Leaving this for reference. Working with #78, I also tried running indexed d4 files. Here, I also got strange results.
I traced it in the code, and did not seem to end up in the same location as the one for the #78, so this seems like it could be a separate issue.
I get consistently very high coverage results for the indexed d4 files. The numbers differs from the unindexed. Occasionally the coverage matches what is found when manually summing the output from d4tools show, but generally it isn't.
Leaving this for reference. Working with #78, I also tried running indexed d4 files. Here, I also got strange results.
I traced it in the code, and did not seem to end up in the same location as the one for the #78, so this seems like it could be a separate issue.
I get consistently very high coverage results for the indexed d4 files. The numbers differs from the unindexed. Occasionally the coverage matches what is found when manually summing the output from
d4tools show
, but generally it isn't.Expected results are:
The bed file: