Bug: Genotypes Not Added in replace_gt_with_sample.sh When Using Probands File

[berntpopp]

Description

When using a probands file with the replace_gt_with_sample.sh script, the genotypes are not correctly added to the output. This issue prevents the script from correctly identifying and processing the proband samples, leading to incomplete or incorrect results.

Steps to Reproduce

1. Run the replace_gt_with_sample.sh script with a probands file specified.
2. Observe that the genotypes are not added to the output as expected.

Expected Behavior

The script should correctly identify the probands from the specified file and include their genotypes in the output.

Actual Behavior

The genotypes are not added to the output when using a probands file.