/dports/biology/vt/vt-0.57721/lib/htslib/cram/ |
H A D | cram_io.c | 1524 if (r->h_meta) { in refs_free() 1527 for (k = kh_begin(r->h_meta); k != kh_end(r->h_meta); k++) { in refs_free() 1530 if (!kh_exist(r->h_meta, k)) in refs_free() 1538 kh_destroy(refs, r->h_meta); in refs_free() 1568 if (!(r->h_meta = kh_init(refs))) in refs_create() 1722 kh_val(r->h_meta, k) = e; in refs_load_fai() 1732 kh_val(r->h_meta, k) = e; in refs_load_fai() 1771 if (!fd->refs || !fd->refs->h_meta) in sanitise_SQ_lines() 1781 if (k == kh_end(fd->refs->h_meta)) in sanitise_SQ_lines() 1824 if (k != kh_end(r->h_meta)) { in refs2id() [all …]
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H A D | cram_structs.h | 621 khash_t(refs) *h_meta; // ref_entry*, index by name
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/dports/biology/bedtools/bedtools2-2.30.0/src/utils/htslib/cram/ |
H A D | cram_io.c | 1524 if (r->h_meta) { in refs_free() 1527 for (k = kh_begin(r->h_meta); k != kh_end(r->h_meta); k++) { in refs_free() 1530 if (!kh_exist(r->h_meta, k)) in refs_free() 1538 kh_destroy(refs, r->h_meta); in refs_free() 1568 if (!(r->h_meta = kh_init(refs))) in refs_create() 1722 kh_val(r->h_meta, k) = e; in refs_load_fai() 1732 kh_val(r->h_meta, k) = e; in refs_load_fai() 1771 if (!fd->refs || !fd->refs->h_meta) in sanitise_SQ_lines() 1781 if (k == kh_end(fd->refs->h_meta)) in sanitise_SQ_lines() 1824 if (k != kh_end(r->h_meta)) { in refs2id() [all …]
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H A D | cram_structs.h | 621 khash_t(refs) *h_meta; // ref_entry*, index by name
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/dports/biology/stacks/stacks-2.4/htslib/cram/ |
H A D | cram_io.c | 1519 if (r->h_meta) { in refs_free() 1522 for (k = kh_begin(r->h_meta); k != kh_end(r->h_meta); k++) { in refs_free() 1525 if (!kh_exist(r->h_meta, k)) in refs_free() 1527 if (!(e = kh_val(r->h_meta, k))) in refs_free() 1533 kh_destroy(refs, r->h_meta); in refs_free() 1563 if (!(r->h_meta = kh_init(refs))) in refs_create() 1717 kh_val(r->h_meta, k) = e; in refs_load_fai() 1727 kh_val(r->h_meta, k) = e; in refs_load_fai() 1776 if (k == kh_end(fd->refs->h_meta)) in sanitise_SQ_lines() 1819 if (k != kh_end(r->h_meta)) { in refs2id() [all …]
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H A D | cram_structs.h | 617 khash_t(refs) *h_meta; // ref_entry*, index by name
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/dports/biology/kallisto/kallisto-0.46.1/ext/htslib/cram/ |
H A D | cram_io.c | 1515 if (r->h_meta) { in refs_free() 1518 for (k = kh_begin(r->h_meta); k != kh_end(r->h_meta); k++) { in refs_free() 1521 if (!kh_exist(r->h_meta, k)) in refs_free() 1523 if (!(e = kh_val(r->h_meta, k))) in refs_free() 1529 kh_destroy(refs, r->h_meta); in refs_free() 1559 if (!(r->h_meta = kh_init(refs))) in refs_create() 1713 kh_val(r->h_meta, k) = e; in refs_load_fai() 1723 kh_val(r->h_meta, k) = e; in refs_load_fai() 1772 if (k == kh_end(fd->refs->h_meta)) in sanitise_SQ_lines() 1816 if (k != kh_end(r->h_meta)) { in refs2id() [all …]
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H A D | cram_structs.h | 617 khash_t(refs) *h_meta; // ref_entry*, index by name
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/dports/biology/freebayes/freebayes-1.3.5/contrib/htslib/cram/ |
