Merge pull request #25 from Illumina/GT-804

GT-804 v2.2b release
Illumina · Jun 15, 2019 · 9648877 · 9648877
2 parents 6a1863b + f912119
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diff --git a/README.md b/README.md
@@ -2,13 +2,7 @@
 
 <!-- vscode-markdown-toc -->
 * [Introduction](#Introduction)
-* [System Requirements](#SystemRequirements)
-	* [Hardware](#Hardware)
-	* [Operating systems](#Operatingsystems)
-	* [Third-party libraries](#ThirdPartyLibraries)
 * [Installation](#Installation)
-	* [Native build](#NativeBuild)
-	* [From Docker image](#FromDockerImage)
 * [Run Paragraph from VCF](#RunParagraphFromVCF)
     * [Example](#Example)
     * [Input requirements](#InputRequirements)
@@ -38,115 +32,9 @@ Please reference Paragraph using:
 
 Genotyping calls in this paper can be found at [paper-data/download-instructions.txt](paper-data/download-instructions.txt)
 
-## <a name='SystemRequirements'></a>System Requirements
-
-### <a name='Hardware'></a>Hardware
-
-A standard workstation with at least 8GB of RAM should be sufficient for compilation and testing of the program.
-
-### <a name='Operatingsystems'></a>Operating systems
-
-Paragrpah is supported on the following systems:
-
-- Ubuntu 16.04 and CentOS 5-7,
-- macOS 10.11+,
-
-Python 3.4+ is required.
-
-We recommend using g++ (6.0+), or a recent version of Clang.
-
-We use the C++11 standard, any Posix compliant compiler supporting this standard
-should be usable.
-
-### <a name='ThirdPartyLibraries'></a>Third-party libraries
-
-Please check [requirements.txt](requirements) for required python modules.
-
-[Boost libraries](http://www.boost.org) version >= 1.5 is required.
-- We prefer to statically link Boost libraries to Paragraph executables:
-
-  ```bash
-  cd ~
-  wget http://downloads.sourceforge.net/project/boost/boost/1.65.0/boost_1_65_0.tar.bz2
-  tar xf boost_1_65_0.tar.bz2
-  cd boost_1_65_0
-  ./bootstrap.sh
-  ./b2 --prefix=$HOME/boost_1_65_0_install link=static install
-  ```
-
-- To point Cmake to your version of Boost use the `BOOST_ROOT` environment variable:
-
-  ```bash
-  export BOOST_ROOT=$HOME/boost_1_65_0_install
-  ```
-
-We have included copies of other dependent libraries in external/. They are:
-- Google Test and Google Mock (v1.8.0)
-- Htslib (v1.9)
-- Spdlog
-
 ## <a name='Installation'></a>Installation
 
-### <a name='NativeBuild'></a>Native buid
-First, checkout the repository like so:
-
-  ```bash
-  git clone https://github.com/Illumina/paragraph.git
-  cd paragraph-tools
-  ```
-
-  Then create a new directory for the program and compile it there:
-
-  ```bash
-  # Create a separate build folder.
-  cd ..
-  mkdir paragraph-tools-build
-  cd paragraph-tools-build
-
-  # Configure
-  # optional:
-  # export BOOST_ROOT=<path-to-boost-installation>
-  cmake ../paragraph-tools
-  # if this doesn't work, run this instead:
-  # cmake ../paragraph-tools -DCMAKE_CXX_COMPILER=`which g++` -DCMAKE_C_COMPILER=`which gcc` -DBOOST_ROOT=$BOOST_ROOT
-
-  # Make, use -j <n> to use n parallel jobs to build, e.g. make -j4
-  make
-  ```
-
-### <a name='FromDockerImage'></a>From Docker Image
-We also provide a [Dockerfile](Dockerfile). To build a Docker image, run the following command inside the source
-  checkout folder:
-
-  ```bash
-  docker build .
-  ```
-
-  Once the image is built you can find out its ID like this:
-
-  ```bash
-  docker images
-  ```
-  ```
-  REPOSITORY                             TAG                 IMAGE ID            CREATED             VIRTUAL SIZE
-  <none>                                 <none>              54c7d4015330        16 seconds ago      1.76 GB
-  ```
-
-  Check the below section for how to run Paragraph, and execute this before running:
-
-  ```bash
-  sudo docker run -v `pwd`:/data 54c7d4015330
-  ```
-
-  The current directory can be accessed as `/data` inside the Docker container.
-
-  The default entry point is `multigrmpy.py`.
-
-  To override the default entrypoint and get an interactive shell, run:
-
-  ```bash
-  sudo docker run --entrypoint /bin/bash -it 54c7d4015330
-  ```
+Please check [doc/Installation.md](doc/Installation.md) for system requirements and installation instructions.
 
