LynchLab
commented
8 years ago It's bad documentation/programming on my part. If you create files with I/O redirection (i.e. command > output), then you don't need any additional files, but if you create files with the output option (i.e. command -o output) then two files should be created, one of which ends with idx. The one caveat is that mapgd only checks the file extension right now to figure out whether or not it needs a separate 'idx' file. This is a dumb way to do things, and I need to fix it. But, in the mean time you can create an idx file with the command "sam2idx" which takes a sam formatted header and converts it to a mapgd formatted header.
-Matt
On Mon, Jun 13, 2016 at 4:21 AM, peterdfields notifications@github.com wrote:
When trying to run the basic example for pooled sequence data I get the following error following calling mapgd pool:
map-file.cc:80: cannot open metapopulation.idx for reading. Error: No such file or directory
Is there an additional indexing step (sorta like samtools index) or should this file been created by the use of mapgd proview?
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When trying to run the basic example for pooled sequence data I get the following error following calling mapgd pool:
map-file.cc:80: cannot open metapopulation.idx for reading. Error: No such file or directory
Is there an additional indexing step (sorta like samtools index) or should this file been created by the use of mapgd proview?