| /dports/biology/samtools/samtools-1.14/ |
| H A D | bam_tview.c | 45 if (!rg_hash) in destroy_rg_hash()
48 for (k = 0; k < kh_end(rg_hash); k++) { in destroy_rg_hash()
49 if (kh_exist(rg_hash, k)) in destroy_rg_hash()
52 kh_destroy(kh_rg, rg_hash); in destroy_rg_hash()
60 khash_t(kh_rg)* rg_hash = kh_init(kh_rg); in khash_t()
61 if (!rg_hash) return NULL; in khash_t()
92 return rg_hash; in khash_t()
99 destroy_rg_hash(rg_hash); in khash_t()
148 if (kh_size(tv->rg_hash) == 0) { in base_tv_init()
168 destroy_rg_hash(tv->rg_hash); in base_tv_destroy()
[all …]
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| H A D | bam_split.c | 69 kh_c2i_t* rg_hash; member
363 retval->rg_hash = kh_init_c2i(); in init()
365 !retval->rg_hash || !retval->rg_index_file_name) { in init()
409 khiter_t iter = kh_put_c2i(retval->rg_hash, retval->rg_id[i], &ret); in init()
416 kh_val(retval->rg_hash,iter) = i; in init()
482 iter = kh_get_c2i(state->rg_hash, rg); in split()
484 iter = kh_end(state->rg_hash); in split()
488 if (iter != kh_end(state->rg_hash)) { in split()
490 int i = kh_val(state->rg_hash,iter); in split()
572 kh_destroy_c2i(status->rg_hash); in cleanup_state()
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| H A D | bam_tview.h | 60 khash_t(kh_rg) *rg_hash;
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| H A D | stats.c | 242 void *rg_hash; // Read groups to include, the array is null-terminated member
1144 if ( stats->rg_hash ) in collect_stats()
1148 khint_t k = kh_get(rg, stats->rg_hash, (const char*)(rg + 1)); in collect_stats()
1149 if ( k == kh_end((kh_rg_t *)stats->rg_hash) ) return; in collect_stats()
2028 stats->rg_hash = kh_init(rg); in init_group_id()
2029 if (!stats->rg_hash) error("Could not initialise RG set\n"); in init_group_id()
2039 kh_put(rg, stats->rg_hash, key, &ret); in init_group_id()
2044 kh_put(rg, stats->rg_hash, key, &ret); in init_group_id()
2128 if ( stats->rg_hash ) kh_destroy(rg, stats->rg_hash); in cleanup_stats()
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| /dports/biology/py-pysam/pysam-0.18.0/samtools/ |
| H A D | bam_split.c | 69 kh_c2i_t* rg_hash; member
363 retval->rg_hash = kh_init_c2i(); in init()
365 !retval->rg_hash || !retval->rg_index_file_name) { in init()
409 khiter_t iter = kh_put_c2i(retval->rg_hash, retval->rg_id[i], &ret); in init()
416 kh_val(retval->rg_hash,iter) = i; in init()
482 iter = kh_get_c2i(state->rg_hash, rg); in split()
484 iter = kh_end(state->rg_hash); in split()
488 if (iter != kh_end(state->rg_hash)) { in split()
490 int i = kh_val(state->rg_hash,iter); in split()
572 kh_destroy_c2i(status->rg_hash); in cleanup_state()
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| H A D | bam_split.c.pysam.c | 71 kh_c2i_t* rg_hash; member
365 retval->rg_hash = kh_init_c2i(); in init()
367 !retval->rg_hash || !retval->rg_index_file_name) { in init()
411 khiter_t iter = kh_put_c2i(retval->rg_hash, retval->rg_id[i], &ret); in init()
418 kh_val(retval->rg_hash,iter) = i; in init()
484 iter = kh_get_c2i(state->rg_hash, rg); in split()
486 iter = kh_end(state->rg_hash); in split()
490 if (iter != kh_end(state->rg_hash)) { in split()
492 int i = kh_val(state->rg_hash,iter); in split()
574 kh_destroy_c2i(status->rg_hash); in cleanup_state()
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| H A D | stats.c | 242 void *rg_hash; // Read groups to include, the array is null-terminated member
1144 if ( stats->rg_hash ) in collect_stats()
1148 khint_t k = kh_get(rg, stats->rg_hash, (const char*)(rg + 1)); in collect_stats()
1149 if ( k == kh_end((kh_rg_t *)stats->rg_hash) ) return; in collect_stats()
2028 stats->rg_hash = kh_init(rg); in init_group_id()
2029 if (!stats->rg_hash) error("Could not initialise RG set\n"); in init_group_id()
2039 kh_put(rg, stats->rg_hash, key, &ret); in init_group_id()
2044 kh_put(rg, stats->rg_hash, key, &ret); in init_group_id()
