February 2018 Commit Log

Number of Commits:
Number of Active Developers:
westram 2018-02-21 11:56 Rev.: 16866

* adds a perl script that allows to overwrite field 'name' with the content of another database field
- helpful e.g. to import trees that use 'acc' or 'full_name' as leafname

99 lines of code changed in 1 file:

westram 2018-02-15 12:51 Rev.: 16861

* reintegrates 'unittest' into 'trunk'
- fixed non-deterministic behavior of add-species:
* 2 sequences in test-DB were identical (changed 1 bp)
* {{{AP_tree_edge}}} cannot be used to store insert-positions (uses pair of {{{AP_tree_nlen}}} instead)
* corrected some undefined behavior (results did depend on compiler version+flags):
- general order of inserts was undefined
- order of initial-insert was undefined (used by complete tree reconstruction)
- bugs fixed:
* not all possible insert-positions were tested
* sometimes species were added at wrong positions
* if multiple species were inserted at the same position, the following optimization
- did modify topology
- now optimizes all multi-inserts globally
- at leaf-positions: includes the leaf (Note: this does not modify the original topology)
* insert order now is "longest sequence first" (was "shortest sequence first")
- fixed unwanted behavior when testing for content of generated files
* adds: log:branches/unittest@16807:16860

676 lines of code changed in 54 files:

westram 2018-02-05 13:03 Rev.: 16835

* updated primer design documentation
- done according to Wolframs IDP paper from 2001

56 lines of code changed in 1 file:

westram 2018-02-02 17:41 Rev.: 16831

* fix sanitizer warning ("left shift of negative value")

8 lines of code changed in 1 file:

January 2018 »

Generated by StatSVN 0.7.0