| /dports/biology/py-pysam/pysam-0.18.0/samtools/ |
| H A D | bedidx.c | 104 hts_pos_t beg, end; in bed_index_core() local
142 static int bed_minoff(const bed_reglist_t *p, hts_pos_t beg, hts_pos_t end) { in bed_minoff()
161 static int bed_overlap_core(const bed_reglist_t *p, hts_pos_t beg, hts_pos_t end) in bed_overlap_core()
175 int bed_overlap(const void *_h, const char *chr, hts_pos_t beg, hts_pos_t end) in bed_overlap()
268 uint64_t beg = 0, end = 0; in bed_read() local
376 static void *bed_insert(void *reg_hash, char *reg, hts_pos_t beg, hts_pos_t end) { in bed_insert()
432 const char *reg; in bed_filter() local
433 hts_pos_t beg, end; in bed_filter() local
491 char reg[1024]; in bed_hash_regions() local
493 int beg, end; in bed_hash_regions() local
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| H A D | bedidx.c.pysam.c | 106 hts_pos_t beg, end; in bed_index_core() local
144 static int bed_minoff(const bed_reglist_t *p, hts_pos_t beg, hts_pos_t end) { in bed_minoff()
163 static int bed_overlap_core(const bed_reglist_t *p, hts_pos_t beg, hts_pos_t end) in bed_overlap_core()
177 int bed_overlap(const void *_h, const char *chr, hts_pos_t beg, hts_pos_t end) in bed_overlap()
270 uint64_t beg = 0, end = 0; in bed_read() local
378 static void *bed_insert(void *reg_hash, char *reg, hts_pos_t beg, hts_pos_t end) { in bed_insert()
434 const char *reg; in bed_filter() local
435 hts_pos_t beg, end; in bed_filter() local
493 char reg[1024]; in bed_hash_regions() local
495 int beg, end; in bed_hash_regions() local
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| /dports/biology/samtools/samtools-1.14/ |
| H A D | bedidx.c | 104 hts_pos_t beg, end; in bed_index_core() local
142 static int bed_minoff(const bed_reglist_t *p, hts_pos_t beg, hts_pos_t end) { in bed_minoff()
161 static int bed_overlap_core(const bed_reglist_t *p, hts_pos_t beg, hts_pos_t end) in bed_overlap_core()
175 int bed_overlap(const void *_h, const char *chr, hts_pos_t beg, hts_pos_t end) in bed_overlap()
268 uint64_t beg = 0, end = 0; in bed_read() local
376 static void *bed_insert(void *reg_hash, char *reg, hts_pos_t beg, hts_pos_t end) { in bed_insert()
432 const char *reg; in bed_filter() local
433 hts_pos_t beg, end; in bed_filter() local
491 char reg[1024]; in bed_hash_regions() local
493 int beg, end; in bed_hash_regions() local
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| /dports/biology/freebayes/freebayes-1.3.5/contrib/htslib/test/ |
| H A D | test-parse-reg.c | 50 void reg_expected(sam_hdr_t *hdr, const char *reg, int flags, in reg_expected()
186 const char *reg = argv[2]; in main() local
189 hts_pos_t beg, end; in main() local
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| /dports/biology/htslib/htslib-1.14/test/ |
| H A D | test-parse-reg.c | 50 void reg_expected(sam_hdr_t *hdr, const char *reg, int flags, in reg_expected()
186 const char *reg = argv[2]; in main() local
189 hts_pos_t beg, end; in main() local
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| /dports/biology/artemis/artemis-17.0.1-11-g3e43d27e/uk/ac/sanger/artemis/components/variant/ |
| H A D | TabixReader.java | 79 int tid, beg, end; field in TabixReader.TIntv
109 private static int reg2bins(final int beg, final int _end, final int[] list) { in reg2bins()
