MA & MSV - Version 2.0.2

• The confidence scores for variant calls now make use of coverage information. Before, the conficance of a call was the number of reads supporting the call. Now it is the number of reads supporting over the the coverage in the region of the call. This helps with making calls in real world data, where coverage is uneven.
• fix for the artifact filter, that removes seeds too far from the median delta distance of all seads in a harmonized SoC. Now the filter only removes seeds if this is advantageous to the SW score of the alignment.

MSV - Version 2.0.1

Revision for MSV.
Only minor changes.

MA - Version 1.1.4

Picked out soft & hard clipping feature from svCaller branch and added it here.

MA - Version 1.1.3

Boolean parameters can now be set to false in the command line interface.

MA - Version 1.1.2

Minor bugfixes for MA.

Version 1.1.1

First full release.

• MA can now recognize short inversions too. A z-drop based heuristic is used as algorithmic
  approach for inversion recognition.
  Regions between seeds showing a z-drop are reverse complemented and realigned using DP.
  If the DP-score is sufficiently high, the region is accepted as inversion and a supplementary alignment
  is provided using the computed DP-path. Similar approaches are used by other aligners too.
• Minor bug fixes.

Version 0.1.2

Version used in the context of the revised manuscript.

Version 0.1.0

Version used in the context of the manuscript.

Version 0.0.1

v0.0.1-alpha

readme stuff