control substitution on

statement ok
SET exon.cram_parse_tags = true;

statement ok
CREATE EXTERNAL TABLE cram STORED AS CRAM LOCATION '$CARGO_MANIFEST_DIR/test-data/datasources/cram/test_input_1_a.cram';

query I
SELECT name, flag, reference, start, end, mapping_quality, cigar, mate_reference, tags."PG" FROM cram LIMIT 1;
----
r000 99 insert 50 59 30 10M insert bull

statement ok
DROP TABLE cram;

statement ok
SET exon.cram_parse_tags = false;

statement ok
CREATE EXTERNAL TABLE cram STORED AS CRAM LOCATION '$CARGO_MANIFEST_DIR/test-data/datasources/cram/test_input_1_a.cram';

query I
SELECT name, flag, reference, start, end, mapping_quality, cigar, mate_reference, tags FROM cram LIMIT 1;
----
r000 99 insert 50 59 30 10M insert [{tag: PG, value: bull}]

statement ok
DROP TABLE cram;

statement ok
CREATE EXTERNAL TABLE cram STORED AS CRAM OPTIONS (fasta_reference '$CARGO_MANIFEST_DIR/test-data/datasources/cram/ce.fa') LOCATION '$CARGO_MANIFEST_DIR/test-data/datasources/cram/0500_mapped.cram';

query I
SELECT name, flag, reference, start, end FROM cram LIMIT 1;
----
match 99 CHROMOSOME_I 1000 1099

statement ok
DROP TABLE cram;

statement ok
CREATE EXTERNAL TABLE cram STORED AS CRAM OPTIONS (fasta_reference '/does/not/exist') LOCATION '$CARGO_MANIFEST_DIR/test-data/datasources/cram/0500_mapped.cram';

statement error
SELECT * FROM cram;

statement ok
DROP TABLE cram;

statement ok
CREATE EXTERNAL TABLE cram STORED AS CRAM OPTIONS (fasta_reference '$CARGO_MANIFEST_DIR/test-data/datasources/two-cram/rand1k.fa', indexed 'true') LOCATION '$CARGO_MANIFEST_DIR/test-data/datasources/two-cram/twolib.sorted.cram';

query I
SELECT * FROM cram WHERE cram_region_filter('rand1k', reference) = true LIMIT 1;
----
read1-1 0 rand1k 1 60 60 60M NULL TCCTAATTCTGGGTAACCGCCGCCTGAAGCCAAAAAATAAGCCGGAGCCAAGGGGGAGTC [] [{tag: AS, value: 60}, {tag: XS, value: 0}]

statement ok
DROP TABLE cram;