Use the gold sample name and the gold alleles for gold evaluations.
hack to workaround premature release of 1.123 with altered classnames
fix syntax error
create bed entry interpreter
make writing of legend file optional
create bed reporter
Allow multiple bed files for DumpIgvXmlMulti
Add bed report creation to CLE plan files

-Also ensure that merging will work correctly
create IGV XML file
prepend https://gscweb.gsc.wustl.edu to files that need to be network accessible
Remove old pre-5.10 way of calling coverage-stats.
Whitespace.
Call TophatAlignmentStats directly.
Unpin perl version in #! lines.
Remove obsolete comment.

This is already directly called.
Call commands directly.
Switch to direct command calls.
Whitespace.
Call command directly.
Remove references to /usr/bin/perl.

`gmt` should use the `genome-perl` now, which should be at least 5.10.