/dports/biology/vt/vt-0.57721/lib/htslib/cram/ |
H A D | cram_codecs.c | 550 cp += safe_itf8_get(cp, data + size, &c->beta.offset); in cram_beta_decode_init() 745 cp += safe_itf8_get(cp, data + size, &c->subexp.k); in cram_subexp_decode_init() 971 cp += safe_itf8_get(cp, data_end, &ncodes); in cram_huffman_decode_init() 1001 l = safe_itf8_get(cp, data_end, &codes[i].symbol); in cram_huffman_decode_init() 1007 cp += safe_itf8_get(cp, data_end, &i); in cram_huffman_decode_init() 1019 l = safe_itf8_get(cp, data_end, &codes[i].len); in cram_huffman_decode_init() 1466 cp += safe_itf8_get(cp, endp, &encoding); in cram_byte_array_len_decode_init() 1467 cp += safe_itf8_get(cp, endp, &sub_size); in cram_byte_array_len_decode_init() 1477 cp += safe_itf8_get(cp, endp, &encoding); in cram_byte_array_len_decode_init() 1478 cp += safe_itf8_get(cp, endp, &sub_size); in cram_byte_array_len_decode_init() [all …]
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H A D | cram_external.c | 333 cp += safe_itf8_get(cp, endp, &i32); in cram_transcode_rg() 335 cp += safe_itf8_get(cp, endp, &i32); in cram_transcode_rg() 338 cp += safe_itf8_get(cp, endp, &i32); in cram_transcode_rg()
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H A D | cram_decode.c | 78 cp += safe_itf8_get(cp, endp, &blk_size); in cram_decode_TD() 150 cp += safe_itf8_get(cp, endp, &hdr->ref_seq_id); in cram_decode_compression_header() 152 cp += safe_itf8_get(cp, endp, &hdr->ref_seq_span); in cram_decode_compression_header() 153 cp += safe_itf8_get(cp, endp, &hdr->num_records); in cram_decode_compression_header() 192 cp += safe_itf8_get(cp, endp, &map_count); in cram_decode_compression_header() 350 cp += safe_itf8_get(cp, endp, &map_count); in cram_decode_compression_header() 364 cp += safe_itf8_get(cp, endp, &encoding); in cram_decode_compression_header() 365 cp += safe_itf8_get(cp, endp, &size); in cram_decode_compression_header() 623 cp += safe_itf8_get(cp, endp, &map_count); in cram_decode_compression_header() 640 cp += safe_itf8_get(cp, endp, &encoding); in cram_decode_compression_header() [all …]
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H A D | cram_io.h | 272 static inline int safe_itf8_get(const char *cp, const char *endp, in safe_itf8_get() function
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/dports/biology/bedtools/bedtools2-2.30.0/src/utils/htslib/cram/ |
H A D | cram_codecs.c | 550 cp += safe_itf8_get(cp, data + size, &c->beta.offset); in cram_beta_decode_init() 745 cp += safe_itf8_get(cp, data + size, &c->subexp.k); in cram_subexp_decode_init() 971 cp += safe_itf8_get(cp, data_end, &ncodes); in cram_huffman_decode_init() 1001 l = safe_itf8_get(cp, data_end, &codes[i].symbol); in cram_huffman_decode_init() 1007 cp += safe_itf8_get(cp, data_end, &i); in cram_huffman_decode_init() 1019 l = safe_itf8_get(cp, data_end, &codes[i].len); in cram_huffman_decode_init() 1466 cp += safe_itf8_get(cp, endp, &encoding); in cram_byte_array_len_decode_init() 1467 cp += safe_itf8_get(cp, endp, &sub_size); in cram_byte_array_len_decode_init() 1477 cp += safe_itf8_get(cp, endp, &encoding); in cram_byte_array_len_decode_init() 1478 cp += safe_itf8_get(cp, endp, &sub_size); in cram_byte_array_len_decode_init() [all …]
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H A D | cram_external.c | 333 cp += safe_itf8_get(cp, endp, &i32); in cram_transcode_rg() 335 cp += safe_itf8_get(cp, endp, &i32); in cram_transcode_rg() 338 cp += safe_itf8_get(cp, endp, &i32); in cram_transcode_rg()