2128 if ( stats->rg_hash ) kh_destroy(rg, stats->rg_hash); in cleanup_stats()
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| H A D | stats.c.pysam.c | 244 void *rg_hash; // Read groups to include, the array is null-terminated member
1146 if ( stats->rg_hash ) in collect_stats()
1150 khint_t k = kh_get(rg, stats->rg_hash, (const char*)(rg + 1)); in collect_stats()
1151 if ( k == kh_end((kh_rg_t *)stats->rg_hash) ) return; in collect_stats()
2030 stats->rg_hash = kh_init(rg); in init_group_id()
2031 if (!stats->rg_hash) error("Could not initialise RG set\n"); in init_group_id()
2041 kh_put(rg, stats->rg_hash, key, &ret); in init_group_id()
2046 kh_put(rg, stats->rg_hash, key, &ret); in init_group_id()
2130 if ( stats->rg_hash ) kh_destroy(rg, stats->rg_hash); in cleanup_stats()
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| /dports/biology/py-pysam/pysam-0.18.0/htslib/ |
| H A D | header.c | 275 if (k < kh_end(hrecs->rg_hash)) { in sam_hrecs_update_hashes()
276 nrg = kh_val(hrecs->rg_hash, k); in sam_hrecs_update_hashes()
304 kh_val(hrecs->rg_hash, k) = nrg; in sam_hrecs_update_hashes()
1510 id_tag = "ID"; hash = hrecs->rg_hash; in check_for_name_update()
1791 if (k != kh_end(hrecs->rg_hash)) in sam_hdr_line_index()
1792 idx = kh_val(hrecs->rg_hash, k); in sam_hdr_line_index()
2320 if (!(hrecs->rg_hash = kh_init(m_s2i))) in sam_hrecs_new()
2391 if (hrecs->rg_hash) in sam_hrecs_free()
2392 kh_destroy(m_s2i, hrecs->rg_hash); in sam_hrecs_free()
2454 return k != kh_end(hrecs->rg_hash) in sam_hrecs_find_type_id()
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| H A D | header.h | 199 khash_t(m_s2i) *rg_hash; //!< Maps RG ID field to rg[] index
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| /dports/biology/freebayes/freebayes-1.3.5/contrib/htslib/ |
| H A D | header.c | 275 if (k < kh_end(hrecs->rg_hash)) { in sam_hrecs_update_hashes()
276 nrg = kh_val(hrecs->rg_hash, k); in sam_hrecs_update_hashes()
304 kh_val(hrecs->rg_hash, k) = nrg; in sam_hrecs_update_hashes()
1505 id_tag = "ID"; hash = hrecs->rg_hash; in check_for_name_update()
1786 if (k != kh_end(hrecs->rg_hash)) in sam_hdr_line_index()
1787 idx = kh_val(hrecs->rg_hash, k); in sam_hdr_line_index()
2315 if (!(hrecs->rg_hash = kh_init(m_s2i))) in sam_hrecs_new()
2386 if (hrecs->rg_hash) in sam_hrecs_free()
2387 kh_destroy(m_s2i, hrecs->rg_hash); in sam_hrecs_free()
2449 return k != kh_end(hrecs->rg_hash) in sam_hrecs_find_type_id()
[all …]
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| H A D | header.h | 199 khash_t(m_s2i) *rg_hash; //!< Maps RG ID field to rg[] index
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| /dports/biology/htslib/htslib-1.14/ |
| H A D | header.c | 275 if (k < kh_end(hrecs->rg_hash)) { in sam_hrecs_update_hashes()
276 nrg = kh_val(hrecs->rg_hash, k); in sam_hrecs_update_hashes()
304 kh_val(hrecs->rg_hash, k) = nrg; in sam_hrecs_update_hashes()
1510 id_tag = "ID"; hash = hrecs->rg_hash; in check_for_name_update()
1791 if (k != kh_end(hrecs->rg_hash)) in sam_hdr_line_index()
1792 idx = kh_val(hrecs->rg_hash, k); in sam_hdr_line_index()
2320 if (!(hrecs->rg_hash = kh_init(m_s2i))) in sam_hrecs_new()
2391 if (hrecs->rg_hash) in sam_hrecs_free()
2392 kh_destroy(m_s2i, hrecs->rg_hash); in sam_hrecs_free()
2454 return k != kh_end(hrecs->rg_hash) in sam_hrecs_find_type_id()
[all …]
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| H A D | header.h | 199 khash_t(m_s2i) *rg_hash; //!< Maps RG ID field to rg[] index
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| /dports/biology/vt/vt-0.57721/lib/htslib/cram/ |
| H A D | sam_header.c | 175 k = kh_put(m_s2i, sh->rg_hash, sh->rg[nrg].name, &r); in sam_hdr_update_hashes()
177 kh_val(sh->rg_hash, k) = nrg; in sam_hdr_update_hashes()
589 k = kh_get(m_s2i, hdr->rg_hash, ID_value); in sam_hdr_find()
590 return k != kh_end(hdr->rg_hash) in sam_hdr_find()
