/dports/biology/sra-tools/sra-tools-2.11.0/tools/fasterq-dump/ |
H A D | raw_read_iter.c | 38 uint32_t seq_spot_id, seq_read_id, read_id; member 71 rc = cmn_iter_add_column( i -> cmn, "SEQ_SPOT_ID", &i -> seq_spot_id ); in make_raw_read_iter() 83 rc = cmn_iter_range( i -> cmn, i -> seq_spot_id ); in make_raw_read_iter() 102 *rc = cmn_read_uint64( iter -> cmn, iter -> seq_spot_id, &rec -> seq_spot_id ); in get_from_raw_read_iter() 146 uint64_t key = rec . seq_spot_id; in write_out_prim()
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H A D | lookup_writer.c | 190 int64_t seq_spot_id, in write_unpacked_to_lookup_writer() argument 194 uint64_t key = make_key( seq_spot_id, seq_read_id ); /* helper.c */ in write_unpacked_to_lookup_writer()
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H A D | lookup_writer.h | 58 int64_t seq_spot_id, uint32_t seq_read_id, const String * bases_as_unpacked_4na );
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H A D | raw_read_iter.h | 50 uint64_t seq_spot_id; member
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H A D | join.h | 87 uint64_t seq_spot_id,
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H A D | sorter.c | 219 uint64_t key = make_key( rec . seq_spot_id, rec . seq_read_id ); /* helper.c */ in producer_thread_func() 231 ErrMsg( "sorter.c get_from_raw_read_iter( %lu ) -> %R", rec . seq_spot_id, rc1 ); in producer_thread_func()
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H A D | join.c | 1511 … rc = lookup_bases( lookup, rec . seq_spot_id, rec . seq_read_id, &buffer, false ); in check_lookup() 1514 … KOutMsg( "lookup_bases( %lu.%u ) --> %R\n", rec . seq_spot_id, rec . seq_read_id, rc ); in check_lookup() 1542 uint64_t seq_spot_id, in check_lookup_this() argument 1557 rc = lookup_bases( lookup, seq_spot_id, seq_read_id, &buffer, false ); in check_lookup_this() 1560 KOutMsg( "lookup_bases( %lu.%u ) --> %R\n", seq_spot_id, seq_read_id, rc ); in check_lookup_this()
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H A D | helper.h | 161 uint64_t make_key( int64_t seq_spot_id, uint32_t seq_read_id );
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H A D | helper.c | 445 uint64_t make_key( int64_t seq_spot_id, uint32_t seq_read_id ) in make_key() argument 447 uint64_t key = seq_spot_id; in make_key()
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/dports/biology/sra-tools/sra-tools-2.11.0/tools/cg-load/ |
H A D | writer-evidence-dnbs.c | 58 int64_t seq_spot_id; member 106 self->algn.seq_spot_id.buffer = &self->match.seq_spot_id; in CGWriterEvdDnbs_Make() 107 self->algn.seq_spot_id.elements = 1; in CGWriterEvdDnbs_Make() 169 … self->data.dnbs[dnb].seq_spot_id = seq_spot_id_1st + self->data.dnbs[dnb].dnb_offset_in_lane_file; in CGWriterEvdDnbs_SetSEQ() 229 self->match.seq_spot_id = cself->data.dnbs[i].seq_spot_id; in CGWriterEvdDnbs_Write()
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H A D | writer-evidence-dnbs.h | 47 int64_t seq_spot_id; member
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H A D | writer-algn.c | 59 int64_t seq_spot_id; member 110 self->algn[i].seq_spot_id.buffer = &self->match[i].seq_spot_id; in CGWriterAlgn_Make() 111 self->algn[i].seq_spot_id.elements = 1; in CGWriterAlgn_Make() 584 self->match[i].seq_spot_id = read->rowid; in CGWriterAlgn_Write_int()