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H A D | cram_decode.c | 78 cp += safe_itf8_get(cp, endp, &blk_size); in cram_decode_TD() 150 cp += safe_itf8_get(cp, endp, &hdr->ref_seq_id); in cram_decode_compression_header() 152 cp += safe_itf8_get(cp, endp, &hdr->ref_seq_span); in cram_decode_compression_header() 153 cp += safe_itf8_get(cp, endp, &hdr->num_records); in cram_decode_compression_header() 192 cp += safe_itf8_get(cp, endp, &map_count); in cram_decode_compression_header() 350 cp += safe_itf8_get(cp, endp, &map_count); in cram_decode_compression_header() 364 cp += safe_itf8_get(cp, endp, &encoding); in cram_decode_compression_header() 365 cp += safe_itf8_get(cp, endp, &size); in cram_decode_compression_header() 623 cp += safe_itf8_get(cp, endp, &map_count); in cram_decode_compression_header() 640 cp += safe_itf8_get(cp, endp, &encoding); in cram_decode_compression_header() [all …]
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H A D | cram_io.h | 272 static inline int safe_itf8_get(const char *cp, const char *endp, in safe_itf8_get() function
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/dports/biology/stacks/stacks-2.4/htslib/cram/ |
H A D | cram_codecs.c | 567 cp += safe_itf8_get(cp, data + size, &c->beta.offset); in cram_beta_decode_init() 764 cp += safe_itf8_get(cp, data + size, &c->subexp.k); in cram_subexp_decode_init() 994 cp += safe_itf8_get(cp, data_end, &ncodes); in cram_huffman_decode_init() 1024 l = safe_itf8_get(cp, data_end, &codes[i].symbol); in cram_huffman_decode_init() 1030 cp += safe_itf8_get(cp, data_end, &i); in cram_huffman_decode_init() 1044 l = safe_itf8_get(cp, data_end, &codes[i].len); in cram_huffman_decode_init() 1496 cp += safe_itf8_get(cp, endp, &encoding); in cram_byte_array_len_decode_init() 1497 cp += safe_itf8_get(cp, endp, &sub_size); in cram_byte_array_len_decode_init() 1507 cp += safe_itf8_get(cp, endp, &encoding); in cram_byte_array_len_decode_init() 1508 cp += safe_itf8_get(cp, endp, &sub_size); in cram_byte_array_len_decode_init() [all …]
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H A D | cram_decode.c | 78 cp += safe_itf8_get(cp, endp, &blk_size); in cram_decode_TD() 150 cp += safe_itf8_get(cp, endp, &hdr->ref_seq_id); in cram_decode_compression_header() 152 cp += safe_itf8_get(cp, endp, &hdr->ref_seq_span); in cram_decode_compression_header() 153 cp += safe_itf8_get(cp, endp, &hdr->num_records); in cram_decode_compression_header() 192 cp += safe_itf8_get(cp, endp, &map_count); in cram_decode_compression_header() 350 cp += safe_itf8_get(cp, endp, &map_count); in cram_decode_compression_header() 364 cp += safe_itf8_get(cp, endp, &encoding); in cram_decode_compression_header() 365 cp += safe_itf8_get(cp, endp, &size); in cram_decode_compression_header() 623 cp += safe_itf8_get(cp, endp, &map_count); in cram_decode_compression_header() 640 cp += safe_itf8_get(cp, endp, &encoding); in cram_decode_compression_header() [all …]
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H A D | cram_external.c | 333 cp += safe_itf8_get(cp, endp, &i32); in cram_transcode_rg() 335 cp += safe_itf8_get(cp, endp, &i32); in cram_transcode_rg() 338 cp += safe_itf8_get(cp, endp, &i32); in cram_transcode_rg()
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H A D | cram_io.h | 272 static inline int safe_itf8_get(const char *cp, const char *endp, in safe_itf8_get() function
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/dports/biology/kallisto/kallisto-0.46.1/ext/htslib/cram/ |