H A D | cram_io.c | 1699 if (r->h_meta) { in refs_free() 1702 for (k = kh_begin(r->h_meta); k != kh_end(r->h_meta); k++) { in refs_free() 1705 if (!kh_exist(r->h_meta, k)) in refs_free() 1713 kh_destroy(refs, r->h_meta); in refs_free() 1743 if (!(r->h_meta = kh_init(refs))) in refs_create() 1901 kh_val(r->h_meta, k) = e; in refs_load_fai() 1911 kh_val(r->h_meta, k) = e; in refs_load_fai() 1955 if (!fd->refs || !fd->refs->h_meta) in sanitise_SQ_lines() 1965 if (k == kh_end(fd->refs->h_meta)) in sanitise_SQ_lines() 2009 if (k != kh_end(r->h_meta)) { in refs2id() [all …]
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H A D | cram_structs.h | 627 khash_t(refs) *h_meta; // ref_entry*, index by name
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/dports/biology/py-pysam/pysam-0.18.0/htslib/cram/ |
H A D | cram_io.c | 2391 if (r->h_meta) { in refs_free() 2394 for (k = kh_begin(r->h_meta); k != kh_end(r->h_meta); k++) { in refs_free() 2397 if (!kh_exist(r->h_meta, k)) in refs_free() 2405 kh_destroy(refs, r->h_meta); in refs_free() 2435 if (!(r->h_meta = kh_init(refs))) in refs_create() 2593 kh_val(r->h_meta, k) = e; in refs_load_fai() 2603 kh_val(r->h_meta, k) = e; in refs_load_fai() 2647 if (!fd->refs || !fd->refs->h_meta) in sanitise_SQ_lines() 2657 if (k == kh_end(fd->refs->h_meta)) in sanitise_SQ_lines() 2701 if (k != kh_end(r->h_meta)) { in refs2id() [all …]
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H A D | cram_structs.h | 685 khash_t(refs) *h_meta; // ref_entry*, index by name
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/dports/biology/htslib/htslib-1.14/cram/ |
H A D | cram_io.c | 2391 if (r->h_meta) { in refs_free() 2394 for (k = kh_begin(r->h_meta); k != kh_end(r->h_meta); k++) { in refs_free() 2397 if (!kh_exist(r->h_meta, k)) in refs_free() 2405 kh_destroy(refs, r->h_meta); in refs_free() 2435 if (!(r->h_meta = kh_init(refs))) in refs_create() 2593 kh_val(r->h_meta, k) = e; in refs_load_fai() 2603 kh_val(r->h_meta, k) = e; in refs_load_fai() 2647 if (!fd->refs || !fd->refs->h_meta) in sanitise_SQ_lines() 2657 if (k == kh_end(fd->refs->h_meta)) in sanitise_SQ_lines() 2701 if (k != kh_end(r->h_meta)) { in refs2id() [all …]
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H A D | cram_structs.h | 685 khash_t(refs) *h_meta; // ref_entry*, index by name
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/dports/biology/iolib/io_lib-io_lib-1-14-10/io_lib/ |
H A D | cram_io.c | 2467 if (r->h_meta) { in refs_free() 2471 while ((hi = HashTableIterNext(r->h_meta, iter))) { in refs_free() 2480 HashTableDestroy(r->h_meta, 0); in refs_free() 2510 r->h_meta = HashTableCreate(16, HASH_DYNAMIC_SIZE | HASH_NONVOLATILE_KEYS); in refs_create() 2511 if (!r->h_meta) in refs_create() 2622 if (!(hi = HashTableAdd(r->h_meta, e->name, strlen(e->name), hd, &n))){ in refs_load_fai() 2680 if (!fd->refs || !fd->refs->h_meta) in sanitise_SQ_lines() 2685 HashItem *hi = HashTableSearch(fd->refs->h_meta, name, 0); in sanitise_SQ_lines() 2734 if ((hi = HashTableSearch(r->h_meta, h->ref[i].name, 0))) { in refs2id() 2777 if (HashTableSearch(r->h_meta, h->ref[i].name, strlen(h->ref[i].name))) in refs_from_header() [all …]
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H A D | cram_structs.h | 630 HashTable *h_meta; // ref_entry*, index by name member
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