Merge pull request #131 from blachlylab/develop

Release v0.14.0+htslib-1.13
blachlylab · Mar 2, 2022 · 2529b13 · 2529b13
2 parents 0f284df + 1176725
commit 2529b13
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diff --git a/.github/workflows/unittests.yml b/.github/workflows/unittests.yml
@@ -2,8 +2,8 @@ name: unittests
 on: [push, pull_request]
 
 jobs:
-  linux-unittests:
-    name: Dub Tests
+  linux-unittests-ldc:
+    name: Dub Tests LDC
     strategy:
       matrix:
         os: [ubuntu-latest]
@@ -73,3 +73,140 @@ jobs:
 
       - name: Upload coverage
         run: bash <(curl -s https://codecov.io/bash)
+
+  linux-unittests-dmd:
+    name: Dub Tests DMD
+    strategy:
+      matrix:
+        os: [ubuntu-latest]
+        dc: [dmd-latest]
+
+    runs-on: ${{ matrix.os }}
+    steps:
+      - uses: actions/checkout@v2
+        with:
+          submodules: recursive
+
+      - name: Install D compiler
+        uses: dlang-community/setup-dlang@v1
+        with:
+          compiler: ${{ matrix.dc }}
+
+      - name: Install htslib deps
+        run: |
+            sudo apt-get update && sudo apt-get install -y build-essential autoconf zlib1g-dev libbz2-dev liblzma-dev libcurl4-openssl-dev libssl-dev
+
+      - name: Get htslib commit
+        id: get-htslib-commit
+        run: echo "::set-output name=sha_short::$(git rev-parse --short :htslib)"
+
+      - name: Cache htslib
+        id: cache-htslib
+        uses: actions/cache@v2
+        with:
+          path: htslib
+          key: ${{ runner.os}}-htslib-${{ steps.get-htslib-commit.outputs.sha_short }}
+
+      - name: Build htslib
+        if: steps.cache-htslib.outputs.cache-hit != 'true'
+        run: |
+            cd htslib
+            autoreconf -i
+            ./configure
+            make
+
+      - name: Install htslib
+        run: |
+            cd htslib
+            sudo make install
+            sudo ldconfig
+
+      - name: Setup additional test files
+        run: |
+            cd htslib
+            cd test
+            cd tabix
+            bgzip -c gff_file.gff > gff_file.gff.gz
+            tabix gff_file.gff.gz
+            bgzip -c bed_file.bed > bed_file.bed.gz
+            tabix bed_file.bed.gz
+            bgzip -c vcf_file.vcf > vcf_file.vcf.gz
+            tabix vcf_file.vcf.gz
+
+      - name: Run tests
+        run: dub -q test -b=unittest-cov
+        env:
+          LIBRARY_PATH: /usr/local/lib
+
+      - name: Run safety tests
+        run: dub -q test -c=unittest-safety
+        env:
+          LIBRARY_PATH: /usr/local/lib
+
+  macos-unittests-dmd:
+    name: Dub Tests DMD
+    strategy:
+      matrix:
+        os: [macos-latest]
+        dc: [dmd-latest]
+
+    runs-on: ${{ matrix.os }}
+    steps:
+      - uses: actions/checkout@v2
+        with:
+          submodules: recursive
+
+      - name: Install D compiler
+        uses: dlang-community/setup-dlang@v1
+        with:
+          compiler: ${{ matrix.dc }}
+
+      - name: Install htslib deps
+        run: |
+            brew install xz autoconf automake
+
+      - name: Get htslib commit
+        id: get-htslib-commit
+        run: echo "::set-output name=sha_short::$(git rev-parse --short :htslib)"
+
+      - name: Cache htslib
+        id: cache-htslib
+        uses: actions/cache@v2
+        with:
+          path: htslib
+          key: ${{ runner.os}}-htslib-${{ steps.get-htslib-commit.outputs.sha_short }}
+
+      - name: Build htslib
+        if: steps.cache-htslib.outputs.cache-hit != 'true'
+        run: |
+            cd htslib
+            autoreconf -i
+            ./configure
+            make
+
+      - name: Install htslib
+        run: |
+            cd htslib
+            sudo make install
+
+      - name: Setup additional test files
+        run: |
+            cd htslib
+            cd test
+            cd tabix
+            bgzip -c gff_file.gff > gff_file.gff.gz
+            tabix gff_file.gff.gz
+            bgzip -c bed_file.bed > bed_file.bed.gz
+            tabix bed_file.bed.gz
+            bgzip -c vcf_file.vcf > vcf_file.vcf.gz
+            tabix vcf_file.vcf.gz
+
+      - name: Run tests
+        run: dub -q test -b=unittest-cov
+        env:
+          LIBRARY_PATH: /usr/local/lib
+
+      - name: Run safety tests
+        run: dub -q test -c=unittest-safety
+        env:
+          LIBRARY_PATH: /usr/local/lib
diff --git a/.gitignore b/.gitignore
@@ -21,12 +21,17 @@ bug_minimal
 sam_iter
 csam_iter
 dhtslib-test-unittest
+coordinates/coordinates-test-unittest
+dhtslib-test-unittest-safety
+chunkby
+cigartest
 
