genomecov -d and -3/-5 options are incompatible, but no error is given

[acvill]

Thank you for maintaining bedtools. It's really excellent software.

An old post on Biostars suggests using the following command to count coverage at the 5' ends of reads:

bedtools genomecov -d -5 -ibam input.bam -g genome.fa > output.txt

I have some stranded transcriptomics data, and I have been using a similar command (bedtools v2.29.2) to extract strand-specific 3' end depth profiles for my alignments:

bedtools genomecov -pc -3 -d -strand + -ibam sample.bam > sample_plus_3p.txt
bedtools genomecov -pc -3 -d -strand - -ibam sample.bam > sample_minus_3p.txt

My expectation when running this command is that I will get a per-base genome coverage report (-d) for the 3' ends (-3) of my paired-end fragments (-pc), with zeros given at all positions where the 3' end of a paired-end read does not fall. No error is given running the above commands, and I indeed get a report listing every position in my genome.

However, I noticed that the exclusion of the -3 option (or inclusion of -5) gives the same results.

tested commands

bedtools genomecov -pc -d -strand + -ibam sample.bam | md5sum
bedtools genomecov -pc -3 -d -strand + -ibam sample.bam | md5sum
bedtools genomecov -pc -5 -d -strand + -ibam sample.bam | md5sum

results

d1ca8002cfe34024374fe9f695c55c64    -
d1ca8002cfe34024374fe9f695c55c64    -
d1ca8002cfe34024374fe9f695c55c64    -

I noticed a similar problem when using the -3 and -5 options in conjunction with BedGraph output (-bga).

My questions:

1. Are the -3 and -5 flags incompatible with -d and -bga, and, if so, why is there no error thrown? (Or, at least, why isn't that mentioned in the documentation?)
2. Is there a correct combination of flags that will give an every-position report that excludes all but the ends of fragments, as I was attempting to implement?

[acvill]

Related issue: https://github.com/arq5x/bedtools2/issues/905

And a Biostars post with more context: https://www.biostars.org/p/9490546/

[acvill]

My workaround: https://www.biostars.org/p/9490546/#9493168