Bug fix and function improvement #510
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This update enhances the bulk RNA-seq alignment pipeline to support and propagate paired-end information throughout the workflow. It introduces paired-end detection for BAM files, updates function signatures and data structures to handle paired-end flags, and ensures that featureCounts and other steps correctly use this information. Validation and output handling for single-end and paired-end data are also improved for robustness.
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This update enhances the bulk RNA-seq alignment pipeline to support and propagate paired-end information throughout the workflow. It introduces paired-end detection for BAM files, updates function signatures and data structures to handle paired-end flags, and ensures that featureCounts and other steps correctly use this information. Validation and output handling for single-end and paired-end data are also improved for robustness.