ProbABEL v0.4.2 released

The ProbABEL development teams is happy to announce the release of ProbABEL v0.4.2. Information on how to get the source code or binaries can be found on the ProbABEL page.

The most important user-visible changes are:
1) Starting with this release the wrapper script has been renamed to probabel. In order not to disrupt any current pipelines a symbolic link is created to the old name. When the user invokes the script with the old name a warning will be printed to encourage them to use the new name. The old name will remain available for several future releases, but will be removed at some point.
2) Improved convergence checks for the Cox PH regression module
3) Fixed a bug where ProbABEL crashed when having large indels in the info file

Thanks to all who made this release possible, by providing code patches, by being beta testers, by suggesting enhancements, or otherwise.
(Please click on "read more", below, for more details.)

Here is the full ChangeLog for this release:

  • The '' script is now simply renamed to 'probabel' (a user shouldn't care what scripting language we use). For at least several releases to come, the old script name will still exist (as a link to the original) and a warning message is displayed when the user runs the .pl script. This should give people time to adjust their pipelines.
  • Fix bug #4919: Too small reading buffers for long alleles in mach info and legend files. Thanks to Daniel Taliun for reporting the bug and providing the patch. Thanks to Xia Shen for testing.
  • Fix bug #4776: Specifying --sep="\t" as an option to pa* doesn't insert a TAB as separator. Now ProbABEL inserts proper tabs when specifying "\t". Thanks to Maksim Struchalin for fixing this bug.
  • Improved convergence checks in the Cox PH regression module. The checks now give similar errors as R does.
  • A minor change in the screen output of ProbABEL. Some of the status messages ("Reading phenotype data" etc.) have been added or move to a slightly different place in the code to help debugging problems with the input data.
  • Fix a bug in the example scripts: an incorrect shell variable was used.
  • For developers: If R is installed, running 'make check' will also compare the results of ProbABEL with those of the same regressions in R.
  • For developers: a start has been made on documenting the internal functions using Doxygen.