handle cluster_count values of zero or less in stage1 setup #456
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…mple fraction (i.e. don't divide by zero)
dozy
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extra tests not yet added |
srl147
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May 7, 2019
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this looks fine, I just checked and samtools view -s ####.0 works on a empty cram file and I assume the downstream checks will happily work on empty fastq file(s)
After discussing this with Marina, why don't you change the logic slightly. A fraction of 0 seems to be interpreted as take everything
if ($cluster_count <= 10000)
p4_params{seed_frac} = sprintf q[%.8f], $id_run + 0.0;
else
$p4_params{seed_frac} = sprintf q[%.8f], (10_000.0 / $cluster_count) + $id_run;
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just use zero for subsample fraction (i.e. don't divide by zero)