229 …public int[] parseReg(final String reg) { // FIXME: NOT working when the sequence name contains : … in parseReg()
243 int col = 0, end = 0, beg = 0; in getIntv() local
298 private int tid, beg, end; field in TabixReader.Iterator
337 public Iterator query(final int tid, final int beg, final int end) { in query()
385 public Iterator query(final String reg) { in query()
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| /dports/biology/py-pysam/pysam-0.18.0/htslib/ |
| H A D | synced_bcf_reader.c | 565 static void _set_variant_boundaries(bcf1_t *rec, hts_pos_t *beg, hts_pos_t *end) in _set_variant_boundaries()
659 hts_pos_t beg, end; in _reader_fill_buffer() local
772 hts_pos_t beg, end; in next_line() local
836 bcf_sr_regions_t *reg = readers->regions; in bcf_sr_seek_start() local
985 static void regions_merge(region_t *reg) in regions_merge()
1000 void _regions_sort_and_merge(bcf_sr_regions_t *reg) in _regions_sort_and_merge()
1135 bcf_sr_regions_t *reg; in bcf_sr_regions_init() local
1210 void bcf_sr_regions_destroy(bcf_sr_regions_t *reg) in bcf_sr_regions_destroy()
1256 static int advance_creg(region_t *reg) in advance_creg()
1265 int bcf_sr_regions_next(bcf_sr_regions_t *reg) in bcf_sr_regions_next()
[all …]
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| /dports/biology/htslib/htslib-1.14/ |
| H A D | synced_bcf_reader.c | 565 static void _set_variant_boundaries(bcf1_t *rec, hts_pos_t *beg, hts_pos_t *end) in _set_variant_boundaries()
659 hts_pos_t beg, end; in _reader_fill_buffer() local
772 hts_pos_t beg, end; in next_line() local
836 bcf_sr_regions_t *reg = readers->regions; in bcf_sr_seek_start() local
985 static void regions_merge(region_t *reg) in regions_merge()
1000 void _regions_sort_and_merge(bcf_sr_regions_t *reg) in _regions_sort_and_merge()
1135 bcf_sr_regions_t *reg; in bcf_sr_regions_init() local
1210 void bcf_sr_regions_destroy(bcf_sr_regions_t *reg) in bcf_sr_regions_destroy()
1256 static int advance_creg(region_t *reg) in advance_creg()
1265 int bcf_sr_regions_next(bcf_sr_regions_t *reg) in bcf_sr_regions_next()
[all …]
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| /dports/sysutils/intel-pcm/pcm-202109/ |
| H A D | utils.h | 363 struct { unsigned int eax, ebx, ecx, edx; } reg; member
378 inline uint32 build_bit_ui(uint32 beg, uint32 end) in build_bit_ui()
394 inline uint32 extract_bits_ui(uint32 myin, uint32 beg, uint32 end) in extract_bits_ui()
415 inline uint64 build_bit(uint32 beg, uint32 end) in build_bit()
430 inline uint64 extract_bits(uint64 myin, uint32 beg, uint32 end) in extract_bits()
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| /dports/sysutils/intel-pcm-devel/pcm-0212b38/ |
| H A D | utils.h | 363 struct { unsigned int eax, ebx, ecx, edx; } reg; member
378 inline uint32 build_bit_ui(uint32 beg, uint32 end) in build_bit_ui()
394 inline uint32 extract_bits_ui(uint32 myin, uint32 beg, uint32 end) in extract_bits_ui()
415 inline uint64 build_bit(uint32 beg, uint32 end) in build_bit()
430 inline uint64 extract_bits(uint64 myin, uint32 beg, uint32 end) in extract_bits()
|
| /dports/lang/mosh/mosh-0.2.7/extlibs/onig-5.9.2/sample/ |
| H A D | listcap.c | 11 node_callback(int group, int beg, int end, int level, int at, void* arg) in node_callback()
31 regex_t* reg; in ex() local
|
| /dports/sysutils/vector/vector-0.10.0/cargo-crates/onig_sys-69.1.0/oniguruma/sample/ |
