Argument parsing corrections #2
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1. Several arguments were incorrectly converted to integer instead of float which rounded them. Arguments (like minhetfreq) that were in range (0, 1) were rounded to 0 and hence always assigned default values during later checks (BS-SNPer.pl:48-55 @ master) 2. It wasn't possible to set any argument to 0 as in this case in later checks (BS-SNPer.pl:48-55 @ master) 0 was interpreted as False and the default value was used in such cases. 3. It doesn't make sense to check @argv == 0 here as it will be empty after GetOptions. What makes sense is checking for files, as there are no default values for them. Although for output files it might be good idea to just construct them based on input filename by adding predefined suffixes, i.e. if $bam == file.bam, $methcg would be file.bam.methcg
galaxy001
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Jan 5, 2021
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which rounded them. Arguments (like minhetfreq) that were in range (0, 1) were
rounded to 0 and hence always assigned default values during later checks
(BS-SNPer.pl:48-55 @ master)
(BS-SNPer.pl:48-55 @ master) 0 was interpreted as False and the default value
was used in such cases.
after GetOptions. What makes sense is checking for files, as there are no
default values for them. Although for output files it might be good idea
to just construct them based on input filename by adding predefined suffixes,
i.e. if $bam == file.bam, $methcg would be file.bam.methcg