control substitution on

statement ok
SET exon.bam_parse_tags = true;

statement ok
CREATE EXTERNAL TABLE bam STORED AS BAM LOCATION '$CARGO_MANIFEST_DIR/test-data/datasources/bam/test.bam';

query T
SELECT name, flag, reference, start, end, mapping_quality, cigar, mate_reference FROM bam LIMIT 1;
----
READ_ID 83 chr1 12203704 12217173 NULL 55M13394N21M chr1

query T
SELECT sequence FROM bam LIMIT 1;
----
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA

query T
SELECT array_element(quality_score, 1) FROM bam LIMIT 5;
----
23
20
37
34
31

query T
SELECT array_length(quality_score) FROM bam LIMIT 5;
----
76
76
76
76
76

query I
SELECT tags."NH", tags."HI", tags."AS", tags."nM", tags."NM", tags."XS", tags."RG" FROM bam LIMIT 1;
----
1 1 149 1 0 45 H7G9G.1

statement ok
DROP TABLE bam;

statement ok
CREATE EXTERNAL TABLE bam STORED AS BAM PARTITIONED BY (sample) LOCATION '$CARGO_MANIFEST_DIR/test-data/datasources/bam-partition';

query T
SELECT name, sample FROM bam WHERE sample = '2' LIMIT 1;
----
READ_ID 2

statement ok
DROP TABLE bam;

query T
SELECT COUNT(*) FROM bam_scan('$CARGO_MANIFEST_DIR/test-data/datasources/bam/test.bam');
----
61

query T
SELECT COUNT(*) FROM bam_scan('$CARGO_MANIFEST_DIR/test-data/datasources/bam-partition');
----
122

statement ok
SET exon.bam_parse_tags = true;

query T
SELECT tags."NH", tags."XS" FROM bam_scan('$CARGO_MANIFEST_DIR/test-data/datasources/bam/test.bam') LIMIT 5;
----
1 45
1 NULL
1 NULL
1 NULL
1 NULL