 ## <a name='RunParagraphFromVCF'></a>Run Paragraph from VCF
 ### <a name='Example'></a>Example
@@ -161,7 +49,7 @@ python3 bin/multigrmpy.py -i share/test-data/round-trip-genotyping/candidates.vc
 
 This runs a simple genotyping example for two test samples.
 *  **candidates.vcf**: this specifies candidate SV events in a vcf format.
-*  **samples.txt**: Manifest that specifies some test BAM files. Tab delimited.
+*  **samples.txt**: Manifest that specifies some test BAM files. Tab or comma delimited.
 *  **dummy.fa** a short dummy reference which only contains `chr1`
 
 The output folder `test` then contains gzipped json for final genotypes:

diff --git a/RELEASES.md b/RELEASES.md
@@ -1,20 +1,22 @@
 # Paragraph Release Notes / Change Log
 
+# Version 2.2b
+
 | Date Y-m-d | Ticket  | Description                                                          |
 |------------|---------|----------------------------------------------------------------------|
+| 2019-06-14 | GT-804  | Simplify README and add static build                    |
+
+# Version 2.2a
+
 | 2019-05-27 | GT-802  | Update license to Apache and fix docker entry                        |
 
-#Version 2.2
+# Version 2.2
 
-| Date Y-m-d | Ticket  | Description                                                          |
-|------------|---------|----------------------------------------------------------------------|
 | 2019-05-11 | GT-743  | Update interface and error handling                                  |
 | 2018-12-11 | GT-696  | Fix newlines in validation scripts (public repo already fixed)       |
 
 # Version 2.1
 
-| Date Y-m-d | Ticket  | Description                                                          |
-|------------|---------|----------------------------------------------------------------------|
 | 2018-12-06 | GT-675  | Fix filters and alignment stats. Change depth test threshold on lower end |
 | 2018-11-08 | GT-660  | Optimize GQ for variant genotypes                                    |
 | 2018-11-02 | GT-656  | Improvement for simple SV genotyping                                 |
@@ -24,8 +26,6 @@
 
 # Version 2.0
 
-| Date Y-m-d | Ticket  | Description                                                          |
-|------------|---------|----------------------------------------------------------------------|
 | 2018-06-27 | GT-490  | Paragraph 2.0 release; disable Poisson depth test by default         |
 | 2018-06-27 | GT-495  | Improved output of phasing information and paths                     |
 | 2018-06-26 | GT-402  | support genotyping on male chrX                                      |
@@ -59,8 +59,6 @@
 
 # Version 1.2
 
-| Date Y-m-d | Ticket  | Description                                                          |
-|------------|---------|----------------------------------------------------------------------|
 | 2018-04-05 | GT-429  | option to turn off exact and graph aligners in grmpy                 |
 | 2018-04-05 | GT-428  | upgrade htslib to version 1.8                                        |
 | 2018-04-04 | GT-427  | GT-427 multigrmpy to generate graph ID if vc2toparagraph does not provide it|
@@ -81,8 +79,6 @@
 
 # Version 1.1
 
-| Date Y-m-d | Ticket  | Description                                                          |
-|------------|---------|----------------------------------------------------------------------|
 | 2018-02-21 | GT-374  | support for read-level validation                                    |
 | 2018-02-19 | GT-379  | configure tool for installation                                      |
 | 2018-02-15 | GT-373  | Speedup bam processing by keeping the file open between the graphs   |

