* 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:
* 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:
* updated primer design documentation
- done according to Wolframs IDP paper from 2001
56 lines of code changed in 1 file:
* fix sanitizer warning ("left shift of negative value")
8 lines of code changed in 1 file: