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open my $fh ... or continue with broken filehandle #73

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mcast opened this issue Jun 13, 2022 · 0 comments

mcast commented Jun 13, 2022

While on Helpdesk debugging a problem probably caused by incorrectly calling this code, I noticed
https://github.com/cancerit/vafCorrect/blob/5.7.2/perl/lib/Sanger/CGP/Vaf/Data/ReadVcf.pm#L102

    open my $fai_fh , '<', $self->{'_g'}.'.fai';
    while (<$fai_fh>) {

If the .fai file is not found, then this error will not be reported in a meaningful way.

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