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CHANGELOG.md

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Structure_threader changelog

Changes since v1.3.9

Plotting

  • Enables the option to draw ALStructure plots from the plot mode.

Changes since v1.3.8

Documentation

  • Clarifies that ALStructure does not currently support Best K estimation.

Plotting

  • Moves the population/individual names on the HTML plot back to the bottom. Somewhere aling the way, plotly must have changed the default to above.

Changes since v1.3.7

Documentation

  • Improves readability and clarifies inline help text for the plot option.

Changes since v1.3.6

Bugfix

  • Corrects a bug with setup.py not working correctly when installing on Windows platforms.

Changes since v1.3.5

Bugfix

  • Adds a corner case to the STRUCTURE results parser for when the option #define ANCESTDIST is set to 1.

Changes since v1.3.4

Bugfix

  • Improves the shebang on alstructure_wrapper.R to improve conda compatibility.

Changes since v1.3.3

Bugfix

  • Forces plotly to version >= 4.1.1 due to a deprecation warning.

Changes since v1.3.2

Bugfix

  • Makes the VCF conversion script handle tri-alellic (and more) SNPs the same way that PLINK does - discard them as NA. I am under the impression that this could be better handled, but for now it will do.

Big thanks to Yamila Paula Cardoso for providing me with a dataset where this bug showed up!


Changes since v1.3.1

Bugfix

  • Fixes a Plotly deprecation warning:
/usr/local/lib/python3.6/dist-packages/plotly/tools.py:465: DeprecationWarning:

plotly.tools.make_subplots is deprecated, please use plotly.subplots.make_subplots instead

Changes since v1.3.0

New feature

  • Structure_threader can now supports passing a VCF file for ALStructure. Not even upstream ALStructure can do this. =-)

Changes since v1.2.15

New feature

  • Structure_threader can now wrap ALStructure!!! This is a major feature and warranted the release of version 1.3.0.

Changes since v1.2.14

Bug Fixes

  • Fixed a bug that occurred when multiple arguments were passed to extra_opts when wrapping fastStructure. Thank you to @oviscanadensis for the superb bug report.

Changes since v1.2.13

Bug Fixes

  • Fixed a bug when parsing yet another variant of STRUCTURE output.

Changes since v1.2.12

Bug Fixes

  • Fixed a bug that caused a crash when MavericK alpha and alphaPropSD parameter values were split with both a comma and a white-space. Thank you to Sophie Gresham for reporting it.

Changes since v1.2.11

New features

  • Adds infrastructure to use Gitlab's CI server parallel to Travis CI.

Bug Fixes

  • The field tests coding was improved to drop some hard-coded paths into dynamic ones.

Changes since v1.2.10

Bug fixes

  • Marks numpy>=1.12.1 dependency. The key issue here being in the version number.

Changes since v1.2.9

Bug fixes

  • Corrects a bug with plotting MavericK "Qmatrix" files that did not have a "population identifier" field.

Changes since v1.2.8

Bug fixes

  • Using the plot function on MavericK results now works as intended.
  • Improved and clarified how the plot input files should be indicated.

Changes since v1.2.7

Bug fixes

  • Structure_threader now always makes a sanity check for mainparams and extraparams.

New features:

  • New option introduced: --seed, which allows the user to define a random seed value. It is not mandatory, and defaults to "1235813".
  • Structure_threader now checks if the RANDOMIZE option is set in the extraparams file. If it is, it gets disabled since random seeds are now handled internally.

Changes since v1.2.6

Bug fixes

  • Corrected a bug when sorting plot order using an "indfile" with more than 10 populations.

Changes since v1.2.5

Bug fixes

  • Improved unit and field tests.
  • Removed a leftover debugging line.

Changes since v1.2.4

Bug fixes

  • Allows a random seed to be passed to STRUCTURE. This seed will be used to generate N seeds, where N is the number of runs. Each will be attached to the appropriate CLI.

Changes since v1.2.3

Bug fixes

  • Added an extra sanity check for write permissions to the output directory.

Changes since v1.2.2

Bug fixes

  • The "skeletons" module was not being packaged in Pypi. This is now fixed.

Changes since v1.2.1

Bug fixes

  • Added more underflow protection.

Changes since v1.2.0

Bug fixes

  • Added an underflow protection.
  • Added a fail-safe in case of MavericK using a single "MainRepeats" parameter.
  • Improved some text strings.

Changes since v1.1.0:

Bug fixes

  • Corrected a few typos in some of the printed messages.
  • Fixed a bug with a nonsensical leading "/" on the windows version.
  • Corrected a bug where MavericK execution stopped due to multiple alpha and alphaPropSD values being set.
  • K plots visualization is now improved when plotting a large number of Ks.

New features:

  • Added option to generate skeleton parameter files (mainparams and extraparams) for STRUCTURE.
  • If wrapping MavericK with TI option turned off, bestK tests are now skipped.
  • Vastly improved unit test suite.
  • New presentation of "bestK" evidence when wrapping MavericK.

Changes since v1.0.1:

Bug fixes:

  • Fixed a broken link in the docs (Thanks to @briantrice for finding it).
  • Fixed a bug with the file prefixes for drawing plots that required the user to be in the directory where the meanQ files were located.
  • Corrected a bug with the way "fastStructure" was spelled
  • Corrected a bug with population delimiters.

New features:

  • Sanity checks errors and warnings are now also colored.

Changes since v1.0.0:

Bug fixes:

  • Fixed issue when best K is 1
  • Fixed missing population separators on static .svg plots when using --use-ind-labels
  • Changed a variable name to avoid conflicts, despite being in a different namespace.
  • Fixed missing population separators on static .svg plots when using --use-ind-labels
  • Fixed key error when providing faststructure format in plot mode

Changes since v0.4.3:

New features:

  • Allow the program to draw the .svg plots only on gray scale (with '-bw' option)
  • Allow the program to show individual label names even when population information is provided (with '--show-ind-labels' option)

Bug fixes:

  • Fixed Qvalue sorting when providing an --ind file with two columns