[Dataspace] Add support to import and store B-Cell Receptor (BCR) dat…

…a - Client Requested Changes 4 (#592)

* Add new queries. Add field descriptions
* Schema updates
* Update sample data

resources/queries/cds/antibody_sequence_header_source.sql

@@ -0,0 +1,11 @@
+SELECT
+    aseq.mab_id,
+    seqs.sequence_id,
+    shed.header,
+    hsrc.source,
+    seqs.sequence_nt,
+    aseq.lineage
+FROM sequence seqs
+         JOIN antibody_sequence AS aseq ON aseq.sequence_id = seqs.sequence_id
+         JOIN sequence_header AS shed ON shed.sequence_id = seqs.sequence_id
+         JOIN header_source AS hsrc ON hsrc.source_id = shed.source_id

resources/queries/cds/lineage_alignment.sql

@@ -0,0 +1,98 @@
+aseq.mab_id,
+algn.sequence_id,
+algn.locus,
+algn.stop_codon,
+algn.vj_in_frame,
+algn.productive,
+algn.rev_comp,
+algn.complete_vdj,
+algn.v_call,
+algn.d_call,
+algn.j_call,
+algn.sequence_alignment,
+algn.germline_alignment,
+algn.sequence_alignment_aa,
+algn.germline_alignment_aa,
+algn.v_alignment_start,
+algn.v_alignment_end,
+algn.d_alignment_start,
+algn.d_alignment_end,
+algn.j_alignment_start,
+algn.j_alignment_end,
+algn.v_sequence_alignment,
+algn.v_sequence_alignment_aa,
+algn.v_germline_alignment,
+algn.v_germline_alignment_aa,
+algn.d_sequence_alignment,
+algn.d_sequence_alignment_aa,
+algn.d_germline_alignment,
+algn.d_germline_alignment_aa,
+algn.j_sequence_alignment,
+algn.j_sequence_alignment_aa,
+algn.j_germline_alignment,
+algn.j_germline_alignment_aa,
+algn.fwr1,
+algn.fwr1_aa,
+algn.cdr1,
+algn.cdr1_aa,
+algn.fwr2,
+algn.fwr2_aa,
+algn.cdr2,
+algn.cdr2_aa,
+algn.fwr3,
+algn.fwr3_aa,
+algn.fwr4,
+algn.fwr4_aa,
+algn.cdr3,
+algn.cdr3_aa,
+algn.junction,
+algn.junction_length,
+algn.junction_aa,
+algn.junction_aa_length,
+algn.v_score,
+algn.d_score,
+algn.j_score,
+algn.v_cigar,
+algn.d_cigar,
+algn.j_cigar,
+algn.v_support,
+algn.d_support,
+algn.j_support,
+algn.v_identity,
+algn.d_identity,
+algn.j_identity,
+algn.v_sequence_start,
+algn.v_sequence_end,
+algn.v_germline_start,
+algn.v_germline_end,
+algn.d_sequence_start,
+2
+algn.d_sequence_end,
+algn.d_germline_start,
+algn.d_germline_end,
+algn.j_sequence_start,
+algn.j_sequence_end,
+algn.j_germline_start,
+algn.j_germline_end,
+algn.fwr1_start,
+algn.fwr1_end,
+algn.cdr1_start,
+algn.cdr1_end,
+algn.fwr2_start,
+algn.fwr2_end,
+algn.cdr2_start,
+algn.cdr2_end,
+algn.fwr3_start,
+algn.fwr3_end,
+algn.fwr4_start,
+algn.fwr4_end,
+algn.cdr3_start,
+algn.cdr3_end,
+algn.np1,
+algn.np1_length,
+algn.np2,
+algn.np2_length,
+algn.run_application,
+aseq.lineage
+FROM alignment AS algn
+JOIN antibody_sequence AS aseq ON algn.sequence_id = aseq.sequence_id

resources/queries/cds/lineage_sequence_germline.sql

@@ -0,0 +1,14 @@
+SELECT
+    aseq.mab_id,
+    sgrm.allele,
+    sgrm.sequence_id,
+    sgrm.percent_identity,
+    sgrm.matches,
+    sgrm.alignment_length,
+    sgrm.score,
+    sgrm.run_application,
+    pref.status AS preferred_status,
+    aseq.lineage
+FROM sequence_germline AS sgrm
+         JOIN antibody_sequence AS aseq ON sgrm.sequence_id = aseq.sequence_id
+         LEFT JOIN preferred_allele AS pref ON pref.sequence_id = sgrm.sequence_id AND pref.allele = sgrm.al