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mourisl / Rascaf

Scaffolding with RNA-seq read alignment
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README clarification #15

Closed pickettbd closed 6 years ago

pickettbd commented 6 years ago

A simple addition to the README might be helpful. When I ran the sample test, it appeared to overwrite the original fasta file. Upon delving into the code, I realized that the parameter provided to rascaf-join with "-o" simply had ".fa" and ".info" appended to it to create the two output files. It just so happened that "-o sample/sample" will cause the original "sample/sample.fa" to be overwritten. I see nothing wrong with the approach, but it would be nice to have known what to expect from the README. It would be a bummer for someone to have their initial assembly fasta file lost forever by being overwritten.

mourisl commented 6 years ago

Thanks for so many good suggestions! It is definitely a disaster if rascaf overwrite the raw assembly file. I just added a test in rascaf-join to throw an error if the output fasta file overwrite the input fasta file.

pickettbd commented 6 years ago

You're welcome! :) I downloaded the changes and tried it on the sample. That's a helpful fix- thank you!