INSDC_coord_len (reference) in projects: dports

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Searched refs:INSDC_coord_len (Results 1 – 25 of 154) sorted by relevance

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/dports/biology/sra-tools/sra-tools-2.11.0/ncbi-vdb/interfaces/align/
H A D	iterator.h	`91 INSDC_coord_len ref_len, 93 INSDC_coord_len read_len, 99 INSDC_coord_len ref_window_len ); 198 INSDC_coord_len len; 341 const char *idstr, INSDC_coord_zero pos, INSDC_coord_len len ); 365 INSDC_coord_zero pos, INSDC_coord_len len ); 399 INSDC_coord_zero pos, int64_t row_id, INSDC_coord_len len ); 439 INSDC_coord_zero first_pos, INSDC_coord_len len ); 455 INSDC_coord_zero pos, INSDC_coord_len len ); 483 INSDC_coord_zero pos, int64_t row_id, INSDC_coord_len *len ); [all …]`
H A D	refseq-mgr.h	`62 INSDC_coord_zero offset, INSDC_coord_len len, 63 uint8_t* buffer, INSDC_coord_len* written); 67 uint32_t seq_id_sz, INSDC_coord_zero offset, INSDC_coord_len len, 68 uint8_t* buffer, INSDC_coord_len* written, const String * accOfParentDb); 76 ALIGN_EXTERN rc_t CC RefSeq_Read(const RefSeq* cself, INSDC_coord_zero offset, INSDC_coord_len len, 77 uint8_t* buffer, INSDC_coord_len* written); 81 ALIGN_EXTERN rc_t CC RefSeq_SeqLength(const RefSeq* cself, INSDC_coord_len* len);`
H A D	writer-reference.h	`89 INSDC_coord_len length, 110 INSDC_coord_len seq_len, 115 INSDC_coord_len allele_len, 126 … rc_t CC ReferenceSeq_Read(const ReferenceSeq* cself, INSDC_coord_zero offset, INSDC_coord_len len, 127 uint8_t* buffer, INSDC_coord_len* ref_len); 137 INSDC_coord_len seq_len, 142 INSDC_coord_len allele_len, 170 INSDC_coord_len overlap_ref_len[3];`
H A D	reader-refseq.h	`56 ALIGN_EXTERN rc_t CC TableReaderRefSeq_SeqLength(const TableReaderRefSeq* cself, INSDC_coord_len* l… 66 …ableReaderRefSeq_Read(const TableReaderRefSeq* cself, INSDC_coord_zero offset, INSDC_coord_len len, 67 uint8_t* buffer, INSDC_coord_len* written);`
/dports/biology/ncbi-vdb/ncbi-vdb-2.11.0/interfaces/align/
H A D	iterator.h	`91 INSDC_coord_len ref_len, 93 INSDC_coord_len read_len, 99 INSDC_coord_len ref_window_len ); 198 INSDC_coord_len len; 341 const char *idstr, INSDC_coord_zero pos, INSDC_coord_len len ); 365 INSDC_coord_zero pos, INSDC_coord_len len ); 399 INSDC_coord_zero pos, int64_t row_id, INSDC_coord_len len ); 439 INSDC_coord_zero first_pos, INSDC_coord_len len ); 455 INSDC_coord_zero pos, INSDC_coord_len len ); 483 INSDC_coord_zero pos, int64_t row_id, INSDC_coord_len *len ); [all …]`
H A D	refseq-mgr.h	`62 INSDC_coord_zero offset, INSDC_coord_len len, 63 uint8_t* buffer, INSDC_coord_len* written); 67 uint32_t seq_id_sz, INSDC_coord_zero offset, INSDC_coord_len len, 68 uint8_t* buffer, INSDC_coord_len* written, const String * accOfParentDb); 76 ALIGN_EXTERN rc_t CC RefSeq_Read(const RefSeq* cself, INSDC_coord_zero offset, INSDC_coord_len len, 77 uint8_t* buffer, INSDC_coord_len* written); 81 ALIGN_EXTERN rc_t CC RefSeq_SeqLength(const RefSeq* cself, INSDC_coord_len* len);`
H A D	writer-reference.h	`89 INSDC_coord_len length, 110 INSDC_coord_len seq_len, 115 INSDC_coord_len allele_len, 126 … rc_t CC ReferenceSeq_Read(const ReferenceSeq* cself, INSDC_coord_zero offset, INSDC_coord_len len, 127 uint8_t* buffer, INSDC_coord_len* ref_len); 137 INSDC_coord_len seq_len, 142 INSDC_coord_len allele_len, 170 INSDC_coord_len overlap_ref_len[3];`
