ekg / fastahack Goto Github PK

Hi,
I'm maintaining this code for the Debian distribution as a predependency for FreeBayes. For the maintenance in Debian it would help a lot if you would consider tagging releases as distributable code. This would enable us to automatically detect new versions and provide users with the latest and greatest code.
Thanks for considering, Andreas.

The destructor for FastaReference assumes that open has been called. If this is not the case, the destructor's call to fclose results in a segfault.

I see that libdisorder is under GPL(v2) but that the rest of the source is not under a free license. Is there any possibility that fastahack could be put under a free license?

This is not working at present, with calls to FastaReference::getSubSequence(...) resulting in embedded \r characters.

The easy fix for users is to not use dos-formatted fasta references, but this should be detected by the indexing and file opening.

This seems like the obvious use case to me, but of course it is relatively easy to workaround. For instance:

$ fastahack -c my_index <ids.txt >sequences.txt
$ paste ids.txt sequences.txt |sed -e 's/^/>/' -e 's/\t/\n/' >sequences.fa

Hi,
I'd like to add an autopkgtest as continuous integration to the Debian package. Fastahack ships with a dir tests but there is no script that is using those fasta files and confirming that the test has passed. It would be helpful if this would such a script would be added or ar least the README file would document what would be considered a valid test.
Thanks, Andreas.

Hi,

We're using FastaHack in one of our production environments. For reproducibility, would it be possible to create a tag or release of the current version of this?
I there are no objections, I'd like to create a bioconda recipe for this piece of software, to increase the ease of use.

Thanks
M