[Gmod-schema-cmts] schema/GMODTools/lib/Bio/GMOD Bulkfiles.pm, 1.10, 1.11

[Don G. <don...@us...>]

Update of /cvsroot/gmod/schema/GMODTools/lib/Bio/GMOD
In directory sc8-pr-cvs2.sourceforge.net:/tmp/cvs-serv13674/lib/Bio/GMOD

Modified Files:
	Bulkfiles.pm 
Log Message:
no_csomesplit changes: files missed by last go (CVS dang your lack of date stamp)

Index: Bulkfiles.pm
===================================================================
RCS file: /cvsroot/gmod/schema/GMODTools/lib/Bio/GMOD/Bulkfiles.pm,v
retrieving revision 1.10
retrieving revision 1.11
diff -C2 -d -r1.10 -r1.11
*** Bulkfiles.pm	7 Apr 2006 21:02:00 -0000	1.10
--- Bulkfiles.pm	15 Oct 2007 16:58:35 -0000	1.11
***************
*** 263,267 ****
--- 263,310 ----
    env GMOD_ROOT=$PWD perl -I./lib/ bin/bulkfiles.pl sgdbulk1
    
+ =head1 no_csomesplit update 
+ 
+   this change is needed to handle partially assembled genomes (the common
+   first draft) with many scaffolds (10,000s of < 1MB  to  100,000s of
+     < 100Kb segments)
+ 
+   The old state assumes a handful of full or nearly full chromosomes implicitly
[...1527 lines suppressed...]
      transposable_element transposable_element_insertion transposable_element_insertion_site transposable_element_pred
      );
-   #$config->{allfeats}= \@allfeats;
  
    %mapchr_pattern= %{ $config->{'mapchr_pattern'} } if ref $config->{'mapchr_pattern'};
--- 2754,2757 ----
***************
*** 2671,2675 ****
  
    ## add these to %ENV before more configs so they get replaced ..
!   @ENV{@ENV_KEYS} = @{%$config}{@ENV_KEYS};
  }
  
--- 2784,2789 ----
  
    ## add these to %ENV before more configs so they get replaced ..
!   foreach my $k (@ENV_KEYS) { defined $$config{$k} and $ENV{$k}= $$config{$k}; }
! 
  }