stdin for show-snps + autotools version in Dependencies

mummer4 / mummer

Mummer alignment tool

Artistic License 2.0

433 stars 108 forks source link

stdin for show-snps + autotools version in Dependencies #200

Open Hajin-Jeon opened 11 months ago

Hajin-Jeon commented 11 months ago

Sometimes, it is convenient to pass data as standard input when using the "show-snps" command. This PR suggests adding the "-s" tag for show-snps, which allows standard input instead of a deltafile.

Furthermore, during the installation of MUMmer, there have been cases where it fails due to version conflicts with autotools. I have added the version information to the Dependencies as mentioned in Issue #12.

gmarcais commented 5 months ago

Hi Hajin,

Thank you for submitted this PR. There are a few different things in this PR.

-s to read from stdin. That is rather unusual flag for that feature, it creates lots of code duplication and I don't think it is necessary: use /dev/stdin as the file name on the command line and it should work.
-H to not output the header, that's fine
-L for min sequence length, fine as well
-I for printing the identity, I don't quite understand yet. It prints identity to a different file?