[med-svn] [Git][med-team/freebayes][upstream] New upstream version 1.3.8
Michael R. Crusoe (@crusoe)
gitlab at salsa.debian.org
Sat Feb 15 11:03:43 GMT 2025
Michael R. Crusoe pushed to branch upstream at Debian Med / freebayes
Commits:
96243c4d by Michael R. Crusoe at 2024-06-07T11:16:40+02:00
New upstream version 1.3.8
- - - - -
16 changed files:
- + .github/ISSUE_TEMPLATE/bug_report.md
- + .github/workflows/ci_test.yml
- + .github/workflows/issue-tracker-bot.yaml
- + .github/workflows/main.yml
- + .github/workflows/support-tracker-bot.yaml
- .gitmodules
- + .travis.yml
- README.md
- RELEASE-NOTES.md
- guix.scm
- meson.build
- src/BedReader.cpp
- src/BedReader.h
- src/version_git.h
- test/t/01_call_variants.t
- test/t/01b_call_variants.t
Changes:
=====================================
.github/ISSUE_TEMPLATE/bug_report.md
=====================================
@@ -0,0 +1,44 @@
+---
+name: Bug report 🐞
+about: Create a report to help us improve
+title: ''
+labels: bug
+assignees: ''
+---
+**Only bug reports!**
+
+The C++ version of Freebayes is in *maintenance* mode. Use the github issue
+tracker to report bugs *only*. For comments, questions and features,
+please use the google group mailing list as stated on the
+[README](https://github.com/freebayes/freebayes/blob/master/README.md)!
+
+**Describe the bug**
+
+A clear and concise description of what the bug is.
+
+**To Reproduce**
+
+Include all steps to reproduce the behavior and paste any complete
+errors from the terminal.
+
+**Expected behavior**
+
+A clear and concise description of what you expected to happen.
+
+**Screenshots**
+
+If applicable, add screenshots to help explain your problem.
+
+**Additional context**
+
+Add any other context about the problem here.
+
+Include a set of BAM/BED files to reproduce the issue
+
++ bonus points if you try to minimize the test case yourself, as issues are often localized:
+ - try to use sambamba or samtools slice to first extract the reference where the error occurs
+ - if that succeeds (the error is still reproducible), continue to crop the file in binary-search fashion
+
+**Finally**
+
+Please check the README and docs carefully. Everyone working on freebayes is doing that for free. Please respect our time (too).
=====================================
.github/workflows/ci_test.yml
=====================================
@@ -0,0 +1,62 @@
+name: CI
+on: [push, pull_request]
+jobs:
+ arch:
+ name: freebayes-CI
+ runs-on: ubuntu-latest
+ strategy:
+ matrix:
+ os: [ubuntu-latest]
+ python-version: [3.8]
+ steps:
+ - name: Update ubuntu
+ run: sudo add-apt-repository ppa:c2d4u.team/c2d4u4.0+ && sudo apt-get update
+ - name: Install dependencies
+ run: sudo apt-get -y -f install samtools bc parallel libvcflib-tools libvcflib-dev fastahack smithwaterman libwfa2-dev
+ - uses: actions/checkout at v3
+ - uses: actions/setup-python at v4
+ with:
+ python-version: ${{ matrix.python-version }}
+ - name: Checkout submodules
+ run: git submodule update --init --recursive
+ - run: pip install meson ninja
+ - name: Configure
+ run: meson setup build/
+ - name: Compile
+ run: ninja -C build/
+ - name: Run tests
+ run: meson test --timeout-multiplier 4 --print-errorlogs -C build/
+
+
+ build-aarch64:
+ name: freebayes-CI aarch64
+ runs-on: ubuntu-latest
+
+ steps:
+ - name: Checkout
+ uses: actions/checkout at v3
+ with:
+ submodules: 'recursive'
+
+ - name: Build
+ uses: uraimo/run-on-arch-action at v2
+ with:
+ arch: aarch64
+ distro: ubuntu20.04
+ githubToken: ${{ github.token }}
+ dockerRunArgs: |
+ --volume "${PWD}:/freebayes"
+ install: |
+ apt-get update -q -y
+ apt-get install -q -y gcc g++ python3.8 python3-pip samtools bc parallel libvcflib-tools libvcflib-dev fastahack smithwaterman
+ pip install meson ninja
+ run: |
+ set -x
+ cd /freebayes
+ # CONFIGURE
+ meson build/
+ #COMPILE
+ ninja -C build/
+ # TEST
+ meson test --timeout-multiplier 4 --print-errorlogs -C build/
+
=====================================
.github/workflows/issue-tracker-bot.yaml
=====================================
@@ -0,0 +1,19 @@
+name: "Close stale issues"
+on:
+ schedule:
+ - cron: "0 1 * * *"
+
+jobs:
+ stale:
+ runs-on: ubuntu-latest
+ steps:
+ - uses: actions/stale at v3
+ with:
+ repo-token: ${{ secrets.GITHUB_TOKEN }}
+ stale-issue-message: 'This issue is marked stale because it has been open 120 days with no activity. Remove stale label or comment or this will be closed in 5 days'
+ close-issue-message: 'This issue was closed for lack of activity. Feel free to re-open if someone feels like working on it.'
