fix: Fix read processing when building consensus reads

[FelixMoelder]

In some cases consensus read calculation fails as read groups may be processed multiple times.
To fix this two major changes have been introduced:

• Read containg softclips will now be skipped and written to the output bam-file directly.
• A new struct GroupEndIndex has been introduced for processing complete read groups.
  The struct manages the end positions of read groups.

Feature:
Existing UMIs will be read from the RX-Tag and added to the description of the consensus reads. These can be converted into actual bam tags by bwa mem (Adding option -C during mapping).