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Searched refs:safe_itf8_get (Results 1 – 25 of 25) sorted by relevance

/dports/biology/vt/vt-0.57721/lib/htslib/cram/
H A Dcram_codecs.c550 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 …]
H A Dcram_external.c333 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()
H A Dcram_decode.c78 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 …]
H A Dcram_io.h272 static inline int safe_itf8_get(const char *cp, const char *endp, in safe_itf8_get() function
/dports/biology/bedtools/bedtools2-2.30.0/src/utils/htslib/cram/
H A Dcram_codecs.c550 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 …]
H A Dcram_external.c333 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()
H A Dcram_decode.c78 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 …]
H A Dcram_io.h272 static inline int safe_itf8_get(const char *cp, const char *endp, in safe_itf8_get() function
/dports/biology/stacks/stacks-2.4/htslib/cram/
H A Dcram_codecs.c567 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 …]
H A Dcram_decode.c78 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 …]
H A Dcram_external.c333 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()
H A Dcram_io.h272 static inline int safe_itf8_get(const char *cp, const char *endp, in safe_itf8_get() function
/dports/biology/kallisto/kallisto-0.46.1/ext/htslib/cram/
H A Dcram_codecs.c568 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 …]
H A Dcram_decode.c78 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 …]
H A Dcram_external.c334 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()
H A Dcram_io.h272 static inline int safe_itf8_get(const char *cp, const char *endp, in safe_itf8_get() function
/dports/biology/iolib/io_lib-io_lib-1-14-10/io_lib/
H A Dcram_decode.c87 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 …]
H A Dcram_codecs.c342 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 …]
H A Dcram_io.h119 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
/dports/biology/freebayes/freebayes-1.3.5/contrib/htslib/cram/
H A Dcram_external.c338 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()
H A Dcram_decode.c88 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 …]
H A Dcram_codecs.c613 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 …]
H A Dcram_io.h273 static inline int safe_itf8_get(const char *cp, const char *endp, in safe_itf8_get() function
/dports/biology/py-pysam/pysam-0.18.0/htslib/cram/
H A Dcram_io.c639 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()
/dports/biology/htslib/htslib-1.14/cram/
H A Dcram_io.c639 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()