Victor Epain (afb8ec7a) at 15 Feb 05:41

Victor Epain (40b66df6) at 15 Feb 05:36

Hello Anita,

The GFA format separates the contig name from its features (LN tag etc.). However, both gplasCC and PlasmidCC transform the contig name by adding to it the sequences tags and their values.

What I proposed is to not adding the contig features to its name.

For example, for a GFA sequence line S: S56 LN:i:9880 dp:f:5.36 gplasCC and plasmidCC are not directly using the contig (sequence) name (which is S56), but transform it to S56_LN:i:9880_dp:f:5.36.

It is not convenient for pipeline tools because the user must use the same transformation as in gplasCC and plasmidCC (and not natural, as you name the column in the tab file Contig_name... which not the contig name again.)

Victor Epain (c04ca203) at 15 Jan 20:41