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