 # DUB
 .dub
 docs.json
 __dummy.html
 docs/
+dub.selections.json
 
 # Code coverage
 *.lst

diff --git a/README.md b/README.md
@@ -1,33 +1,34 @@
+![alt text](/logo/dhtslib_logo.png "dhtslib")
+
 dhtslib
 =======
 
 [![unittests](https://github.com/blachlylab/dhtslib/actions/workflows/unittests.yml/badge.svg)](https://github.com/blachlylab/dhtslib/actions/workflows/unittests.yml)
 [![codecov.io](https://codecov.io/github/blachlylab/dhtslib/coverage.svg?branch=develop)](https://codecov.io/github/blachlylab/dhtslib?branch=develop)
 
-# Overview
 
 `dhtslib` provides D bindings, high-level abstractions, and additional functionality for [htslib](https://github.com/samtools/htslib), the most widely-used library for manipulation of high-throughput sequencing data. We currently support linux and OSX. Windows support is still in progress (see #38). More extensive documentation can be found at our [gitbook](https://blachlylab.gitbook.io/dhtslib/).
 
-# Installation
+## Installation
 
 Add `dhtslib` as a dependency to `dub.json`:
 
 ```
     "dependencies": {
-        "dhtslib": "~>0.12.3+htslib-1.10",
+        "dhtslib": "~>0.13.3+htslib-1.13",
     }
 ```
-(version number 0.12.3 is example, `+htslib-1.10` represents the compatible htslib version; see https://dub.pm/package-format-json)
+(version number 0.13.3 is example, `+htslib-1.13` represents the compatible htslib version; see https://dub.pm/package-format-json)
 
-# Requirements
+## Requirements
 
-## htslib
-A system installation of htslib >= v1.10 is required. You can find detailed install instructions [here](htslib.md).
+### htslib
+A system installation of htslib >= v1.13 is required. You can find detailed install instructions [here](htslib.md).
 
-# Usage
+## Usage
 `dhtslib` usage information and examples can be found [here](usage.md).
 
-## Dhtslib API (OOP Wrappers)
+### Dhtslib API (OOP Wrappers)
 
 Object-oriented, idomatic D wrappers are available for:
 
@@ -47,7 +48,7 @@ Additional functionality is provided for:
 All htslib bindings can be found under the `htslib` namespace (in prior versions they were under `dhtlsib.htslib`). These can be used directly as you would with `htslib`.
 
 
-## htslib API
+### htslib API
 
 Direct bindings to htslib C API are available as submodules under the `htslib` namespace. Naming remains the same as the original `.h` include files. For example, `import htslib.faidx` for direct access to the C function calls. Where the OOP wrappers manage their own data along the the D garbage collector, these functions use traditional C memory management (or lack thereof). The current compatible htslib versions are 1.10+.
 
@@ -82,7 +83,7 @@ Missing or work-in-progress:
 
 [dstep](https://github.com/jacob-carlborg/dstep) has matured and is an incredibly powerful tool for machine-assisted C-to-D translation. We've used dstep for the majority of bindings in the since version v0.11.0. After dstep translation, we port inline functions by hand as they are not translated, tweak some macros into templates (done although dstep already does an amazing job on simple `#define` macros translating to D templates!),  and update the documentation comments to ddoc format.
 
-# FAQ
+## FAQ
 
 **Q**: Does this work with the latest htslib?
 
@@ -106,16 +107,16 @@ However, the development resources poured into `htslib` overall are tremendous,
 It's easy to get a segfault by using the direct C API incorrectly. Or possibly correctly. We have tried to eliminate most of this (use after free, etc.) in the OOP wrappers via refernece counting. If you are getting a segfault you cannot understand when using purely the high-level D API, please post an issue.
 
 
-# Bugs and Warnings
+## Bugs and Warnings
 
 Do not call `hts_log_*` with `ctx` as anything other than a string literal from a destructor, as it is potentialy allocating via `toStringz`
 
 
-# Programs made with dhtslib
+## Programs made with dhtslib
 1. [fade](https://github.com/blachlylab/fade): Fragmentase Artifact Detection and Elimination
 2. [recontig](https://github.com/blachlylab/recontig): a program to convert different bioinformatics data types from one reference naming convention to another i.e UCSC to ensembl (chr1 to 1)
 
-# Related projects
+## Related projects
 
 1. [gff3d](https://github.com/blachlylab/gff3d): GFF3 record reader/writer
-2. [dklib](https://github.com/blachlylab/dklib): Templatized port of attractivechaos' klib, used extensively in htslib
+2. [dklib](https://github.com/blachlylab/dklib): Templatized port of attractivechaos' klib, used extensively in htslib