Fix --save_output_as_bam flag#2154

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save-output-bam

Commits on Mar 9, 2026

Fix --save_output_as_bam: duplicate emissions, skipped variant calling, unnecessary conversions

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Update changelog with PR #2154

FriederikeHanssen
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Commits on Mar 12, 2026

Merge origin/dev into save-output-bam

FriederikeHanssen
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Remove stale CRAM_TO_BAM_RECAL reference from docs

FriederikeHanssen
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claude
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Fix markduplicates: produce BAM natively when --save_output_as_bam

FriederikeHanssen
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claude
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Clean up dead config and unused parameters

FriederikeHanssen
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Fix missing BAM index in bam_markduplicates

FriederikeHanssen
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Update save_output_as_bam snapshot: remove BAM_TO_CRAM_MAPPING

FriederikeHanssen
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claude
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Update test snapshots for --save_output_as_bam changes

FriederikeHanssen
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claude
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Commits on Mar 20, 2026