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/dports/biology/sra-tools/sra-tools-2.11.0/tools/vdb-validate/ |
H A D | check-corrupt.cpp | 190 int64_t seq_spot_id = *p_seq_spot_id; in runChecks() local 191 if (seq_spot_id == 0) in runChecks() 194 ss << "SECONDARY_ALIGNMENT:" << sa_row_id << " has SEQ_SPOT_ID = " << seq_spot_id; in runChecks() 267 …rc = VCursorCellDataDirect ( seq_cursor, seq_spot_id, seq_read_len_idx, NULL, (const void**)&p_seq… in runChecks() 269 …DB_ROW_ERROR("VCursorCellDataDirect() failed on SEQUENCE table, READ_LEN column", seq_spot_id, rc); in runChecks() 274 …AD_ID value (" << seq_read_id << ") - 1 based, is out of SEQUENCE:" << seq_spot_id << " READ_LEN r… in runChecks() 282 …_OFFSET length (" << pa_row_len << ") does not match its SEQUENCE:" << seq_spot_id << " READ_LEN["… in runChecks()
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H A D | vdb-validate.c | 1828 int64_t seq_spot_id; in ridc_align_seq_pri_sec() local 1843 seq_spot_id = *(const int64_t *)data_ptr; in ridc_align_seq_pri_sec() 1845 if (seq_spot_id == 0) in ridc_align_seq_pri_sec() 1853 ordered &= last_seq_spot_id <= seq_spot_id; in ridc_align_seq_pri_sec() 1854 last_seq_spot_id = seq_spot_id; in ridc_align_seq_pri_sec() 1856 seq_spot_id_pairs[i].first = seq_spot_id; in ridc_align_seq_pri_sec() 1873 seq_spot_read_id_pairs[i].first = seq_spot_id; in ridc_align_seq_pri_sec() 1890 int64_t seq_spot_id = seq_spot_id_pairs[i].first; in ridc_align_seq_pri_sec() local 1901 "name=%s,SPOT_ID=%ld", dbname, seq_spot_id)); in ridc_align_seq_pri_sec() 1939 "name=%s,ROW_ID=%ld", dbname, seq_spot_id)); in ridc_align_seq_pri_sec() [all …]
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/dports/biology/sra-tools/sra-tools-2.11.0/tools/sra-pileup/ |
H A D | sam-unaligned.c | 321 int64_t seq_spot_id; in get_mate_info() local 322 … rc = matecache_lookup_unaligned( mc, ids->db_idx, mate_id, mate_ref_pos, &ref_idx, &seq_spot_id ); in get_mate_info() 630 int64_t seq_spot_id; in dump_seq_row_sam_filtered() local 632 …c = matecache_lookup_unaligned( mc, ids->db_idx, align_id, &mate_ref_pos, &ref_idx, &seq_spot_id ); in dump_seq_row_sam_filtered() 666 … rc = KOutMsg( "%ld.%.*s\t", seq_spot_id, spot_group_len, spot_group ); in dump_seq_row_sam_filtered() 672 rc = KOutMsg( "%ld\t", seq_spot_id ); in dump_seq_row_sam_filtered() 1095 int64_t seq_spot_id; in dump_seq_row_fastx_filtered() local 1096 …c = matecache_lookup_unaligned( mc, ids->db_idx, align_id, &mate_ref_pos, &ref_idx, &seq_spot_id ); in dump_seq_row_fastx_filtered() 1112 … rc = dump_name( opts, seq_spot_id, spot_group, spot_group_len ); /* sam-dump-opts.c */ in dump_seq_row_fastx_filtered()
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H A D | sam-dump-opts.c | 1441 rc_t dump_name( const samdump_opts * opts, int64_t seq_spot_id, in dump_name() argument 1449 rc = KOutMsg( "%.*s-1:%lu", spot_group_len, spot_group, seq_spot_id ); in dump_name() 1451 rc = KOutMsg( "%lu", seq_spot_id ); in dump_name() 1459 … rc = KOutMsg( "%s.%lu.%.*s", opts->qname_prefix, seq_spot_id, spot_group_len, spot_group ); in dump_name() 1462 rc = KOutMsg( "%s.%lu", opts->qname_prefix, seq_spot_id ); in dump_name() 1468 rc = KOutMsg( "%lu.%.*s", seq_spot_id, spot_group_len, spot_group ); in dump_name() 1471 rc = KOutMsg( "%lu", seq_spot_id ); in dump_name()
