fix build.yml

Author: brentp

.github/workflows/build.yml

@@ -12,7 +12,7 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-18.04, macos-10.15]
-        nimversion:
+        version:
         - stable
         - devel
 
@@ -48,7 +48,7 @@ jobs:
       run: |
         sudo apt-get update
         sudo apt-get -qy install bwa make build-essential cmake libncurses-dev ncurses-dev libbz2-dev lzma-dev liblzma-dev \
-             curl libssl-dev libtool autoconf automake libcurl4-openssl-dev
+             curl libssl-dev libtool autoconf automake libcurl4-openssl-dev zlib1g-dev
 
     # Setup htslib
     - name: Install htslib (linux)
@@ -57,28 +57,31 @@ jobs:
         cd
         git clone --recursive https://github.com/samtools/htslib.git
         cd htslib && git checkout 1.11 && autoheader && autoconf && ./configure --enable-libcurl
-        cd
-        make -j 4 -C htslib install
-        echo "::set-env name=LD_LIBRARY_PATH::${LD_LIBRARY_PATH}:${HOME}/htslib"
-        ls -lh $HOME/htslib/*.so
+        sudo make -j 4 install
+        sudo ldconfig
+        #echo "::set-env name=LD_LIBRARY_PATH::${LD_LIBRARY_PATH}:${HOME}/htslib"
+        #ls -lh $HOME/htslib/*.so
+
+    - name: Install hstlib (macos)
+      if: runner.os == 'macOS'
+      run: |
+        brew install htslib
 
     - name: Install d4 
-        export HTSLIB=system
+      run: |
+        #export HTSLIB=system
         git clone https://github.com/38/d4-format
         cd d4-format
-        cargo build --release
+        cargo build --release --all-features
+        cd d4binding/ && cargo build --release && cd ..
         sudo cp ../d4-format/target/release/libd4binding.* /usr/local/lib
         sudo cp ./d4binding/include/d4.h /usr/local/include/
+        sudo (ldconfig || true)
 
 
-    - name: Install hstlib (macos)
-      if: runner.os == 'macOS'
-      run: |
-        brew install htslib
-
-    - uses: iffy/install-nim@v1.1
+    - uses: iffy/install-nim@v4.1.1
       with:
-        nimversion: ${{ matrix.nimversion }}
+        version: ${{ matrix.version }}
 
     - uses: actions-rs/toolchain@v1
       with:

depthstat.nim

@@ -18,7 +18,7 @@ proc add*[T](c: var CountStat, value: T) {.inline.} =
   if value.int > c.counts.high.int:
     c.counts[c.counts.high].inc
   elif value < 0:
-    raise newException(IndexError, "error setting negative depth value:" & $value)
+    raise newException(IndexDefect, "error setting negative depth value:" & $value)
   else:
     c.counts[value].inc
 

mosdepth.nim

@@ -765,7 +765,7 @@ proc threshold_args*(ts: string): seq[int] =
 
 
 proc check_cram_has_ref(cram_path: string, fasta:string) =
-  if fasta != "" and exists_file(fasta):
+  if fasta != "" and fileExists(fasta):
     return
   if cram_path.ends_with(".cram"):
     stderr.write_line("[mosdepth] ERROR: specify a reference file (or set REF_PATH env var) for decoding CRAM")