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Uninitialized values in GenomeIndex.pm #127

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robmaz opened this issue Oct 2, 2018 · 1 comment
Open

Uninitialized values in GenomeIndex.pm #127

robmaz opened this issue Oct 2, 2018 · 1 comment
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@robmaz
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robmaz commented Oct 2, 2018

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.
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@magicDGS
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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 #33, which is already implemented but the class is still there and the argument still in the map).

robmaz pushed a commit that referenced this issue Jan 14, 2019
GenomeIndex.pm: remove checks for obsolete args
5c719af 
should also fix issue #127
robmaz added a commit that referenced this issue Jan 21, 2019
@robmaz
Rm fix remaining bugs (#132)
4ab579e 
* distmap: fix trim-args type
--trim-args should expect a string argument

* GenomeIndex.pm: remove checks for obsolete args
should also fix issue #127

* HadoopMapping.pm: mktemp needs template arg

* HadoopMapping.pm: exec to see mapper return code
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@magicDGS @robmaz