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lines changed Original file line number Diff line number Diff line change 4444# ' gsubExpression would be ":.*". This would retrieve the string after the colon as the barcode.
4545# ' @param bamFlag A vector of bam flags to be used for reading in fragments from input bam files. Should be in the format of a
4646# ' `scanBamFlag` passed to `ScanBam` in Rsamtools.
47- # ' @param offsetPlus The numeric offset to apply to a "+" stranded Tn5 insertion to account for the precise Tn5 binding site.
47+ # ' @param offsetPlus The numeric offset to apply to the start (left-most Tn5 insertion) of a fragment to account for the precise Tn5 binding site.
4848# ' This parameter only applies to bam file input and it is assumed that fragment files have already been offset which is the standard from 10x output.
4949# ' See Buenrostro et al. Nature Methods 2013.
50- # ' @param offsetMinus The numeric offset to apply to a "-" stranded Tn5 insertion to account for the precise Tn5 binding site.
50+ # ' @param offsetMinus The numeric offset to apply to the end (right-most Tn5 insertion) of a fragment to account for the precise Tn5 binding site.
5151# ' This parameter only applies to bam file input and it is assumed that fragment files have already been offset which is the standard from 10x output.
5252# ' See Buenrostro et al. Nature Methods 2013.
5353# ' @param addTileMat A boolean value indicating whether to add a "Tile Matrix" to each ArrowFile. A Tile Matrix is a counts matrix that,
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