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edits
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NOTE: This tool does not properly work on templates that have more than 2 segments. It does not properly match reads when more than 2 reads have the same read name.
NOTE: This tool does not properly work on templates that have more than 2 segments. It does not properly match reads when more than 2 reads have the same read name.
NOTE: Dedup cannot read from stdin since it reads the input file twice.
Potential future features:
Potential future features:
This code assumes that at most 1000 bases are clipped at the start of a read.
This code assumes that at most 1000 bases are clipped at the start of a read.
Deduping requires two passes through the file, so cannot read from stdin.
==Handling Recalibration==
==Handling Recalibration==
== Required Parameters ==
== Required Parameters ==
{{inBAMInputFile}}
{{inBAMInputFile|noStdin=1}}
Note: The input file must be sorted by coordinate.
Note: The input file must be sorted by coordinate.
