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Add Genomics API counters for Dataflow UI display. #41
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Hi Nicole, On line 122 in DataflowWorkarounds.java it is currently written as:
It would be preferred as follows, or maybe a variable that can be assigned:
~p |
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On line 125 of the same file, it is currently written as:
Could we expand it just for clarification purposes:
~p |
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Looks nice, I'll try it once merged. Thanks, |
Its now in the codelabs repository.
--machineType does not have a default of n1-standard-4 in all contexts.
Now that we are doing client-side filtering for strict shard boundaries, we need to ensure that we are requesting the field that the filter will check.
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Hi Nicole, Unfortunately it throws an error, since I cannot give it a range on a specific chromosome :( It wants a string for the reference, and I only want to count the reads within a specific range. Is there a solution? Thanks, |
Contributor
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@pgrosu The API flavor of this pipeline was written as a very simplistic variant with just taking the reference and not ranges. The main purpose of this was to try the BAM file reading, not so much the API access. I will add more sophistication to the API side handling to make it compatible with what BAM reading part accepts. |
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Aha, thanks Ilia - I'll wait :) It was this part of the script that caused me think otherwise initially: if [ "$1" = "bam" ]; then
bam_argument="--BAMFilePath=$BAM_FILE_PATH"
fi
if [ "$2" = "cloud" ]; then
additional_arguments="--stagingLocation=${STAGING} --numWorkers=1 --runner=BlockingDataflowPipelineRunner"
else
additional_arguments="--numWorkers=1"
fiThanks, |
deflaux
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Mar 13, 2015
Add Genomics API counters for Dataflow UI display.
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Thanks Nicole :) |
jiridanek
pushed a commit
to jiridanek/dataflow-java
that referenced
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Jan 18, 2016
Add Genomics API counters for Dataflow UI display.
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