|adaptorAlign||Align adaptors to reads|
|chopReads||Chop adaptors off reads|
|consensusReadSeq||Consensus read sequence|
|expectedDist||Calculate expected distances|
|getScoreThresholds||Get score thresholds for adaptor alignments|
|multiReadAlign||Multiple read alignment|
|sam2ranges||SAM to genomic ranges|
|tuneAlignment||Tune alignment parameters|
|umiGroup||Group equivalent UMIs|
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