problem with bedfile and index file

[xzhuo]

Hi Clayton,

I can run maf_extract with no problem using interval and not provide kct index file.

However, I got error with option --bed :

 NoMethodError: undefined method `read_bed_intervals' for main:Object
   (root) at /home/xiaoyu/.rvm/gems/jruby-1.7.19/gems/bio-maf-1.0.1-java/bin/maf_extract:160
     load at org/jruby/RubyKernel.java:1087
   (root) at /home/xiaoyu/.rvm/gems/jruby-1.7.19/bin/maf_extract:1
     eval at org/jruby/RubyKernel.java:1107
   (root) at /home/xiaoyu/.rvm/gems/jruby-1.7.19/bin/jruby_executable_hooks:15

and there is another error if I provide index kct file:

NoMethodError: undefined method `close' for "chrUn_KI270753v1.kct":String
   close at /home/xiaoyu/.rvm/gems/jruby-1.7.19/gems/bio-maf-1.0.1-java/lib/bio/maf/index.rb:118
    each at org/jruby/RubyArray.java:1613
   close at /home/xiaoyu/.rvm/gems/jruby-1.7.19/gems/bio-maf-1.0.1-java/lib/bio/maf/index.rb:118
  (root) at /home/xiaoyu/.rvm/gems/jruby-1.7.19/gems/bio-maf-1.0.1-java/bin/maf_extract:189
    load at org/jruby/RubyKernel.java:1087
  (root) at /home/xiaoyu/.rvm/gems/jruby-1.7.19/bin/maf_extract:1
    eval at org/jruby/RubyKernel.java:1107
  (root) at /home/xiaoyu/.rvm/gems/jruby-1.7.19/bin/jruby_executable_hooks:15

I am using ruby 1.9.3 with jruby as you recommended. Could you help me out?

Thanks!

-Xiaoyu