a7cb599945
-Throw a UserException if a Locus or ActiveRegion walker is run with -dcov < 200, since low dcov values can result in problematic downsampling artifacts for locus-based traversals. -Read-based traversals continue to have no minimum for -dcov, since dcov for read traversals controls the number of reads per alignment start position, and even a dcov value of 1 might be safe/desirable in some circumstances. -Also reorganize the global downsampling defaults so that they are specified as annotations to the Walker, LocusWalker, and ActiveRegionWalker classes rather than as constants in the DownsamplingMethod class. -The default downsampling settings have not been changed: they are still -dcov 1000 for Locus and ActiveRegion walkers, and -dt NONE for all other walkers. |
||
|---|---|---|
| .. | ||
| R | ||
| c | ||
| chainFiles | ||
| doc | ||
| java | ||
| keys | ||
| packages | ||
| perl | ||
| scala | ||
| testdata | ||