H A D | cram_codecs.c | 568 cp += safe_itf8_get(cp, data + size, &c->beta.offset); in cram_beta_decode_init() 766 cp += safe_itf8_get(cp, data + size, &c->subexp.k); in cram_subexp_decode_init() 995 cp += safe_itf8_get(cp, data_end, &ncodes); in cram_huffman_decode_init() 1025 l = safe_itf8_get(cp, data_end, &codes[i].symbol); in cram_huffman_decode_init() 1033 cp += safe_itf8_get(cp, data_end, &i); in cram_huffman_decode_init() 1050 l = safe_itf8_get(cp, data_end, &codes[i].len); in cram_huffman_decode_init() 1488 cp += safe_itf8_get(cp, endp, &encoding); in cram_byte_array_len_decode_init() 1489 cp += safe_itf8_get(cp, endp, &sub_size); in cram_byte_array_len_decode_init() 1499 cp += safe_itf8_get(cp, endp, &encoding); in cram_byte_array_len_decode_init() 1500 cp += safe_itf8_get(cp, endp, &sub_size); in cram_byte_array_len_decode_init() [all …]
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H A D | cram_decode.c | 78 cp += safe_itf8_get(cp, endp, &blk_size); in cram_decode_TD() 150 cp += safe_itf8_get(cp, endp, &hdr->ref_seq_id); in cram_decode_compression_header() 152 cp += safe_itf8_get(cp, endp, &hdr->ref_seq_span); in cram_decode_compression_header() 153 cp += safe_itf8_get(cp, endp, &hdr->num_records); in cram_decode_compression_header() 192 cp += safe_itf8_get(cp, endp, &map_count); in cram_decode_compression_header() 351 cp += safe_itf8_get(cp, endp, &map_count); in cram_decode_compression_header() 365 cp += safe_itf8_get(cp, endp, &encoding); in cram_decode_compression_header() 366 cp += safe_itf8_get(cp, endp, &size); in cram_decode_compression_header() 623 cp += safe_itf8_get(cp, endp, &map_count); in cram_decode_compression_header() 640 cp += safe_itf8_get(cp, endp, &encoding); in cram_decode_compression_header() [all …]
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H A D | cram_external.c | 334 cp += safe_itf8_get(cp, endp, &i32); in cram_transcode_rg() 336 cp += safe_itf8_get(cp, endp, &i32); in cram_transcode_rg() 339 cp += safe_itf8_get(cp, endp, &i32); in cram_transcode_rg()
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H A D | cram_io.h | 272 static inline int safe_itf8_get(const char *cp, const char *endp, in safe_itf8_get() function
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/dports/biology/iolib/io_lib-io_lib-1-14-10/io_lib/ |
H A D | cram_decode.c | 87 cp += safe_itf8_get(cp, endp, &blk_size); in cram_decode_TD() 161 cp += safe_itf8_get(cp, endp, &hdr->ref_seq_id); in cram_decode_compression_header() 170 cp += safe_itf8_get(cp, endp, &hdr->num_records); in cram_decode_compression_header() 204 cp += safe_itf8_get(cp, endp, &map_count); in cram_decode_compression_header() 334 cp += safe_itf8_get(cp, endp, &map_count); in cram_decode_compression_header() 349 cp += safe_itf8_get(cp, endp, &encoding); in cram_decode_compression_header() 350 cp += safe_itf8_get(cp, endp, &size); in cram_decode_compression_header() 583 cp += safe_itf8_get(cp, endp, &map_count); in cram_decode_compression_header() 596 cp += safe_itf8_get(cp, endp, &m->key); in cram_decode_compression_header() 600 cp += safe_itf8_get(cp, endp, &encoding); in cram_decode_compression_header() [all …]
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H A D | cram_codecs.c | 342 l = safe_itf8_get(cp, (char *)b->data + b->uncomp_size, (int32_t *)out); in cram_external_decode_int() 818 cp += safe_itf8_get(cp, data + size, &c->subexp.offset); in cram_subexp_decode_init() 819 cp += safe_itf8_get(cp, data + size, &c->subexp.k); in cram_subexp_decode_init() 1089 cp += safe_itf8_get(cp, data_end, &ncodes); in cram_huffman_decode_init() 1112 l = safe_itf8_get(cp, data_end, &i32); in cram_huffman_decode_init() 1122 cp += safe_itf8_get(cp, data_end, &i); in cram_huffman_decode_init() 1137 l = safe_itf8_get(cp, data_end, &codes[i].len); in cram_huffman_decode_init() 1626 cp += safe_itf8_get(cp, endp, &encoding); in cram_byte_array_len_decode_init() 1627 cp += safe_itf8_get(cp, endp, &sub_size); in cram_byte_array_len_decode_init() 1637 cp += safe_itf8_get(cp, endp, &encoding); in cram_byte_array_len_decode_init() [all …]
