added min depth as command line option#2235
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This currently treats each file separately for depth filtering purposes, however as the output is for the sum over all files I think it should count a location if the sum of all positions comes over the threshold. This would be similar to running: I suspect the program is mostly used with only one input, but if you do supply more that one I'd guess it's with the intention of seeing the coverage over the merged files. |
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Updated to use depth based on all input files. |
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Fixes #1563
Added min-depth command line option with default value 1. With this value, it works as previous versions.
When value other than 1 is given, new value is used for the min depth check and any position in a file which has depth below it are ignored. The quality values for such positions are also ignored.
Note: The depth is per file / input.