| /dports/biology/sra-tools/sra-tools-2.11.0/tools/bam-loader/ |
| H A D | alignment-writer.c | 100 if (data->mate_ref_pos == 0) { in WriteSecondaryRecord()
249 self->data.mate_ref_pos.buffer = &self->mate_ref_pos; in AlignmentRecordInit()
250 self->data.mate_ref_pos.elements = 1; in AlignmentRecordInit()
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| H A D | alignment-writer.h | 61 INSDC_coord_zero mate_ref_pos; member
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| H A D | loader-imp.c | 2579 data.mate_ref_pos = mpos; in ProcessBAM()
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| /dports/biology/sra-tools/sra-tools-2.11.0/ncbi-vdb/libs/loader/ |
| H A D | alignment-writer.c | 100 if (data->mate_ref_pos == 0) { in WriteSecondaryRecord()
252 self->data.mate_ref_pos.buffer = &self->mate_ref_pos; in AlignmentRecordInit()
253 self->data.mate_ref_pos.elements = 1; in AlignmentRecordInit()
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| H A D | common-writer.c | 1771 data.mate_ref_pos = mpos; in ArchiveFile()
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| /dports/biology/ncbi-vdb/ncbi-vdb-2.11.0/libs/loader/ |
| H A D | alignment-writer.c | 100 if (data->mate_ref_pos == 0) { in WriteSecondaryRecord()
252 self->data.mate_ref_pos.buffer = &self->mate_ref_pos; in AlignmentRecordInit()
253 self->data.mate_ref_pos.elements = 1; in AlignmentRecordInit()
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| H A D | common-writer.c | 1771 data.mate_ref_pos = mpos; in ArchiveFile()
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| /dports/biology/sra-tools/sra-tools-2.11.0/tools/sra-pileup/ |
| H A D | sam-unaligned.c | 308 INSDC_coord_zero * const mate_ref_pos ) in get_mate_info() argument
314 *mate_ref_pos = 0; in get_mate_info()
322 … rc = matecache_lookup_unaligned( mc, ids->db_idx, mate_id, mate_ref_pos, &ref_idx, &seq_spot_id ); in get_mate_info()
326 *mate_ref_pos += 1; in get_mate_info()
365 *mate_ref_pos = ( pos + 1 ); in get_mate_info()
629 INSDC_coord_zero mate_ref_pos; in dump_seq_row_sam_filtered() local
632 …rc = matecache_lookup_unaligned( mc, ids->db_idx, align_id, &mate_ref_pos, &ref_idx, &seq_spot_id … in dump_seq_row_sam_filtered()
703 rc = KOutMsg( "%s\t%li\t", mate_ref_name, mate_ref_pos + 1 ); in dump_seq_row_sam_filtered()
870 INSDC_coord_zero mate_ref_pos; in dump_seq_prim_row_sam() local
874 … rc = KOutMsg( "%.*s\t%li\t", mate_ref_name_len, mate_ref_name, mate_ref_pos ); in dump_seq_prim_row_sam()
[all …]
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| H A D | sam-aligned.c | 1470 INSDC_coord_zero mate_ref_pos = 0; in print_alignment_sam_ps() local
1498 …rc = matecache_lookup_same_ref( mc, atx->db_idx, mate_align_id, &mate_ref_pos, &sam_flags, &tlen ); in print_alignment_sam_ps()
1546 … rc = read_INSDC_coord_zero( id, cursor, atx->mate_ref_pos_idx, &mate_ref_pos, 0, "MATE_REF_POS" ); in print_alignment_sam_ps()
1725 … rc = KOutMsg( "%.*s\t%u\t%d\t", mate_ref_name_len, mate_ref_name, mate_ref_pos + 1, tlen ); in print_alignment_sam_ps()
1732 rc = KOutMsg( "*\t%u\t%d\t", mate_ref_pos, tlen ); in print_alignment_sam_ps()
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| /dports/biology/sra-tools/sra-tools-2.11.0/tools/cg-load/ |
| H A D | writer-algn.c | 66 INSDC_coord_zero mate_ref_pos; member
146 self->algn[i].mate_ref_pos.buffer = &self->match[i].mate_ref_pos; in CGWriterAlgn_Make()
147 self->algn[i].mate_ref_pos.elements = 1; in CGWriterAlgn_Make()
624 self->match[i].mate_ref_pos = data->map[mate].offset; in CGWriterAlgn_Write_int()
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| /dports/biology/sra-tools/sra-tools-2.11.0/ncbi-vdb/interfaces/loader/ |
| H A D | alignment-writer.h | 61 INSDC_coord_zero mate_ref_pos; member
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| /dports/biology/ncbi-vdb/ncbi-vdb-2.11.0/interfaces/loader/ |
| H A D | alignment-writer.h | 61 INSDC_coord_zero mate_ref_pos; member
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| /dports/biology/sra-tools/sra-tools-2.11.0/ncbi-vdb/interfaces/align/ |
| H A D | writer-alignment.h | 126 TableWriterData mate_ref_pos; member
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| /dports/biology/ncbi-vdb/ncbi-vdb-2.11.0/interfaces/align/ |
| H A D | writer-alignment.h | 126 TableWriterData mate_ref_pos; member
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| /dports/biology/sra-tools/sra-tools-2.11.0/ncbi-vdb/libs/align/ |
| H A D | writer-alignment.c | 283 TW_COL_WRITE(cself->base, cself->cols[ewalgn_cn_MATE_REF_POS], data->mate_ref_pos); in TableWriterAlgn_Write()
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| /dports/biology/ncbi-vdb/ncbi-vdb-2.11.0/libs/align/ |
| H A D | writer-alignment.c | 283 TW_COL_WRITE(cself->base, cself->cols[ewalgn_cn_MATE_REF_POS], data->mate_ref_pos); in TableWriterAlgn_Write()
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