The bamCountAll function takes a bamReader object and returns a data.frame. The data.frame contains the counts for all contained reference sequences.
An instance of bamReader. Must be opened and contain initialized index.
Logical. Determines the amount of textual output during runtime.
The method returns a data.frame. Each row contains count data for one reference sequence. Each column contains the counts for one CIGAR-OP type ("M", "I","N","S","H","P","=","X"). Columns with the total number of aligns, the refid (ID) and the length of the reference sequence (LN), as retrieved by 'getRefData' are added.
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