Discrepancy in example output

[jdeligt]

I installed through conda and ran covtobed -m 0 -x 5 test/demo.bam on the git repo;

EMPTY 0 414 0
NC_001416.1 0 2 0
NC_001416.1 2 6 1
NC_001416.1 6 7 2
NC_001416.1 7 12 3
NC_001416.1 12 18 4
NC_001416.1 169 170 4
NC_001416.1 201 206 4
NC_001416.1 206 207 3
NC_001416.1 207 214 4
NC_001416.1 514 539 4
NC_001416.1 539 540 3
NC_001416.1 540 569 4
NC_001416.1 596 609 4
NC_001416.1 1120 1999 0
NC_001416.1 2653 2674 4
NC_001416.1 2674 2686 3
NC_001416.1 2686 2762 2
NC_001416.1 2762 2771 1
NC_001416.1 2771 2800 0

Please update the example to match what is in the repo.

[telatin]

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

[jdeligt]

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.

[telatin]

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

[jdeligt]

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