CracTools::Interval::Query::File - Acts like CracTools::Interval::Query but read interval from files and return lines of the file matching the query.


version 1.251


Add an otpion that gives an method wich can parsed the return line.


  Arg [file] : String - file path
  Arg [type] : String - file type (bed,sam,gff,gtf)

  Example     : my $gffQuery = CracTools::GFF::Query->new('annotations.gff');
  Description : Create a new GFF Query object
  ReturnType  : CracTools::GFF::Query
  Exceptions  : none


Return an array reference of intervals associated with the line.

Interval structure is described by get_interval_sub


Return a line of a file at a give seek position.



Overload _processReturnValue() method to retrieve lines from files using seek positions.


Interval must be : 1-base coordinate system Closed intervals


We transform BED annotation postions to base-1 positions, and closed intervals


  • Nicolas PHILIPPE <>

  • Jérôme AUDOUX <>

  • Sacha BEAUMEUNIER <>


This software is Copyright (c) 2017 by IRMB/INSERM (Institute for Regenerative Medecine and Biotherapy / Institut National de la Santé et de la Recherche Médicale) and AxLR/SATT (Lanquedoc Roussilon / Societe d'Acceleration de Transfert de Technologie).

This is free software, licensed under:

  The GNU Affero General Public License, Version 3, November 2007