Merge pull request #402 from pangenome/wfmash-local-inv

wfmash v0.16.0

Dockerfile

@@ -50,16 +50,13 @@ RUN wget https://github.com/samtools/bcftools/releases/download/1.19/bcftools-1.
 RUN git clone --recursive https://github.com/waveygang/wfmash \
     && cd wfmash \
     && git pull \
-    && git checkout 251f4e1d7770723d3495e9d7b443f941798d4174 \
+    && git checkout 2243583d2f4272ce5254be9ffc508d492dd8b6f8 \
     && git submodule update --init --recursive \
     && sed -i 's/-march=native/-march=sandybridge/g' src/common/wflign/deps/WFA2-lib/Makefile \
     && cmake -H. -DCMAKE_BUILD_TYPE=Generic -DEXTRA_FLAGS='-march=sandybridge -Ofast' -Bbuild && cmake --build build -- -j $(nproc) \
     && cp build/bin/wfmash /usr/local/bin/wfmash \
     # Libraries aren't getting installed
-    && cp build/lib/libwfa2cpp.so.0 /usr/local/lib/ \
-    && cp build/lib/libwfa2cpp.so /usr/local/lib/ \
-    && cp build/lib/libwfa2.so.0 /usr/local/lib/ \
-    && cp build/lib/libwfa2.so /usr/local/lib/ \
+    && cp build/lib/* /usr/local/lib/ \
     && cd ../ \
     && rm -rf wfmash
 

pggb

@@ -590,7 +590,7 @@ if [[ "$input_paf" == false ]]; then
         "$input_fasta" \
         --lower-triangular \
         --hg-filter-ani-diff $hg_filter_ani_diff \
-        -i "$prefix_mappings_paf".mappings.$mapper.paf --invert-filtering \
+        -i "$prefix_mappings_paf".mappings.$mapper.paf \
         > "$prefix_paf".alignments.$mapper.paf) 2> >(tee -a "$log_file")
   fi
 fi