591 ? hdr->rg[kh_val(hdr->rg_hash, k)].ty in sam_hdr_find()
882 if (!(sh->rg_hash = kh_init(m_s2i))) in sam_hdr_new()
1027 if (hdr->rg_hash) in sam_hdr_free()
1028 kh_destroy(m_s2i, hdr->rg_hash); in sam_hdr_free()
1088 khint_t k = kh_get(m_s2i, hdr->rg_hash, rg); in sam_hdr_find_rg()
1089 return k == kh_end(hdr->rg_hash) in sam_hdr_find_rg()
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| H A D | sam_header.h | 199 khash_t(m_s2i) *rg_hash; //!< Maps RG ID field to rg[] index
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| /dports/biology/bedtools/bedtools2-2.30.0/src/utils/htslib/cram/ |
| H A D | sam_header.c | 175 k = kh_put(m_s2i, sh->rg_hash, sh->rg[nrg].name, &r); in sam_hdr_update_hashes()
177 kh_val(sh->rg_hash, k) = nrg; in sam_hdr_update_hashes()
589 k = kh_get(m_s2i, hdr->rg_hash, ID_value); in sam_hdr_find()
590 return k != kh_end(hdr->rg_hash) in sam_hdr_find()
591 ? hdr->rg[kh_val(hdr->rg_hash, k)].ty in sam_hdr_find()
882 if (!(sh->rg_hash = kh_init(m_s2i))) in sam_hdr_new()
1027 if (hdr->rg_hash) in sam_hdr_free()
1028 kh_destroy(m_s2i, hdr->rg_hash); in sam_hdr_free()
1088 khint_t k = kh_get(m_s2i, hdr->rg_hash, rg); in sam_hdr_find_rg()
1089 return k == kh_end(hdr->rg_hash) in sam_hdr_find_rg()
[all …]
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| H A D | sam_header.h | 199 khash_t(m_s2i) *rg_hash; //!< Maps RG ID field to rg[] index
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| /dports/biology/stacks/stacks-2.4/htslib/cram/ |
| H A D | sam_header.c | 175 k = kh_put(m_s2i, sh->rg_hash, sh->rg[nrg].name, &r); in sam_hdr_update_hashes()
177 kh_val(sh->rg_hash, k) = nrg; in sam_hdr_update_hashes()
589 k = kh_get(m_s2i, hdr->rg_hash, ID_value); in sam_hdr_find()
590 return k != kh_end(hdr->rg_hash) in sam_hdr_find()
591 ? hdr->rg[kh_val(hdr->rg_hash, k)].ty in sam_hdr_find()
882 if (!(sh->rg_hash = kh_init(m_s2i))) in sam_hdr_new()
1027 if (hdr->rg_hash) in sam_hdr_free()
1028 kh_destroy(m_s2i, hdr->rg_hash); in sam_hdr_free()
1088 khint_t k = kh_get(m_s2i, hdr->rg_hash, rg); in sam_hdr_find_rg()
1089 return k == kh_end(hdr->rg_hash) in sam_hdr_find_rg()
[all …]
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| H A D | sam_header.h | 199 khash_t(m_s2i) *rg_hash; //!< Maps RG ID field to rg[] index
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| /dports/biology/kallisto/kallisto-0.46.1/ext/htslib/cram/ |
| H A D | sam_header.c | 174 k = kh_put(m_s2i, sh->rg_hash, sh->rg[nrg].name, &r); in sam_hdr_update_hashes()
176 kh_val(sh->rg_hash, k) = nrg; in sam_hdr_update_hashes()
588 k = kh_get(m_s2i, hdr->rg_hash, ID_value); in sam_hdr_find()
589 return k != kh_end(hdr->rg_hash) in sam_hdr_find()
590 ? hdr->rg[kh_val(hdr->rg_hash, k)].ty in sam_hdr_find()
882 if (!(sh->rg_hash = kh_init(m_s2i))) in sam_hdr_new()
1027 if (hdr->rg_hash) in sam_hdr_free()
1028 kh_destroy(m_s2i, hdr->rg_hash); in sam_hdr_free()
1088 khint_t k = kh_get(m_s2i, hdr->rg_hash, rg); in sam_hdr_find_rg()
1089 return k == kh_end(hdr->rg_hash) in sam_hdr_find_rg()
[all …]
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| H A D | sam_header.h | 199 khash_t(m_s2i) *rg_hash; //!< Maps RG ID field to rg[] index
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| /dports/biology/iolib/io_lib-io_lib-1-14-10/io_lib/ |
| H A D | sam_header.c | 177 if (!HashTableAdd(sh->rg_hash, sh->rg[nrg].name, 0, hd, NULL)) in sam_hdr_update_hashes()
593 hi = HashTableSearch(hdr->rg_hash, ID_value, strlen(ID_value)); in sam_hdr_find()
900 if (!(sh->rg_hash = HashTableCreate(16, HASH_FUNC_HSIEH | in sam_hdr_new()
1056 if (hdr->rg_hash) in sam_hdr_free()
1057 HashTableDestroy(hdr->rg_hash, 0); in sam_hdr_free()
1117 HashItem *hi = HashTableSearch(hdr->rg_hash, rg, 0); in sam_hdr_find_rg()
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| H A D | sam_header.h | 200 HashTable *rg_hash; //!< Hash table indexed by ID: field member
|