Mpileup maxcnt tweak. #1269
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Mpileup maxcnt tweak. #1269
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In htslib: We can now count the depth anywhere along the read rather than only at the left end. It's not buffering reads up so it doesn't know what's about to come, so for any individual column it'll still favour reads that end near a column than start near a column, but by counting at the right hand end we avoid the boom & bust approach to before where the coverage could plumet to zero immediately following a large spike. With iter->depth_pos = 1.0 the coverage ends up being a minimum of maxcnt (assuming the true coverage is higher), rather than a maximum of maxcnt. So we go over-depth, but avoid the drop outs. This is enabled in Samtools using -d max_depth.fraction. Eg -d10000.9 will compute depth 90% of the way along the sequence rather than at the start.
This only affects VCF / BCF output, which has been deprecated and removed from the usage and the man page. Hence this option is now a red herring / pit fall.
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Uses samtools/htslib#1084
By default no change in behaviour, but the -d option now doubles up as a location too.
-d 10is equiv to-d 10.0meaning left end.-d 10.7means use depth 70% of the way through the read.