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robmaz / distmap

Sequence alignment on Hadoop
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Uninitialized values in GenomeIndex.pm #127

Open robmaz opened 6 years ago

robmaz commented 6 years ago

Running with --index-only writes the following warnings: ... Copying executables Use of uninitialized value in -e at /home/vetlinux02/.linuxbrew/Cellar/distmap/HEAD-fee4cef/bin/../lib/perl5/site_perl/GenomeIndex.pm line 222. Use of uninitialized value in -e at /home/vetlinux02/.linuxbrew/Cellar/distmap/HEAD-fee4cef/bin/../lib/perl5/site_perl/GenomeIndex.pm line 226. Use of uninitialized value in -e at /home/vetlinux02/.linuxbrew/Cellar/distmap/HEAD-fee4cef/bin/../lib/perl5/site_perl/GenomeIndex.pm line 230. Use of uninitialized value in -e at /home/vetlinux02/.linuxbrew/Cellar/distmap/HEAD-fee4cef/bin/../lib/perl5/site_perl/GenomeIndex.pm line 235. Creating Archive ...

magicDGS commented 6 years ago

This is related with #78 (trying to copy the picard jar/s if provided) and also trying to copy the trimming-script (I think that it is related to https://github.com/robmaz/distmap/issues/33, which is already implemented but the class is still there and the argument still in the map).