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revision 1.2, Sun Jul 15 04:08:16 2007 UTC revision 1.3, Wed Aug 8 18:43:37 2007 UTC
# Line 64  Line 64 
64      if (! defined("$dir/full.ali"))   { return undef }      if (! defined("$dir/full.ali"))   { return undef }
65    
66      my($ali,$core_ali);      my($ali,$core_ali);
67      (open(ALI,"<$dir/full.ali") && ($ali = &gjoseqlib::read_fasta(\*ALI)))      open(ALI,"<$dir/full.ali") || die "could not open $dir/full.ali";
68          || return undef;      ($ali = &gjoseqlib::read_fasta(\*ALI)) || die "$dir/full.ali is not well-formatted fasta";
69      close(ALI);      close(ALI);
70    
71      if (open(ALI,"<$dir/core.ali") && ($core_ali = &gjoseqlib::read_fasta(\*ALI)))      if (open(ALI,"<$dir/core.ali") && ($core_ali = &gjoseqlib::read_fasta(\*ALI)))
# Line 85  Line 85 
85          $ali      = [grep { ! $deleted{$_->[0]} } @$ali];          $ali      = [grep { ! $deleted{$_->[0]} } @$ali];
86          $core_ali = $core_ali ? [grep { ! $deleted{$_->[0]} } @$core_ali] : undef;          $core_ali = $core_ali ? [grep { ! $deleted{$_->[0]} } @$core_ali] : undef;
87      }      }
88    
89      if (@$ali < 2)         { return undef }      if (@$ali < 2)         { return undef }
90    
91      my @coords = ();      my @coords = ();

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