diff --git a/data/download-instructions.txt b/data/download-instructions.txt
diff --git a/doc/Installation.md b/doc/Installation.md
@@ -0,0 +1,127 @@
+# Installation of Paragraph
+
+* [System Requirements](#SystemRequirements)
+	* [Hardware](#Hardware)
+	* [Operating systems](#Operatingsystems)
+	* [Third-party libraries](#ThirdPartyLibraries)
+* [Static Build](#StaticBuild)
+* [Installation](#Installation)
+	* [Native build](#NativeBuild)
+	* [From Docker image](#FromDockerImage)
+
+## <a name='SystemRequirements'></a>System Requirements
+
+### <a name='Hardware'></a>Hardware
+
+A standard workstation with at least 8GB of RAM should be sufficient for compilation and testing of the program.
+
+### <a name='Operatingsystems'></a>Operating systems
+
+Paragrpah is supported on the following systems:
+
+- Ubuntu 16.04 and CentOS 5-7,
+- macOS 10.11+,
+
+Python 3.6+ is required.
+
+We recommend using g++ (6.0+), or a recent version of Clang.
+
+We use the C++11 standard, any Posix compliant compiler supporting this standard
+should be usable.
+
+### <a name='ThirdPartyLibraries'></a>Third-party libraries
+
+Please check [requirements](../requirements.txt) for required python modules.
+
+We have included copies of other dependent libraries in external/. They are:
+- Google Test and Google Mock (v1.8.0)
+- Htslib (v1.9)
+- Spdlog
+
+## <a name='Static Build'></a>Static Build
+
+We provide a static build that works for GCC 5.2+ under linux environment. No installation is required for the static build.
+
+Download the static build under "release" tag of the github repo.
+
+## <a name='Installation'></a>Installation
+
+### <a name='NativeBuild'></a>Native buid
+
+[Boost libraries](http://www.boost.org) version >= 1.5 is required.
+- We prefer to statically link Boost libraries to Paragraph executables:
+
+  ```bash
+  cd ~
+  wget http://downloads.sourceforge.net/project/boost/boost/1.65.0/boost_1_65_0.tar.bz2
+  tar xf boost_1_65_0.tar.bz2
+  cd boost_1_65_0
+  ./bootstrap.sh
+  ./b2 --prefix=$HOME/boost_1_65_0_install link=static install
+  ```
+
+- To point Cmake to your version of Boost use the `BOOST_ROOT` environment variable:
+
+  ```bash
+  export BOOST_ROOT=$HOME/boost_1_65_0_install
+  ```
+
+Once you have boost installed, checkout the repository like so:
+
+  ```bash
+  git clone https://github.com/Illumina/paragraph.git
+  cd paragraph-tools
+  ```
+
+  Then create a new directory for the program and compile it there:
+
+  ```bash
+  # Create a separate build folder.
+  cd ..
+  mkdir paragraph-tools-build
+  cd paragraph-tools-build
+
+  # Configure
+  # optional:
+  # export BOOST_ROOT=<path-to-boost-installation>
+  cmake ../paragraph-tools
+  # if this doesn't work, run this instead:
+  # cmake ../paragraph-tools -DCMAKE_CXX_COMPILER=`which g++` -DCMAKE_C_COMPILER=`which gcc` -DBOOST_ROOT=$BOOST_ROOT
+
+  # Make, use -j <n> to use n parallel jobs to build, e.g. make -j4
+  make
+  ```
+
+### <a name='FromDockerImage'></a>From Docker Image
+We also provide a [Dockerfile](Dockerfile). To build a Docker image, run the following command inside the source
+  checkout folder:
+
+  ```bash
+  docker build .
+  ```
+
+  Once the image is built you can find out its ID like this:
+
+  ```bash
+  docker images
+  ```
+  ```
+  REPOSITORY                             TAG                 IMAGE ID            CREATED             VIRTUAL SIZE
+  <none>                                 <none>              54c7d4015330        16 seconds ago      1.76 GB
+  ```
+
+  Check the below section for how to run Paragraph, and execute this before running:
+
+  ```bash
+  sudo docker run -v `pwd`:/data 54c7d4015330
+  ```
+
+  The current directory can be accessed as `/data` inside the Docker container.
+
+  The default entry point is `multigrmpy.py`.
+
+  To override the default entrypoint and get an interactive shell, run:
+
+  ```bash
+  sudo docker run --entrypoint /bin/bash -it 54c7d4015330
+  ```
diff --git a/src/python/bin/multigrmpy.py b/src/python/bin/multigrmpy.py
@@ -326,11 +326,11 @@ def run(args):
                 line = line.rstrip()
                 if line.startswith('#'):
                     line = line[1:]
-                f = line.split('\t')
+                fields = re.split('\t|,', line)
                 if id_index == -1:
-                    id_index = f.index("id")
+                    id_index = fields.index("id")
                     continue
-                sample_names.append(f[id_index])
+                sample_names.append(fields[id_index])
         if args.input.endswith("vcf") or args.input.endswith("vcf.gz"):
             grmpyOutput = vcfupdate.read_grmpy(result_json_path)
             result_vcf_path = os.path.join(args.output, "genotypes.vcf.gz")