H A D	reader-refseq.h	`56 ALIGN_EXTERN rc_t CC TableReaderRefSeq_SeqLength(const TableReaderRefSeq* cself, INSDC_coord_len* l… 66 …ableReaderRefSeq_Read(const TableReaderRefSeq* cself, INSDC_coord_zero offset, INSDC_coord_len len, 67 uint8_t* buffer, INSDC_coord_len* written);`
/dports/biology/sra-tools/sra-tools-2.11.0/ncbi-vdb/libs/sraxf/
H A D	syn_quality.c	55 static INSDC_coord_len sum_read_len(size_t const count, INSDC_coord_len const const lengths) in sum_read_len() 57 INSDC_coord_len result = 0; in sum_read_len() 92 , INSDC_coord_len const const length in gen_syn_quality() 174 , SAFE_BASE(COL_LEN, INSDC_coord_len) in syn_quality_read_drvr() 262 INSDC_coord_len length[] = { 20, 40 }; in UnitTest_0Read_NoFilter() 280 INSDC_coord_len length[] = { 20, 40 }; in UnitTest_1Read_NoFilter() 303 INSDC_coord_len length[] = { 20, 40 }; in UnitTest_2Read_NoFilter() 326 INSDC_coord_len length[] = { 20, 40 }; in UnitTest_1Read_Pass() 349 INSDC_coord_len length[] = { 20, 40 }; in UnitTest_1Read_Fail() 372 INSDC_coord_len length[] = { 20, 40 }; in UnitTest_2Read_Pass() [all …]
/dports/biology/ncbi-vdb/ncbi-vdb-2.11.0/libs/sraxf/
H A D	syn_quality.c	55 static INSDC_coord_len sum_read_len(size_t const count, INSDC_coord_len const const lengths) in sum_read_len() 57 INSDC_coord_len result = 0; in sum_read_len() 92 , INSDC_coord_len const const length in gen_syn_quality() 174 , SAFE_BASE(COL_LEN, INSDC_coord_len) in syn_quality_read_drvr() 262 INSDC_coord_len length[] = { 20, 40 }; in UnitTest_0Read_NoFilter() 280 INSDC_coord_len length[] = { 20, 40 }; in UnitTest_1Read_NoFilter() 303 INSDC_coord_len length[] = { 20, 40 }; in UnitTest_2Read_NoFilter() 326 INSDC_coord_len length[] = { 20, 40 }; in UnitTest_1Read_Pass() 349 INSDC_coord_len length[] = { 20, 40 }; in UnitTest_1Read_Fail() 372 INSDC_coord_len length[] = { 20, 40 }; in UnitTest_2Read_Pass() [all …]
/dports/biology/sra-tools/sra-tools-2.11.0/ncbi-vdb/libs/align/
H A D	reader-wgs.c	`103 rc_t TableReaderWGS_SeqLength(TableReaderWGS const const self, int64_t row, INSDC_coord_len const… in TableReaderWGS_SeqLength() 139 INSDC_coord_len const len, in TableReaderWGS_Read() 141 INSDC_coord_len *const written) in TableReaderWGS_Read() 153 INSDC_coord_len const max = self->read->len; in TableReaderWGS_Read() 159 INSDC_coord_len const end = offset + len; in TableReaderWGS_Read() 160 INSDC_coord_len const N = end < max ? (end - offset) : (max - offset); in TableReaderWGS_Read()`
H A D	reader-wgs.h	`43 rc_t TableReaderWGS_SeqLength(const TableReaderWGS* cself, int64_t row, INSDC_coord_len* len); 54 INSDC_coord_zero offset, INSDC_coord_len len, 55 uint8_t* buffer, INSDC_coord_len* written);`
H A D	refseq-mgr.c	`119 INSDC_coord_len len, uint8_t buffer, 120 INSDC_coord_len written); 139 INSDC_coord_len len, 141 INSDC_coord_len written); 145 INSDC_coord_len result); 190 INSDC_coord_len const len, 192 INSDC_coord_len const written); 196 INSDC_coord_len const result); 355 INSDC_coord_len const length, in RefSeq_RefSeq_read() 364 INSDC_coord_len const length, in RefSeq_WGS_read() [all …]`
