To keep the README short, I explicited the truncation with [...].

Thanks for updating it, I was mainly referring to a line that is not just missing but discordant;

Original

NC_001416.1 1112 1120 4
NC_001416.1 1120 1999 0

Actual

NC_001416.1 596 609 4
NC_001416.1 1120 1999 0

This suggests that data has changed in the repo without the Readme being updated accordingly.
Or that functionaility changed, adding a test folder with the test output generated with the data and code in the repo can prevent things like that from happening.
I see that you have started a README in the test output. Please include the full test output and potential output files from example commaands here and populate it with a test suite or script.

I added new synthetic BAM files to allow for automated tests. In particular "test_cov.bam" has reference chromosomes named after the coverage of the only peak expected (e.g. reference 5X is expected to produce a single BED feature of 5X coverage).

https://github.com/telatin/covtobed/wiki/Testing

All good, missed that, sorry. Thanks for that.