--minmap_arg arg not present in conda install

BGI-Qingdao / TGS-GapCloser

A gap-closing software tool that uses long reads to enhance genome assembly.

GNU General Public License v3.0

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--minmap_arg arg not present in conda install #36

Closed charlesfeigin closed 3 years ago

charlesfeigin commented 3 years ago

Hi!

Excited to use your program. I installed the conda version (1.1.1) and noticed that the --minmap_arg is no longer present (and shows as unrecognized options in the err file). I am hoping to gap-fill an assembly using PacBio HiFi reads and was planning to use --minmap_arg '-x asm20' as suggested in the github page example. Do you know what an equivalent set of options would be in v1.1.1? Thanks!

Best, Charles

cchd0001 commented 3 years ago

Hi ,

please change the line 313 in tgsgapcloser, from MINIMAP2_PARAM=" -x ava-pb " to MINIMAP2_PARAM="-x asm20 ", and set --tgstype pb