Consensus calling the UMI-bases uses hardcoded error rates

[nh13]

When calling consensus on UMI sequences (the RX tag), the --error-rate-pre-umi and --error-rate-post-umi parameters don't seem to be used. In UmiConsensusCaller.scala, the SimpleConsensusCaller is created with default values (private val consensusBuilder = new SimpleConsensusCaller() at line 198) and then used to build the consensus UMI at line 486. Meanwhile, the main read consensus caller in VanillaUmiConsensusCaller.scala does pass through the user-specified error rates:

new ConsensusCaller(errorRatePreLabeling = options.errorRatePreUmi, errorRatePostLabeling = options.errorRatePostUmi)

Is this intentional, or should the UMI consensus also use these parameters?

[coderabbitai]

📝 CodeRabbit Plan Mode

Generate an implementation plan and prompts that you can use with your favorite coding agent.

• Create Plan

Examples

• Example 1
• Example 2

🔗 Similar Issues

Related Issues

• Strand not taken into account inside GroupReadsByUmi #1084
• Generate consensus reads without using UMIs #1077
• Clarification on UMI read structure and processing #1101
• No way to dedup down to single strand #1094

🔗 Related PRs

#1116 - fix: the consensus RX (UMI) should be called from filtered records only [merged]

👤 Suggested Assignees

• SPPearce
• bounlu
• feylix
• nh13

---

🧪 Issue enrichment is currently in early access.

To disable automatic issue enrichment, add the following to your .coderabbit.yaml:

issue_enrichment:
  auto_enrich:
    enabled: false