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apetkau / core-phylogenomics

Pipeline for identifying core SNPs and building a phylogenetic tree
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Some line options generated for lib/reads2sams.pl are incorrect #7

Open apetkau opened 10 years ago

apetkau commented 10 years ago

Some of the command line options, like -i -k 13 -s 6 and --map -n 24 -f samsoft -r -1 -y 0.5 are incorrect for lib/reads2sams.pl are incorrect. They should have quotes around the strings passed to -i and -m or --map. Also, --map should be --map_opts.

apetkau commented 10 years ago

This has more to do with how I am printing the commands, the actual command line options are passed correctly to the software.