speed up flagging with ItervalTree

[Keiran Raine]

Most of the flagging code is looking for simple "hit" lookups in tabix files. This can be handled in exactly the same way as the input generation speed up.

Will have additional advantages as current code wraps each query with an eval which is expensive:

cgpPindel/perl/lib/Sanger/CGP/PindelPostProcessing/FragmentFilterRules.pm

Lines 339 to 349 in da79133

 my $ret = eval{ 
   my $iter = $vcf_flagging_unmatched_normals_tabix->query_full($CHROM,$from,$to); 
   return $PASS if(!defined $iter); # no valid entries (chromosome not in index) so must pass 
   while($iter->next){ 
     return $FAIL; 
   } 
   return $PASS; 
 }; 
 if($@) { 
   die $@; 
 } 

Should be able to hide this in the reuse_unmatched_normals_tabix and reuse_repeats_tabix functions. Needs to be applied in both FilterRules.pm and FragmentFilterRules.pm.