From 980069ad422cb2c91c1629d1cc118c077052a307 Mon Sep 17 00:00:00 2001
From: AndreaGuarracino <andreaguarracino@outlook.com>
Date: Wed, 31 Jan 2024 09:59:54 -0600
Subject: [PATCH 1/3] update wfmash

---
 Dockerfile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Dockerfile b/Dockerfile
index c927b85..1b981ed 100644
--- a/Dockerfile
+++ b/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) \

From bf686f298cc85dfae615ff25b36be837b6908b66 Mon Sep 17 00:00:00 2001
From: AndreaGuarracino <andreaguarracino@outlook.com>
Date: Wed, 31 Jan 2024 10:21:52 -0600
Subject: [PATCH 2/3] update odgi and smoothxg

---
 Dockerfile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Dockerfile b/Dockerfile
index 1b981ed..8343c47 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -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 \

From c1fbd6f11a2bf37eb1b3ef04318cf984ed4a2fc8 Mon Sep 17 00:00:00 2001
From: AndreaGuarracino <andreaguarracino@outlook.com>
Date: Wed, 31 Jan 2024 12:48:22 -0600
Subject: [PATCH 3/3] odgi stats -sgdl

---
 pggb | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/pggb b/pggb
index ec6c9c7..1ff8306 100755
--- a/pggb
+++ b/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