Merge commit '2b8a884e60d499b9bf603d6d6cb54459e22f53ab' as 'svtools/b…

…in/svtyper'

svtools/bin/svtyper/.gitignore

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+# Compiled source #
+###################
+*.com
+*.class
+*.dll
+*.exe
+*.o
+*.so
+
+# Packages #
+############
+# it's better to unpack these files and commit the raw source
+# git has its own built in compression methods
+*.7z
+*.dmg
+*.gz
+*.iso
+*.jar
+*.rar
+*.tar
+*.zip
+
+# Logs and databases #
+######################
+*.log
+*.sql
+*.sqlite
+
+# OS generated files #
+######################
+*~
+\#*\#
+.DS_Store
+.DS_Store?
+._*
+.Spotlight-V100
+.Trashes
+Icon?
+ehthumbs.db
+Thumbs.db

svtools/bin/svtyper/.travis.yml

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+language: python
+python:
+    - "2.7"
+
+install:
+  - if [[ "$TRAVIS_PYTHON_VERSION" == "2.7" ]]; then
+      wget https://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh -O miniconda.sh;
+    else
+      wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh;
+    fi
+  - bash miniconda.sh -b -p $HOME/miniconda
+  - export PATH="$HOME/miniconda/bin:$PATH"
+  - hash -r
+  - conda config --set always_yes yes --set changeps1 no
+  - conda update -q conda
+  # Useful for debugging any issues with conda
+  - conda info -a
+
+  - deps='pysam'
+  - conda create -q -c bioconda -n test-environment python=$TRAVIS_PYTHON_VERSION $deps
+  - source activate test-environment
+
+script:
+    - cd test && ./test.sh
+    - python test_svtyper.py
+
+# # command to install dependencies
+# install:
+#   # We do this conditionally because it saves us some downloading if the
+#   # version is the same.
+#   - if [[ "$TRAVIS_PYTHON_VERSION" == "2.7" ]]; then
+#       wget https://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh -O miniconda.sh;
+#     else
+#       wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh;
+#     fi
+#   - bash miniconda.sh -b -p $HOME/miniconda
+#   - export PATH="$HOME/miniconda/bin:$PATH"
+#   - hash -r
+#   - conda config --set always_yes yes --set changeps1 no
+#   - conda update -q conda
+#   # Useful for debugging any issues with conda
+#   - conda info -a
+
+#   - deps='libgfortran pip nose coverage statsmodels numpy pandas scipy'
+#   - conda create -q -n test-environment python=$TRAVIS_PYTHON_VERSION $deps
+#   - source activate test-environment
+
+# # command to run tests
+# script: 
+# # FIXME If these were modules, this shouldn't be necessary
+#     nosetests --all-modules --traverse-namespace --with-coverage --cover-inclusive --with-id -v
+# after_success:
+#     - pip install coveralls
+#     - coveralls

svtools/bin/svtyper/LICENSE

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+The MIT License (MIT)
+
+Copyright (c) 2014 Colby Chiang
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
+

