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fix(quant): Aligned.toTranscriptome.out.bam record for record as STAR (primary draw, pair-level soft-clip budget, MAPQ, mate order, merged CIGAR, deletions, alignment order) - #315

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fix/parity-residualsfrom
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fix(quant): Aligned.toTranscriptome.out.bam record for record as STAR (primary draw, pair-level soft-clip budget, MAPQ, mate order, merged CIGAR, deletions, alignment order)#315
BenjaminDEMAILLE wants to merge 8 commits into
fix/parity-residualsfrom
fix/transcriptome-bam-records

fix(quant): transcriptome order for single-end reads; BySJout draws a…

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