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csq: only print > max consequences for 1 sample.#585

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brentp wants to merge 1 commit into
samtools:developfrom
brentp:limit-warning
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csq: only print > max consequences for 1 sample.#585
brentp wants to merge 1 commit into
samtools:developfrom
brentp:limit-warning

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@brentp brentp commented Apr 4, 2017

I'm seeing redundant warnings like this:

Warning: --ncsq 16 is too small to annotate NA12878 at 5:50057729 with 17-th csq
Warning: --ncsq 16 is too small to annotate NA12891 at 5:50057729 with 17-th csq
Warning: --ncsq 16 is too small to annotate NA12892 at 5:50057729 with 17-th csq
Warning: --ncsq 16 is too small to annotate NA12878 at 5:96101031 with 17-th csq
Warning: --ncsq 16 is too small to annotate NA12892 at 5:96101031 with 17-th csq
Warning: --ncsq 16 is too small to annotate NA12878 at 5:96101031 with 18-th csq
Warning: --ncsq 16 is too small to annotate NA12892 at 5:96101031 with 18-th csq
Warning: --ncsq 16 is too small to annotate NA12878 at 5:96101031 with 19-th csq
Warning: --ncsq 16 is too small to annotate NA12892 at 5:96101031 with 19-th csq
Warning: --ncsq 16 is too small to annotate NA12878 at 5:96101031 with 20-th csq
Warning: --ncsq 16 is too small to annotate NA12892 at 5:96101031 with 20-th csq
Warning: --ncsq 16 is too small to annotate NA12878 at 5:96101031 with 21-th csq
Warning: --ncsq 16 is too small to annotate NA12892 at 5:96101031 with 21-th csq
Warning: --ncsq 16 is too small to annotate NA12878 at 5:138221989 with 17-th csq
Warning: --ncsq 16 is too small to annotate NA12891 at 5:138221989 with 17-th csq
...

This limits to show only the first warning. I'm happy to change this but this was the smallest change I could see that would be effective.

pd3 added a commit that referenced this pull request Apr 5, 2017
Specifically, giving -q, --quiet once prints the following warnings
only once, giving it twice it supresses all warnings:
Warning: --ncsq 16 is too small to annotate NA12877 at 22:30953295 with 20-th csq

This commit replaces
#585
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pd3 commented Apr 5, 2017

Sometimes it is useful to have the full information, it is not redundant. This commit gives more control over what will be reported bbe709e

@pd3 pd3 closed this Apr 5, 2017
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