The pileup created by htslib seems to default to about 8000 max depth, the same as samtools mpileup if you don't add a -d flag. This PR sets it the i32::max_value() which I think it the more expected behavior, this could cause memory issues with very high depth bams. But I still think that is more expected and those bams should be down sampled with a different tool rather than a hard cutoff here.
only base-depth is affected by this change. All other tools don't rely on pileup engine.
The pileup created by htslib seems to default to about 8000 max depth, the same as
samtools mpileupif you don't add a-dflag. This PR sets it thei32::max_value()which I think it the more expected behavior, this could cause memory issues with very high depth bams. But I still think that is more expected and those bams should be down sampled with a different tool rather than a hard cutoff here.only
base-depthis affected by this change. All other tools don't rely on pileup engine.