svtools/bin/svtyper/README.md

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+SVTyper
+=======
+[![GitHub license](https://img.shields.io/badge/license-MIT-blue.svg)](https://raw.githubusercontent.com/hall-lab/svtyper/master/LICENSE)
+[![Build Status](https://travis-ci.org/hall-lab/svtyper.svg?branch=master)](https://travis-ci.org/hall-lab/svtyper)
+
+Bayesian genotyper for structural variants
+
+## Example
+
+```
+svtyper \
+    -i sv.vcf \
+    -B sample.bam \
+    -l sample.bam.json \
+    > sv.gt.vcf
+```
+
+## Overview
+
+SVTyper performs breakpoint genotyping of structural variants (SVs) using whole genome sequencing data. Users must supply a VCF file of sites to genotype (which may be generated by [LUMPY](https://github.com/arq5x/lumpy-sv)) as well as a BAM/CRAM file of Illumina paired-end reads aligned with [BWA-MEM](https://github.com/lh3/bwa). SVTyper assesses discordant and concordant reads from paired-end and split-read alignments to infer genotypes at each site. Algorithm details and benchmarking are described in [Chiang et al., 2015](http://www.nature.com/nmeth/journal/vaop/ncurrent/full/nmeth.3505.html).
+
+![NA12878 heterozygous deletion](etc/het.png?raw=true "NA12878 heterozygous deletion")
+
+## Installation
+
+Requirements
+- Python 2.7 or newer
+- Pysam 0.8.1 or newer
+
+Clone the repository
+```
+git clone git@github.com:hall-lab/svtyper.git
+```
+
+Test the installation
+```
+cd svtyper/test
+
+../svtyper \
+    -i example.vcf \
+    -B NA12878.target_loci.sorted.bam \
+    -l NA12878.bam.json
+    > test.vcf
+```
+
+## Troubleshooting
+
+Many common issues are related to abnormal insert size distributions in the BAM file. SVTyper provides methods to assess and visualize the characteristics of sequencing libraries.
+
+Running SVTyper with the `-l` flag creates a JSON file with essential metrics on a BAM file. SVTyper will sample the first N reads for the file (1 million by default) to parse the libraries, read groups, and insert size histograms. This can be done in the absence of a VCF file.
+```
+svtyper \
+    -B my.bam \
+    -l my.bam.json
+```
+
+The [lib_stats.R](scripts/lib_stats.R) script produces insert size histograms from the JSON file
+```
+scripts/lib_stats.R my.bam.json my.bam.json.pdf
+```
+![Insert size histogram](etc/my.bam.json.png?raw=true "Insert size histogram")
+
+
+## Citation
+
+C Chiang, R M Layer, G G Faust, M R Lindberg, D B Rose, E P Garrison, G T Marth, A R Quinlan, and I M Hall. SpeedSeq: ultra-fast personal genome analysis and interpretation. Nat Meth 12, 966–968 (2015). doi:10.1038/nmeth.3505.
+
+http://www.nature.com/nmeth/journal/vaop/ncurrent/full/nmeth.3505.html

svtools/bin/svtyper/requirements.txt

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+pysam

svtools/bin/svtyper/scripts/lib_stats.R

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+#!/usr/bin/env Rscript
+
+# print usage
+usage <- function() {
+    cat(
+'usage: lib_stats.R <file>
+lib_stats.R
+author: Colby Chiang (colbychiang@wustl.edu)
+description: Plot a library information for BAM file
+positional arguments:
+  <input JSON>               JSON file of library info, created by SVTyper
+  <output PDF>               path to output pdf
+')
+}
+
+# Draw a histogram from a text file
+args <- commandArgs(trailingOnly=TRUE)
+file <- args[1]
+filename <- basename(args[1])
+output <- args[2]
+
+# Check input args
+if (is.na(file) || is.na(output)) {
+    usage()
+    quit(save='no', status=1)
+}
+
+# install R packages if needed
+options(repos=structure(c(CRAN="http://cran.wustl.edu")))
+list.of.packages <- c("jsonlite")
+new.packages <- list.of.packages[!(list.of.packages %in% installed.packages()[,"Package"])]
+if(length(new.packages)) install.packages(new.packages)
+library(jsonlite)
+
+bam <- fromJSON(file)
+
+pdf(output, h=6, w=8)
+for (sample in bam) {
+    ins <- as.data.frame(t(sample$libraryArray$histogram))
+
+    for (i in 1:ncol(ins)) {
+        plot(as.numeric(row.names(ins)), ins[,i], type='h', xlab='Insert size (bp)', ylab='Number of read-pairs', main=paste0('LB: ', sample$libraryArray$library_name[i], '\nprevalence: ', round(100*sample$libraryArray$prevalence[i],1), "%"), col='steelblue', bty='l')
+        abline(v=sample$libraryArray$mean[i], col='red', lty=1)
+        legend('topright', c(paste0('mean: ', round(sample$libraryArray$mean[i],1)), paste0('sd: ', round(sample$libraryArray$sd[i],1))), lty=c(1, 0), col=c('red'))
+    }
+}
+dev.off()
+