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  1. 1000 Genomes Project Pilot 1 SNP Calling
  2. 830 - BasicMapper::main()
  3. 830 - BestAlignment::ClearPositions()
  4. 830 - BestAlignment::EvaluateAlignment() (detailed comparison)
  5. 830 - BestAlignment::EvaluateAlignment() (main loop)
  6. 830 - BestAlignment::IterateCache()
  7. 830 - BestAlignment::MaqAlignment()
  8. 830 - BestAlignment::isNewPosition()
  9. 830 - Haplotyper::ConditionOnData()
  10. 830 - Haplotyper::ImputeGenotypes()
  11. 830 - Haplotyper::ImputeGenotypes() (edge)
  12. 830 - Haplotyper::ImputeGenotypes() (internal)
  13. 830 - Haplotyper::RandomSetup()
  14. 830 - Haplotyper::SampleChromosomes()
  15. 830 - Haplotyper::SampleHaplotypes()
  16. 830 - Haplotyper::SampleOneHaplotype()
  17. 830 - Haplotyper::ScoreLeftConditional()
  18. 830 - Haplotyper::ScoreLeftConditional() (smart, complicated)
  19. 830 - Haplotyper::SetupPrior()
  20. 830 - Haplotyper::SummarizeOptions()
  21. 830 - Haplotyper::Transpose()
  22. 830 - MINIMAC::main()
  23. 830 - MaqIndex::BuildIndex()
  24. 830 - MaqIndex::CompareToIndex()
  25. 830 - MaqIndex::GetWord()
  26. 830 - MaqIndex::LookupWord()
  27. 830 - MarkovModel::Condition()
  28. 830 - MarkovModel::CountErrors()
  29. 830 - MarkovModel::CountErrorsAndRecombinants()
  30. 830 - MarkovModel::CountRecombinants()
  31. 830 - MarkovModel::Impute()
  32. 830 - MarkovModel::Transpose()
  33. 830 - MarkovModel::WalkLeft()
  34. 830 - MarkovModel::WalkRight()
  35. AWS Credentials
  36. AWS Resources
  37. Abecasis Group Awards
  38. Abecasis Lab
  39. Alan Kwong
  40. Amazon Single Node
  41. Amazon Snapshot
  42. Amazon Storage
  43. An example of using libcsg
  44. Analyses of Indels
  45. Ancestry
  46. Ann Arbor Travel Basics
  47. Arf
  48. BAFRegress
  49. BAM
  50. BAM Review Action Items

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