Bug: Empty Outputs in Tumor-Only Analysis with Numbered GEN[1] Fields

[berntpopp]

Description

Empty outputs are generated in tumor-only analysis when including numbered GEN[1] fields with a higher number than 0. This issue needs to be investigated and resolved to ensure correct output generation.

Steps to Reproduce

1. Run the script with a tumor-only analysis configuration.
2. Include numbered GEN[1] fields with a higher number than 0.
3. Observe that the output is empty.

Expected Behavior

The script should generate the correct output even when numbered GEN[1] fields with a higher number than 0 are included.

Actual Behavior

The output is empty when numbered GEN[1] fields with a higher number than 0 are included in tumor-only analysis.

Proposed Solution

Investigate and fix the issue causing empty outputs in this scenario.

Impact

Fixing this issue will ensure that the script generates the correct output for tumor-only analysis, even when including numbered GEN[1] fields with higher numbers.

Additional Notes

• Ensure backward compatibility with existing functionality.
• Update the documentation to reflect the correct handling of numbered GEN[1] fields in tumor-only analysis.

[berntpopp]

SnpSift extractFields odes not handle missing indices well and has no setting for this, thus keep wildcards only (maybe document this) and handle splitting posthoc (Excel generation). We should add some kind of check for indices >0.

[berntpopp]

Catch errors from the main command and log them for debugging.

Relates to #52