object Coverage extends BDGCommandCompanion

Coverage (accessible as the command 'coverage' through the CLI) takes two arguments, an INPUT and OUTPUT, and calculates the number of reads from INPUT at every location in the file. Optional arguments are only_negative_strands, only_positive_strands and collapse. only_negative_strands and only_positive_strands save coverage computed from only negative and positive strands, respectively. Collapse specifies whether saved coverage should merge neighboring coverage with the same counts to one record.

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  4. def apply(cmdLine: Array[String]): BDGCommand
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  7. val commandDescription: String
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  8. val commandName: String
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