address VS-152, remove extra headers from extract #7466
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RoriCremer
reviewed
Sep 13, 2021
| import htsjdk.variant.vcf.VCFHeaderLine; | ||
| import htsjdk.variant.vcf.VCFHeaderLineType; | ||
| import htsjdk.samtools.SAMSequenceDictionary; | ||
| import htsjdk.variant.vcf.*; |
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was this intentional? Are we changing styles?
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intellij autoformatting -- I didn't even know we had an official style :D but happy to change it back
…aded in the __SAMPLES table
ahaessly
approved these changes
Sep 13, 2021
| @@ -121,7 +121,7 @@ def get_all_sample_ids(fq_destination_table_samples): | |||
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| def create_extract_samples_table(fq_destination_table_samples, fq_sample_name_table, fq_sample_mapping_table): | |||
| sql = f"CREATE OR REPLACE TABLE `{fq_destination_table_samples}` AS (" \ | |||
| f"SELECT m.sample_id, m.sample_name FROM `{fq_sample_name_table}` s JOIN `{fq_sample_mapping_table}` m ON (s.sample_name = m.sample_name) " \ | |||
| f"SELECT m.sample_id, m.sample_name, s.is_loaded FROM `{fq_sample_name_table}` s JOIN `{fq_sample_mapping_table}` m ON (s.sample_name = m.sample_name) " \ | |||
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this should be m.is_loaded the s table might be the temp table with only sample names
…aded in the __SAMPLES table
RoriCremer
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that referenced
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Sep 20, 2021
* address VS-152, remove extra headers from extract * explicit imports * fixed inconsistency between prepare and extract with respect to is_loaded in the __SAMPLES table * fixed inconsistency between prepare and extract with respect to is_loaded in the __SAMPLES table
This was referenced Mar 17, 2023
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