Changes

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.

Potential future features:

Potential future features:

== 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.