Tidy readClassList and quantData#565

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lingminhao wants to merge 25 commits intodevel_pre_v4from

tidy_readClassFile_quantData

Commits on Apr 15, 2026

convert quantData into an object storing list of S4 object
lingminhao
committed
Refactor quantData: remove countMatrix and replace with list columns [columnIds, columnCounts] in readClassDt
lingminhao
committed

Commits on Apr 16, 2026

remove redundant stored data in quantData
lingminhao
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add readToTranscriptMaps to final se when trackReads is TRUE
lingminhao
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Add gene and unique count matrix helpers from quantData
lingminhao
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add colnames and colData to readClassList
lingminhao
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name readClassList, quantData, readToTranscriptMaps, and distTables lists by sample names
lingminhao
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add nonuniqueCounts to quantData & se.

lingminhao
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claude
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refactor generateUniqueCountsFromQuantData to return SummarizedExperiment

lingminhao
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claude
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refactor transcriptToGeneExpression to compute gene counts as uniqueCounts + incompatibleCounts + nonuniqueCounts

lingminhao
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claude
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refactor constructQuantData class using claude

lingminhao
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claude
committed

Commits on Apr 17, 2026