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fls-bioinformatics-core / auto_process_ngs

Scripts and utilities for automatic processing & management of Illumina NGS sequencing data.
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Fix bug when creating Fastqs in mock analysis projects without specifying lanes #914

Closed pjbriggs closed 10 months ago

pjbriggs commented 10 months ago

Fixes a bug in the MockAnalysisProject.create method (in the mock module) when making Fastqs without explicitly specifying a lane in the names (e.g. because merging across lanes is being simulated).

Without the fix the Fastq read headers have the lane set to None (creating an invalid read header and potentially breaking code which tries to extract information from it). The fix is to have the lane number default to 1 if not otherwise specified.