI); in tbx_index_build3()
282 int tbx_index_build2(const char *fn, const char *fnidx, int min_shift, const tbx_conf_t *conf) in tbx_index_build2() argument
284 return tbx_index_build3(fn, fnidx, min_shift, 0, conf); in tbx_index_build2()
292 tbx_t *tbx_index_load2(const char *fn, const char *fnidx) in tbx_index_load2() argument
299 tbx->idx = fnidx? hts_idx_load2(fn, fnidx) : hts_idx_load(fn, HTS_FMT_TBI); in tbx_index_load2()
330 hts_log_error("Invalid index header for %s", fnidx ? fnidx : fn); in tbx_index_load2()
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| /dports/biology/kallisto/kallisto-0.46.1/ext/htslib/ |
| H A D | tbx.c | 265 int tbx_index_build3(const char *fn, const char *fnidx, int min_shift, int n_threads, const tbx_con… in tbx_index_build3() argument
276 ret = hts_idx_save_as(tbx->idx, fn, fnidx, min_shift > 0? HTS_FMT_CSI : HTS_FMT_TBI); in tbx_index_build3()
281 int tbx_index_build2(const char *fn, const char *fnidx, int min_shift, const tbx_conf_t *conf) in tbx_index_build2() argument
283 return tbx_index_build3(fn, fnidx, min_shift, 0, conf); in tbx_index_build2()
291 tbx_t *tbx_index_load2(const char *fn, const char *fnidx) in tbx_index_load2() argument
298 tbx->idx = fnidx? hts_idx_load2(fn, fnidx) : hts_idx_load(fn, HTS_FMT_TBI); in tbx_index_load2()
331 __func__, fnidx ? fnidx : fn); in tbx_index_load2()
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| /dports/biology/emboss/EMBOSS-6.6.0/ajax/core/ |
| H A D | ajbamindex.c | 843 char *fnidx = NULL; in ajBamIndexLoad() local
863 strcpy(fnidx, fn); strcat(fnidx, ".bai"); in ajBamIndexLoad()
864 fp = fopen(fnidx, "rb"); in ajBamIndexLoad()
872 strcpy(fnidx, fn); in ajBamIndexLoad()
873 fnidx[strlen(fn)-1] = 'i'; in ajBamIndexLoad()
874 fp = fopen(fnidx, "rb"); in ajBamIndexLoad()
878 free(fnidx); in ajBamIndexLoad()
907 char *fnidx; in ajBamIndexBuild() local
931 strcpy(fnidx, fn); strcat(fnidx, ".bai"); in ajBamIndexBuild()
938 free(fnidx); in ajBamIndexBuild()
[all …]
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| /dports/biology/vt/vt-0.57721/lib/htslib/htslib/ |
| H A D | tbx.h | 71 int tbx_index_build2(const char *fn, const char *fnidx, int min_shift, const tbx_conf_t *conf);
72 …int tbx_index_build3(const char *fn, const char *fnidx, int min_shift, int n_threads, const tbx_co…
74 tbx_t *tbx_index_load2(const char *fn, const char *fnidx);
|