allow spark confs as cmdline flags

hammerlab / guacamole

Spark-based variant calling, with experimental support for multi-sample somatic calling (including RNA) and local assembly

Apache License 2.0

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allow spark confs as cmdline flags #598

Closed ryan-williams closed 7 years ago

ryan-williams commented 7 years ago

forcing everything to go through GUAC_SPARK_CONFS props files was too restrictive; now we'll pick out arg-pairs of the form --conf spark.… and send them to spark, sending everything else to guacamole.

also fixed a GUAC_SPARK_CONFS bug where defaulting to conf/ dir didn't work when one file was specified.

coveralls commented 7 years ago

Coverage remained the same at 78.671% when pulling 3d76bcd847ebaeabb339a9bf635acbb12857e252 on ryan-williams:sc into 738996d8cfcc4bbcabf2138cf269b965dff5b190 on hammerlab:master.