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H A D | sam-aligned.c | 1473 const int64_t * seq_spot_id; in print_alignment_sam_ps() local 1489 …rc = read_int64_ptr( id, cursor, atx->cmn.seq_spot_id_idx, &seq_spot_id, &seq_spot_id_len, "SEQ_SP… in print_alignment_sam_ps() 1580 … rc = matecache_insert_unaligned( mc, atx->db_idx, key, pos, atx->ref_idx, *seq_spot_id ); in print_alignment_sam_ps() 1601 … rc = dump_name( opts, *seq_spot_id, spot_group, spot_group_len ); /* sam-dump-opts.c */ in print_alignment_sam_ps() 1604 rc = dump_name( opts, *seq_spot_id, NULL, 0 ); /* sam-dump-opts.c */ in print_alignment_sam_ps() 1873 const int64_t * seq_spot_id; in print_alignment_fastx() local 1876 …rc_t rc = read_int64_ptr( rec->id, cursor, atx->cmn.seq_spot_id_idx, &seq_spot_id, &seq_spot_id_le… in print_alignment_fastx() 1884 … rc = matecache_insert_unaligned( mc, atx->db_idx, rec->id, pos, atx->ref_idx, *seq_spot_id ); in print_alignment_fastx() 1904 … rc = dump_name( opts, *seq_spot_id, spot_grp, spot_grp_len ); /* sam-dump-opts.c */ in print_alignment_fastx() 1907 rc = dump_name( opts, *seq_spot_id, NULL, 0 ); /* sam-dump-opts.c */ in print_alignment_fastx()
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H A D | sam-dump-opts.h | 297 rc_t dump_name( const samdump_opts * opts, int64_t seq_spot_id,
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/dports/biology/sra-tools/sra-tools-2.11.0/ncbi-vdb/interfaces/align/ |
H A D | writer-alignment.h | 92 TableWriterData seq_spot_id; member
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H A D | align.vschema | 132 * "seq_spot_id" [ DATA ] 137 T NCBI:align:project_from_sequence #1 < ascii col> ( I64 seq_spot_id, INSDC:coord:one seq_read_id )
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/dports/biology/ncbi-vdb/ncbi-vdb-2.11.0/interfaces/align/ |
H A D | writer-alignment.h | 92 TableWriterData seq_spot_id; member
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/dports/biology/sra-tools/sra-tools-2.11.0/ncbi-vdb/libs/ngs/ |
H A D | CSRA1_Alignment.c | 900 int64_t seq_spot_id; in CSRA1_AlignmentIteratorNext() local 905 …TRY ( seq_spot_id = NGS_CursorGetInt64 ( self -> secondary_curs, ctx, self -> cur_row, align_SEQ_S… in CSRA1_AlignmentIteratorNext() 907 if ( seq_spot_id > 0 ) in CSRA1_AlignmentIteratorNext()
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/dports/biology/ncbi-vdb/ncbi-vdb-2.11.0/libs/ngs/ |
H A D | CSRA1_Alignment.c | 900 int64_t seq_spot_id; in CSRA1_AlignmentIteratorNext() local 905 …TRY ( seq_spot_id = NGS_CursorGetInt64 ( self -> secondary_curs, ctx, self -> cur_row, align_SEQ_S… in CSRA1_AlignmentIteratorNext() 907 if ( seq_spot_id > 0 ) in CSRA1_AlignmentIteratorNext()
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/dports/biology/sra-tools/sra-tools-2.11.0/ncbi-vdb/libs/align/ |
H A D | writer-alignment.c | 255 TW_COL_WRITE(cself->base, cself->cols[ewalgn_cn_SEQ_SPOT_ID], data->seq_spot_id); in TableWriterAlgn_Write()
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/dports/biology/ncbi-vdb/ncbi-vdb-2.11.0/libs/align/ |
H A D | writer-alignment.c | 255 TW_COL_WRITE(cself->base, cself->cols[ewalgn_cn_SEQ_SPOT_ID], data->seq_spot_id); in TableWriterAlgn_Write()
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