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H A D | cram_io.h | 119 static inline int safe_itf8_get(const char *cp, const char *endp, in safe_itf8_get() function 342 #define safe_itf8_get uint7_get_32 macro
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/dports/biology/freebayes/freebayes-1.3.5/contrib/htslib/cram/ |
H A D | cram_external.c | 338 cp += safe_itf8_get(cp, endp, &i32); in cram_transcode_rg() 340 cp += safe_itf8_get(cp, endp, &i32); in cram_transcode_rg() 343 cp += safe_itf8_get(cp, endp, &i32); in cram_transcode_rg()
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H A D | cram_decode.c | 88 cp += safe_itf8_get(cp, endp, &blk_size); in cram_decode_TD() 164 cp += safe_itf8_get(cp, endp, &hdr->ref_seq_id); in cram_decode_compression_header() 182 cp += safe_itf8_get(cp, endp, &hdr->num_records); in cram_decode_compression_header() 183 cp += safe_itf8_get(cp, endp, &hdr->num_landmarks); in cram_decode_compression_header() 218 cp += safe_itf8_get(cp, endp, &map_count); in cram_decode_compression_header() 346 cp += safe_itf8_get(cp, endp, &map_count); in cram_decode_compression_header() 362 cp += safe_itf8_get(cp, endp, &encoding); in cram_decode_compression_header() 363 cp += safe_itf8_get(cp, endp, &size); in cram_decode_compression_header() 506 cp += safe_itf8_get(cp, endp, &map_count); in cram_decode_compression_header() 523 cp += safe_itf8_get(cp, endp, &encoding); in cram_decode_compression_header() [all …]
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H A D | cram_codecs.c | 613 cp += safe_itf8_get(cp, data + size, &c->u.beta.offset); in cram_beta_decode_init() 826 cp += safe_itf8_get(cp, data + size, &c->u.subexp.k); in cram_subexp_decode_init() 1102 cp += safe_itf8_get(cp, data_end, &ncodes); in cram_huffman_decode_init() 1138 l = safe_itf8_get(cp, data_end, &i32); in cram_huffman_decode_init() 1146 cp += safe_itf8_get(cp, data_end, &i); in cram_huffman_decode_init() 1158 l = safe_itf8_get(cp, data_end, &codes[i].len); in cram_huffman_decode_init() 1679 cp += safe_itf8_get(cp, endp, &encoding); in cram_byte_array_len_decode_init() 1680 cp += safe_itf8_get(cp, endp, &sub_size); in cram_byte_array_len_decode_init() 1690 cp += safe_itf8_get(cp, endp, &encoding); in cram_byte_array_len_decode_init() 1691 cp += safe_itf8_get(cp, endp, &sub_size); in cram_byte_array_len_decode_init() [all …]
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H A D | cram_io.h | 273 static inline int safe_itf8_get(const char *cp, const char *endp, in safe_itf8_get() function
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/dports/biology/py-pysam/pysam-0.18.0/htslib/cram/ |
H A D | cram_io.c | 639 static int64_t safe_itf8_get(char **cp, const char *endp, int *err) { in safe_itf8_get() function 5026 vv->varint_get32 = safe_itf8_get; in cram_init_varint() 5027 vv->varint_get32s = safe_itf8_get; in cram_init_varint()
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/dports/biology/htslib/htslib-1.14/cram/ |
H A D | cram_io.c | 639 static int64_t safe_itf8_get(char **cp, const char *endp, int *err) { in safe_itf8_get() function 5026 vv->varint_get32 = safe_itf8_get; in cram_init_varint() 5027 vv->varint_get32s = safe_itf8_get; in cram_init_varint()
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