Hi,
I'm reviving this old thread as it shows up on the internet search and perfectly fits.
I followed the above instructions and was able to extract the gfa files. Now I want to re-pack the files after editing them.
I found:
https://gbatemp.net/threads/release-gfa ... ld.468131/https://github.com/jam1garner/gfa-packerand with a bit of luck:
https://web.archive.org/web/*/http://ww ... ress/bpe.cNow I wasn't able to get this all working and the file I want to re-compress 'TF01.bfres -> TF01.gfa' is definitely above 1MB
I did glanze over both the python script and the c-source of bpe and I'm not sure if this 1MB limit is easy to overcome or not. Just changing the defines might work or not
#define BLOCKSIZE 10000 /* maximum block size */
#define HASHSIZE 8192 /* size of hash table */
#define MAXCHARS 220 /* char set per block */
#define THRESHOLD 3 /* minimum pair count */
I might be experienced enough to get this working but first I want to ask here if there is not an obviously better or more recent way of doing this?
Cheers!