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Bug? PairHMM outputs to stdout instead of stderr
I'm using 3.3-0-g37228af.
This command gets around a feature that looks like a bug to me:
gatk -T HaplotypeCaller -R ref.fa -I in.bam -o /dev/stdout 2> log.txt | grep -v -e PairHMM -e "JNI call" | bgzip -s - > out.vcf.gz
As you see, one has to remove three lines of the stdout stream written by PairHMM. Like all other logging information, they should go to stderr.
The three lines look like this:
Using un-vectorized C++ implementation of PairHMM Time spent in setup for JNI call : 3.3656100000000003E-4 Total compute time in PairHMM computeLikelihoods() : 0.008854789