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Commits on Mar 21, 2016

• New default options.

  jirihon

  committedMar 21, 2016
  ae0ce20

• Minimal score has to be positive value.

  jirihon

  committedMar 21, 2016
  52e3dea

Commits on Mar 19, 2016

• Added examples to score, strand and density methods as suggested by Bioc developers when we published triplex.

  jirihon

  committedMar 19, 2016
  326def8

• Strand docu.

  jirihon

  committedMar 19, 2016
  9a7f855

• Added support for strand option and by default searching on both strands.

  jirihon

  committedMar 19, 2016
  3a44f76

Commits on Mar 17, 2016

• Meeting R CMD check and BiocCheck requirements.

  jirihon

  committedMar 17, 2016
  59fd1f2

• Fixed docu to loop_sd_factor.

  jirihon

  committedMar 17, 2016
  c60ec62

• Added support for loop lengths mean and standard deviation penalization factors.

  jirihon

  committedMar 17, 2016
  362b12b

Commits on Mar 16, 2016

• Now supporting mismatches only INSIDE run.

  jirihon

  committedMar 16, 2016
  6ffa7df

• Updated run regexp and docu in respect to the previous commit.

  jirihon

  committedMar 16, 2016
  a91a9aa

Commits on Mar 15, 2016

• New option: maximum number of all defects in total.

  jirihon

  committedMar 15, 2016
  5dd5b29

• Added support for bulges and mismatches in multiple runs. But still solving support for mismatches on the edge positions in run.

  jirihon

  committedMar 15, 2016
  d6441bd

Commits on Mar 14, 2016

• Typo.

  jirihon

  committedMar 14, 2016
  899402b

• Performance improvement when default scoring system is enabled and custom scoring function is specified.

  jirihon

  committedMar 14, 2016
  df27896

• Rethinked: one toggle option for all internal scoring functions. Much easier to understand for the end user.

  jirihon

  committedMar 14, 2016
  bb5aa36

• New option to disable internal scoring functions.

  jirihon

  committedMar 14, 2016
  7b1ca0a

Commits on Mar 3, 2016

• Add option to set minimal PQS score.

  jirihon

  committedMar 3, 2016
  b04ec28

• Changed docu to density vector. Code typo.

  jirihon

  committedMar 3, 2016
  7097f63

Commits on Feb 22, 2016

• Added option for user defined scoring function.

  jirihon

  committedFeb 22, 2016
  70870e6

Commits on Feb 17, 2016

• Progress status implemented.

  jirihon

  committedFeb 17, 2016
  df97175

• Refactoring and documentation.

  jirihon

  committedFeb 17, 2016
  023f034

• Initial pqsfinder package.

  jirihon

  committedFeb 17, 2016
  fc2b6a1

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