Merge pull request #371 from pangenome/update-stuff

update wfmash/smoothxg/odgi

Dockerfile

@@ -46,7 +46,7 @@ RUN apt-get update \
 RUN git clone --recursive https://github.com/waveygang/wfmash \
     && cd wfmash \
     && git pull \
-    && git checkout 0b191bb84ffdfd257354c1aa82a7f1e13dc536d0 \
+    && git checkout e7850f9e9ba743a350b36b5e51ae8c414fba717d \
     && 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) \
@@ -72,7 +72,7 @@ RUN git clone --recursive https://github.com/ekg/seqwish \
 RUN git clone --recursive https://github.com/pangenome/smoothxg \
     && cd smoothxg \
     && git pull \
-    && git checkout 9970e0df187c5e1234ace61243f30ddccbbbbdd8 \
+    && git checkout ea362342bc4301f767727467953bafcaf147172b \
     && git submodule update --init --recursive \
     && sed -i 's/-msse4.1/-march=sandybridge -Ofast/g' deps/spoa/CMakeLists.txt \
     && sed -i 's/-march=native/-march=sandybridge -Ofast/g' deps/spoa/CMakeLists.txt \

pggb

@@ -684,12 +684,12 @@ fi
 
 if [[ $do_stats == true ]]; then
     $timer -f "$fmt" odgi build -t $threads -P -g "$prefix_seqwish".seqwish.gfa -o "$prefix_seqwish".seqwish.og 2> >(tee -a "$log_file")
-    odgi stats -i "$prefix_seqwish".seqwish.og -m > "$prefix_seqwish".seqwish.og.stats.yaml 2>&1 | tee -a "$log_file"
-    odgi stats -i "$prefix_smoothed_output".final.og -m  > "$prefix_smoothed_output".final.og.stats.yaml 2>&1 | tee -a "$log_file"
+    odgi stats -i "$prefix_seqwish".seqwish.og -m -sgdl > "$prefix_seqwish".seqwish.og.stats.yaml 2>&1 | tee -a "$log_file"
+    odgi stats -i "$prefix_smoothed_output".final.og -m  -sgdl > "$prefix_smoothed_output".final.og.stats.yaml 2>&1 | tee -a "$log_file"
     if [[ $consensus_spec != false ]]; then
         for consensus_graph in "$prefix_smoothed_output"*.cons*.gfa; do
             odgi build -t $threads -P -g "$consensus_graph" -o "$consensus_graph".og 2> >(tee -a "$log_file")
-            odgi stats -i "$consensus_graph".og -m >"$consensus_graph".og.stats.yaml 2>&1 | tee -a "$log_file"
+            odgi stats -i "$consensus_graph".og -m -sgdl >"$consensus_graph".og.stats.yaml 2>&1 | tee -a "$log_file"
         done
     fi
 fi