Sequence filters break when running full RSpec suite under JRuby

[csw]

Not sure why, but the "sequence_filter" tests fail when running rspec but pass when running rspec -e sequence_filter. Investigating.

[csw]

Bug occurs, causing sequence_filter tests to fail, under JRuby 1.7.0.preview1 when running rake spec, or rspec -t bug on the repro branch.

Can be avoided by any of the following:

• running the sequence_filter tests alone,
• disabling any of the three sets of #fetch_blocks tests marked :bug
• setting @sequence_filter = nil in the Parser constructor
• testing @sequence_filter rather than sequence_filter in #parse_block_data.

Maybe some kind of compiler bug?

[csw]

Implemented workaround for this. Leaving bug open for working out JRuby bug report.

[csw]

To reproduce:

$ git clone https://github.com/csw/bioruby-maf.git
$ cd bioruby-maf
$ git checkout jruby-sequence-filter-bug
$ rvm use jruby-head [or equivalent]
$ bundle install
$ rspec -e sequence_filter
[passes]
$ rspec -t bug
[fails]

[csw]

Filed JRUBY-6768.

[csw]

This is now fixed on jruby master.