Clearly label the number of reads in the CountReads output #6449
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@lbergelson A quick one for you |
lbergelson
reviewed
Feb 10, 2020
| @@ -39,6 +39,7 @@ public void apply( final GATKRead read, final ReferenceContext referenceContext, | |||
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| @Override | |||
| public Object onTraversalSuccess() { | |||
| logger.info("CountReads counted " + count + " total reads"); | |||
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@droazen This should probably print a non-logger number directly to standard out as well shouldn't it? So that people can capture it programmatically/ incase logging is turned off.
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This PR is just to label the value output by the tool, which was confusing users. If we want to support actual piping of the output, which is not something we typically do, we'd probably want an actual test case to prove that it works. This seems beyond the scope of this particular PR.
lbergelson
reviewed
Feb 10, 2020
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@droazen One comment, this is definitely an improvement over not specifying anything, but maybe we want more?
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