epruesse / SINA

SINA - Reference based multiple sequence alignment
https://sina.readthedocs.io
GNU General Public License v3.0
40 stars 4 forks source link

Support arb 7.0 #103

Open a1an77 opened 2 years ago

a1an77 commented 2 years ago

SINA does not compile against the recently released arb 7.0. There is a change in the API which can be fixed by the following patch (using the new recommended version of the copy function). Not sure if the default version of the copy function has relevant differences wrt the old one.

diff -ru SINA-1.7.2/src/query_arb.cpp SINA-1.7.2-patched/src/query_arb.cpp
--- SINA-1.7.2/src/query_arb.cpp    2020-12-13 21:00:11.000000000 +0100
+++ SINA-1.7.2-patched/src/query_arb.cpp    2021-10-26 16:21:30.255924518 +0200
@@ -809,7 +809,7 @@
     GBDATA *gbsource = other.data->getGBDATA(name);
     gbdest = GB_create_container(data->gbspec, "species");
     if ((gbsource != nullptr) && (gbdest != nullptr)) {
-        GB_copy(gbdest,gbsource);
+        GB_copy_std(gbdest,gbsource);
         data->gblast = gbdest;
         if (mark) {
             GB_write_flag(gbdest, 1);