| H A D | listcap.c | 11 node_callback(int group, int beg, int end, int level, int at, void* arg) in node_callback()
31 regex_t* reg; in ex() local
|
| /dports/editors/xi-core/xi-editor-0.3.0/rust/cargo-crates/onig_sys-69.1.0/oniguruma/sample/ |
| H A D | listcap.c | 11 node_callback(int group, int beg, int end, int level, int at, void* arg) in node_callback()
31 regex_t* reg; in ex() local
|
| /dports/biology/ugene/ugene-40.1/src/libs_3rdparty/samtools/src/samtools/ |
| H A D | bam2depth.c | 38 int i, n, tid, beg, end, pos, *n_plp, baseQ = 0, mapQ = 0; in main() local
40 char *reg = 0; // specified region in main() local
|
| /dports/misc/broot/broot-1.7.0/cargo-crates/onig_sys-69.7.0/oniguruma/sample/ |
| H A D | listcap.c | 11 node_callback(int group, int beg, int end, int level, int at, void* arg) in node_callback()
31 regex_t* reg; in ex() local
|
| /dports/devel/git-delta/delta-0.9.2/cargo-crates/onig_sys-69.6.0/oniguruma/sample/ |
| H A D | listcap.c | 11 node_callback(int group, int beg, int end, int level, int at, void* arg) in node_callback()
31 regex_t* reg; in ex() local
|
| /dports/emulators/qemu/qemu-6.2.0/roms/edk2/MdeModulePkg/Universal/RegularExpressionDxe/oniguruma/sample/ |
| H A D | listcap.c | 11 node_callback(int group, int beg, int end, int level, int at, void* arg) in node_callback()
31 regex_t* reg; in ex() local
|
| /dports/security/cargo-audit/rustsec-cargo-audit-v0.15.2/cargo-audit/cargo-crates/onig_sys-69.7.0/oniguruma/sample/ |
| H A D | listcap.c | 11 node_callback(int group, int beg, int end, int level, int at, void* arg) in node_callback()
31 regex_t* reg; in ex() local
|
| /dports/emulators/qemu5/qemu-5.2.0/roms/edk2/MdeModulePkg/Universal/RegularExpressionDxe/oniguruma/sample/ |
| H A D | listcap.c | 11 node_callback(int group, int beg, int end, int level, int at, void* arg) in node_callback()
31 regex_t* reg; in ex() local
|
| /dports/sysutils/uefi-edk2-bhyve/edk2-edk2-stable202102/MdeModulePkg/Universal/RegularExpressionDxe/oniguruma/sample/ |
| H A D | listcap.c | 11 node_callback(int group, int beg, int end, int level, int at, void* arg) in node_callback()
31 regex_t* reg; in ex() local
|
| /dports/devel/oniguruma/oniguruma-6.9.7.1/sample/ |
| H A D | listcap.c | 11 node_callback(int group, int beg, int end, int level, int at, void* arg) in node_callback()
31 regex_t* reg; in ex() local
|
| /dports/www/xh/xh-0.14.1/cargo-crates/onig_sys-69.7.0/oniguruma/sample/ |
| H A D | listcap.c | 11 node_callback(int group, int beg, int end, int level, int at, void* arg) in node_callback()
31 regex_t* reg; in ex() local
|
| /dports/www/zola/zola-0.15.2/cargo-crates/onig_sys-69.7.1/oniguruma/sample/ |
| H A D | listcap.c | 11 node_callback(int group, int beg, int end, int level, int at, void* arg) in node_callback()
31 regex_t* reg; in ex() local
|
| /dports/sysutils/edk2/edk2-edk2-stable202102/MdeModulePkg/Universal/RegularExpressionDxe/oniguruma/sample/ |
| H A D | listcap.c | 11 node_callback(int group, int beg, int end, int level, int at, void* arg) in node_callback()
31 regex_t* reg; in ex() local
|
| /dports/textproc/bat/bat-0.18.3/cargo-crates/onig_sys-69.6.0/oniguruma/sample/ |
| H A D | listcap.c | 11 node_callback(int group, int beg, int end, int level, int at, void* arg) in node_callback()
31 regex_t* reg; in ex() local
|