/dports/biology/ncbi-vdb/ncbi-vdb-2.11.0/libs/align/
H A D	reader-wgs.c	`103 rc_t TableReaderWGS_SeqLength(TableReaderWGS const const self, int64_t row, INSDC_coord_len const… in TableReaderWGS_SeqLength() 139 INSDC_coord_len const len, in TableReaderWGS_Read() 141 INSDC_coord_len *const written) in TableReaderWGS_Read() 153 INSDC_coord_len const max = self->read->len; in TableReaderWGS_Read() 159 INSDC_coord_len const end = offset + len; in TableReaderWGS_Read() 160 INSDC_coord_len const N = end < max ? (end - offset) : (max - offset); in TableReaderWGS_Read()`
H A D	reader-wgs.h	`43 rc_t TableReaderWGS_SeqLength(const TableReaderWGS* cself, int64_t row, INSDC_coord_len* len); 54 INSDC_coord_zero offset, INSDC_coord_len len, 55 uint8_t* buffer, INSDC_coord_len* written);`
H A D	refseq-mgr.c	`119 INSDC_coord_len len, uint8_t buffer, 120 INSDC_coord_len written); 139 INSDC_coord_len len, 141 INSDC_coord_len written); 145 INSDC_coord_len result); 190 INSDC_coord_len const len, 192 INSDC_coord_len const written); 196 INSDC_coord_len const result); 355 INSDC_coord_len const length, in RefSeq_RefSeq_read() 364 INSDC_coord_len const length, in RefSeq_WGS_read() [all …]`
/dports/biology/sra-tools/sra-tools-2.11.0/ncbi-vdb/libs/sra/
H A D	reader-cmn.h	`55 const INSDC_coord_len spot_len; 57 const INSDC_coord_len read_len; 62 const INSDC_coord_len label_len; 140 const char read_label, INSDC_coord_len* read_label_sz, 141 INSDC_coord_zero* read_start, INSDC_coord_len* read_len);`
H A D	reader-abi.c	`68 const INSDC_coord_len trim_len; 222 … const char read_label, INSDC_coord_len* read_label_sz, in AbsolidReader_SpotReadInfo() 223 … INSDC_coord_zero* read_start, INSDC_coord_len* read_len) in AbsolidReader_SpotReadInfo() 226 INSDC_coord_len rl; in AbsolidReader_SpotReadInfo() 268 INSDC_coord_len read_label_sz = 0; 325 INSDC_coord_len read_len = 0; 360 INSDC_coord_len j = 0, read_len = 0; 375 INSDC_coord_len i; 407 INSDC_coord_len j = 0; 414 INSDC_coord_len read_len = 0; [all …]`
/dports/biology/ncbi-vdb/ncbi-vdb-2.11.0/libs/sra/
H A D	reader-cmn.h	`55 const INSDC_coord_len spot_len; 57 const INSDC_coord_len read_len; 62 const INSDC_coord_len label_len; 140 const char read_label, INSDC_coord_len* read_label_sz, 141 INSDC_coord_zero* read_start, INSDC_coord_len* read_len);`
H A D	reader-abi.c	`68 const INSDC_coord_len trim_len; 222 … const char read_label, INSDC_coord_len* read_label_sz, in AbsolidReader_SpotReadInfo() 223 … INSDC_coord_zero* read_start, INSDC_coord_len* read_len) in AbsolidReader_SpotReadInfo() 226 INSDC_coord_len rl; in AbsolidReader_SpotReadInfo() 268 INSDC_coord_len read_label_sz = 0; 325 INSDC_coord_len read_len = 0; 360 INSDC_coord_len j = 0, read_len = 0; 375 INSDC_coord_len i; 407 INSDC_coord_len j = 0; 414 INSDC_coord_len read_len = 0; [all …]`
/dports/biology/sra-tools/sra-tools-2.11.0/ncbi-vdb/libs/axf/
