<opt
  name="fbbulk-r3b" 
  relid="3b"
>
  <!-- see site_defaults for more included configs -->
  <include>site_defaults</include>

  <title>FlyBase Chado DB r3.2.2</title>
  <about>
   Configurations to extract feature and sequence data for
   bulk files from FlyBase chado databases, including various
   release information.
  </about>

  <doc name="Release.txt"><![CDATA[
    D. melanogaster euchromatin genome data from FlyBase
    Release  ${rel}.   This release is data maintenance,
    correcting intron and UTR positions (off-by-1), 
    and adds D.pseudoobscura r2.1 synteny and ortholog features. 
    See release notes at <a href="http://flybase.net/${release_url}">
    http://flybase.net/${release_url}</a>
  ]]></doc>

  <include>fbreleases</include>

  <org>dmel</org>
  <species>Drosophila melanogaster</species>
  
  <!-- oct04: patch for utr fmax < fmin when 0 length -->
  <utrpatch>1</utrpatch>
  <!-- oct04: patch for intron  fmin - no+1,fmax, add+1 -->
  <intronpatch>1</intronpatch>
  
  <!-- this featurewriter patt failed to retype pseudogenes .. why? -->
  <rename_child_type>pseudogene|\w+RNA</rename_child_type>

  <!-- db.name  is release-dependent ; use fbreleases -->
  <db
    driver="Pg"
    name="dmel_chado"
    host="localhost"
    port="7302"
    user=""
    password=""
    />
  
  <!-- use to add parent ids to features FBgn|FBti ; NOT these - FBan|CG|CR -->
  <idpattern>(FBgn|FBti)\d+</idpattern>

  <!-- note 19nov04 - override scaffold default featmap.
      fb dmel chado scaffold residues come from
      chromosome dna; but had out-of-date errors, safer to use
      chromosome, not fromdb for these? 
  -->
  <featmap
    name="scaffold"   
    alt_name0 = "golden_path_region" 
    alt_name1 = "golden_path_fragment" 
    alt_name2 = "databank_scaffold"
    alt_name3 = "scaffold"
    alt_name4 = "supercontig"
    types="golden_path_region scaffold"
    typelabel="scaffold"
    NOT_fromdb="1"
    />
  <featmap name="dummy" note="here for xml parser" />

</opt>

