differencestest.pileup

1       3000721 A       W       4       4       60      33      5       28      1
1       3000727 G       K       24      24      60      32      5       27      1
1       3000767 T       K       21      21      60      29      5       24      1
1       3001443 G       A       96      96      60      23      23      0       2
1       3002052 C       T       48      48      60      7       7       0       2
1       3004103 C       T       45      45      60      6       6       0       1
1       3004121 *       +AC/*   99      99      60      5       2       3       1
1       3004918 C       T       53      54      30      15      2       2       1
1       3004919 C       G       29      57      30      15      5       10      1
1       3004964 T       A       31      45      27      7       1       6       1

import.sh

mongoimport -d pileup -c pileup -type tsv --stopOnError -f chrID,chrLOC,refBase,conBase,consQual,SNPQual,maxMapqual,numbReadBases,numberMajorRead,numberMinorRead,strain differencestest.pileup

mongoit.rb

require 'mongo'
require 'mongoid'

Mongoid.configure do |config|
  name = "pileup"
  host = "localhost"
  config.master = Mongo::Connection.new.db(name)
  config.persist_in_safe_mode = false
end

class Entry
  include Mongoid::Document

  store_in :pileup

  field :chrID
  field :chrLOC
  field :refBase
  field :conBase
  field :consqual
  field :SNPQual
  field :maxMapqual
  field :numbReadBases
  field :numberMajorRead
  field :numberMinorRead
  field :strain

  index [[:chrID, Mongo::ASCENDING], [:charLOC, Mongo::ASCENDING]]
end

query.rb

Entry.only(:chrID, :chrLOC, :strain).where(:chrID => 1).where(:chrLOC.gt => 13000757).where(:chrLOC.lt => 13000808).to_a

# Profiler
#=> { "ts" : "Wed Jul 07 2010 16:18:59 GMT-0400 (EST)", "info" : "query pileup.$cmd ntoreturn:1 command: { count: \"pileup\", query: { chrID: 1, chrLOC: { $lt: 13000808 } }, fields: { chrID: 1, chrLOC: 1, strain: 1, _type: 1 } } reslen:57 bytes:41", "millis" : 0 }

query.sql

--- sample query

SELECT strain, chrID, chrLOC FROM akrdba WHERE chrID = 1 and chrpos > 13000757 AND chrpos < 13000808