H A D	ref-tbl-sub-select.c	59 INSDC_coord_zero offset, INSDC_coord_len ref_len, 78 INSDC_coord_len seq_len; 101 INSDC_coord_zero offset, INSDC_coord_len ref_len, in REFERENCE_TABLE_sub_select() 105 INSDC_coord_len num_read; in REFERENCE_TABLE_sub_select() 140 INSDC_coord_len* sl; in REFERENCE_TABLE_sub_select() 247 INSDC_coord_len num_read = 0; in ALIGN_CMN_TABLE_sub_select() 275 num_read += (INSDC_coord_len)rslt->elem_count; in ALIGN_CMN_TABLE_sub_select() 289 const INSDC_coord_len* rl; in ALIGN_CMN_TABLE_sub_select() 309 INSDC_coord_len left = ref_len - num_read; in ALIGN_CMN_TABLE_sub_select() 325 const INSDC_coord_len* al_ref_len; in ALIGN_CMN_TABLE_sub_select() [all …]
H A D	cigar.c	213 bsize = (INSDC_coord_len)bsz; in cigar_string() 457 INSDC_coord_len a = ref_len; in right_soft_clip() 490 INSDC_coord_len count; in cigar_impl() 500 INSDC_coord_len count; in cigar_impl() 560 INSDC_coord_len cnt; in cigar_impl_2() 1237 INSDC_coord_len result; in left_soft_clip_impl() 1274 INSDC_coord_len result; in left_soft_clip_impl_2() 1367 INSDC_coord_len result = 0; in right_soft_clip_impl() 1368 INSDC_coord_len left = 0; in right_soft_clip_impl() 1499 INSDC_coord_len* result; in right_soft_clip_4_impl() [all …]
/dports/biology/ncbi-vdb/ncbi-vdb-2.11.0/libs/axf/
H A D	ref-tbl-sub-select.c	59 INSDC_coord_zero offset, INSDC_coord_len ref_len, 78 INSDC_coord_len seq_len; 101 INSDC_coord_zero offset, INSDC_coord_len ref_len, in REFERENCE_TABLE_sub_select() 105 INSDC_coord_len num_read; in REFERENCE_TABLE_sub_select() 140 INSDC_coord_len* sl; in REFERENCE_TABLE_sub_select() 247 INSDC_coord_len num_read = 0; in ALIGN_CMN_TABLE_sub_select() 275 num_read += (INSDC_coord_len)rslt->elem_count; in ALIGN_CMN_TABLE_sub_select() 289 const INSDC_coord_len* rl; in ALIGN_CMN_TABLE_sub_select() 309 INSDC_coord_len left = ref_len - num_read; in ALIGN_CMN_TABLE_sub_select() 325 const INSDC_coord_len* al_ref_len; in ALIGN_CMN_TABLE_sub_select() [all …]
H A D	cigar.c	213 bsize = (INSDC_coord_len)bsz; in cigar_string() 457 INSDC_coord_len a = ref_len; in right_soft_clip() 490 INSDC_coord_len count; in cigar_impl() 500 INSDC_coord_len count; in cigar_impl() 560 INSDC_coord_len cnt; in cigar_impl_2() 1237 INSDC_coord_len result; in left_soft_clip_impl() 1274 INSDC_coord_len result; in left_soft_clip_impl_2() 1367 INSDC_coord_len result = 0; in right_soft_clip_impl() 1368 INSDC_coord_len left = 0; in right_soft_clip_impl() 1499 INSDC_coord_len* result; in right_soft_clip_4_impl() [all …]
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/sra/readers/sra/test/
H A D	csra_span_check.cpp	112 CVDBColumnBits<sizeof(INSDC_coord_len)8> col_max_seq_len; 114 CVDBColumnBits<sizeof(INSDC_coord_len)8> col_overlap_len; 124 return CVDBValueFor<INSDC_coord_len>(cursor, 1, col_max_seq_len); in GetRowSize() 160 CVDBValueFor<INSDC_coord_len> OVERLAP_REF_LEN(TVDBRowId row) const in OVERLAP_REF_LEN() 162 return CVDBValueFor<INSDC_coord_len>(cursor, row, col_overlap_len); in OVERLAP_REF_LEN() 175 CVDBColumnBits<sizeof(INSDC_coord_len)8> col_len; 181 INSDC_coord_len REF_LEN(TVDBRowId row) const in REF_LEN() 183 return CVDBValueFor<INSDC_coord_len>(cursor, row, col_len); in REF_LEN() 376 col_max_seq_len = CVDBColumnBits<sizeof(INSDC_coord_len)8>(cursor, "MAX_SEQ_LEN"); in SRef() 381 col_overlap_len = CVDBColumnBits<sizeof(INSDC_coord_len)*8>(cursor, "OVERLAP_REF_LEN"); in SRef() [all …]

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