From b6853c837c43dd10c5b41fc828e17cde3b463c27 Mon Sep 17 00:00:00 2001
From: Andrew D Smith <andrewds@usc.edu>
Date: Thu, 12 Jun 2025 20:29:14 -0700
Subject: [PATCH 1/3] src/abismal: updating submodule

---
 src/abismal | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/abismal b/src/abismal
index 022c31e0..38d8087c 160000
--- a/src/abismal
+++ b/src/abismal
@@ -1 +1 @@
-Subproject commit 022c31e0faa2229b0aad65d781b0dca26cdbc3a0
+Subproject commit 38d8087c07e14f8c84cdc7d6ce12dcca43d024b8

From 251cccae61c2e5a70987883f6f4263e176922c7c Mon Sep 17 00:00:00 2001
From: Andrew D Smith <andrewds@usc.edu>
Date: Thu, 12 Jun 2025 20:30:48 -0700
Subject: [PATCH 2/3] .github/workflows/dnmtools_release_linux.yml: adding
 forgotten gsl dependency and using threads to build htslib

---
 .github/workflows/dnmtools_release_linux.yml | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/dnmtools_release_linux.yml b/.github/workflows/dnmtools_release_linux.yml
index 42502cf3..55ec3b16 100644
--- a/.github/workflows/dnmtools_release_linux.yml
+++ b/.github/workflows/dnmtools_release_linux.yml
@@ -23,8 +23,9 @@ jobs:
         env:
           SCRIPT: |
             export DEBIAN_FRONTEND=noninteractive && \
-            apt-get update && apt-get install --no-install-recommends -y automake && \
+            apt-get update && apt-get install --no-install-recommends -y automake libgsl-dev && \
             find /usr -name libz.so -exec rm {} \; && \
+            find /usr -name libgsl\*.so -exec rm {} \; && \
             git clone --recursive https://github.com/samtools/htslib.git && \
             cd htslib && \
             autoreconf -i && \
@@ -35,7 +36,7 @@ jobs:
                 --disable-lzma \
                 --disable-ref-cache \
                 LDADD="-L/usr/local/lib" && \
-            make CFLAGS="-Wall -O2 -fvisibility=hidden" libhts.a && \
+            make -j4 CFLAGS="-Wall -O2 -fvisibility=hidden" libhts.a && \
             cp libhts.a /usr/local/lib/ && \
             cp -r ../htslib /usr/local/include/ && \
             cd /workspace && \
@@ -48,7 +49,7 @@ jobs:
       - name: Get version number
         id: get-vn
         run: |
-          awk '/AC_INIT/ {print "vn="$2}' configure.ac | sed -e "s/\[//; s/\]//; s/,//" >> "$GITHUB_OUTPUT"
+          awk '/AC_INIT/ {print "vn="$2}' configure.ac | sed "s/\[//; s/\]//; s/,//" >> "$GITHUB_OUTPUT"
         env:
           GH_TOKEN: ${{ github.token }}
       - name: Upload the binary

From e0dccb9f98b3ce2bf56a6deba469708c4feda503 Mon Sep 17 00:00:00 2001
From: Andrew D Smith <andrewds@usc.edu>
Date: Thu, 12 Jun 2025 20:31:09 -0700
Subject: [PATCH 3/3] .github/workflows/dnmtools_release_macos.yml: using
 threads to build htslib

---
 .github/workflows/dnmtools_release_macos.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/dnmtools_release_macos.yml b/.github/workflows/dnmtools_release_macos.yml
index 1000cf1a..481ee31d 100644
--- a/.github/workflows/dnmtools_release_macos.yml
+++ b/.github/workflows/dnmtools_release_macos.yml
@@ -36,7 +36,7 @@ jobs:
             --disable-ref-cache \
             --without-libdeflate \
             LDADD="-L/usr/local/lib"
-          make CFLAGS="-Wall -O2 -fvisibility=hidden" libhts.a
+          make -j4 CFLAGS="-Wall -O2 -fvisibility=hidden" libhts.a
           sudo cp libhts.a /opt/dnmtools/lib
       - name: Build dnmtools
         run: |