+ days-before-stale: 120
+ days-before-close: 5
+ exempt-issue-labels: "bug,build,enhancement,help wanted,in progress"
+ debug-only: false
+ operations-per-run: 100
=====================================
.github/workflows/main.yml
=====================================
@@ -0,0 +1,36 @@
+# This is a basic workflow to help you get started with Actions
+
+name: CI
+
+# Controls when the action will run.
+on:
+ # Triggers the workflow on push or pull request events but only for the master branch
+ push:
+ branches: [ master ]
+ pull_request:
+ branches: [ master ]
+
+ # Allows you to run this workflow manually from the Actions tab
+ workflow_dispatch:
+
+# A workflow run is made up of one or more jobs that can run sequentially or in parallel
+jobs:
+ # This workflow contains a single job called "build"
+ build:
+ # The type of runner that the job will run on
+ runs-on: ubuntu-latest
+
+ # Steps represent a sequence of tasks that will be executed as part of the job
+ steps:
+ # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
+ - uses: actions/checkout at v2
+
+ # Runs a single command using the runners shell
+ - name: Run a one-line script
+ run: echo Hello, world!
+
+ # Runs a set of commands using the runners shell
+ - name: Run a multi-line script
+ run: |
+ echo Add other actions to build,
+ echo test, and deploy your project.
=====================================
.github/workflows/support-tracker-bot.yaml
=====================================
@@ -0,0 +1,20 @@
+name: "Close support issues"
+on:
+ schedule:
+ - cron: "0 1 * * *"
+
+jobs:
+ stale:
+ runs-on: ubuntu-latest
+ steps:
+ - uses: actions/stale at v3
+ with:
+ repo-token: ${{ secrets.GITHUB_TOKEN }}
+ stale-issue-message: 'This issue is marked stale because it has been open 30 days with no activity. Remove stale label or comment or this will be closed in 5 days'
+ close-issue-message: 'This issue was closed for lack of activity. Feel free to re-open if someone feels like working on it.'
+ days-before-stale: 30
+ days-before-close: 5
+ only-labels: "please file bugs only - use google groups instead"
+ exempt-issue-labels: "build,enhancement,help wanted,in progress"
+ debug-only: false
+ operations-per-run: 100
=====================================
.gitmodules
=====================================
@@ -4,6 +4,12 @@
[submodule "bash-tap"]
path = test/bash-tap
url = https://github.com/illusori/bash-tap.git
-[submodule "contrib/vcflib"]
- path = contrib/vcflib
- url = https://github.com/vcflib/vcflib.git
+[submodule "contrib/smithwaterman"]
+ path = contrib/smithwaterman
+ url = https://github.com/ekg/smithwaterman.git
+[submodule "contrib/fastahack"]
+ path = contrib/fastahack
+ url = https://github.com/ekg/fastahack.git
+[submodule "contrib/multichoose"]
+ path = contrib/multichoose
+ url = git at github.com:vcflib/multichoose.git
=====================================
.travis.yml
=====================================
@@ -0,0 +1,26 @@
+language: cpp
+os: linux
+dist: focal
+addons:
+ apt:
+ packages:
+ - bc
+ - samtools
+ - parallel
+ - meson
+ - ninja-build
+ - libvcflib-tools
+ - vcftools
+jobs:
+ include:
+ - arch: amd64
+ compiler: gcc
+ - arch: arm64
+ compiler: gcc
+ - arch: arm64
+ compiler: clang
+script:
+ - if [ "$TRAVIS_CPU_ARCH" = arm64 ]; then meson_opts="-Doptimization=0"; fi
+ - meson build/ $meson_opts
+ - ninja -C build/
+ - meson test --timeout-multiplier 8 --print-errorlogs -C build/
=====================================
README.md
=====================================
@@ -2,7 +2,8 @@
## user manual and guide
-[](https://github.com/freebayes/freebayes/actions) [](https://travis-ci.com/freebayes/freebayes) [](https://anaconda.org/bioconda/freebayes) [](https://anaconda.org/bioconda/freebayes) [](https://github.com/brewsci/homebrew-bio) [](https://www.gnu.org/software/guix/packages/F/) [](https://packages.debian.org/testing/freebayes) [](https://matrix.to/#/#vcflib:matrix.org)
+[](https://github.com/freebayes/freebayes/actions) [](https://travis-ci.com/freebayes/freebayes)
+[](https://anaconda.org/bioconda/freebayes) [](https://github.com/brewsci/homebrew-bio) [](https://packages.guix.gnu.org/packages/freebayes/) [](https://packages.debian.org/testing/freebayes) [](https://matrix.to/#/#vcflib:matrix.org)
--------
## Overview
@@ -482,6 +483,10 @@ Freebayes can target AMD64 and ARM64 (with Neon extensions).
Recently we added the meson build system which can be run with
+ meson build/ --buildtype release
+
+For development/debugging use
+
meson build/ --buildtype debug
or to setup with clang instead
=====================================
RELEASE-NOTES.md
=====================================
@@ -4,6 +4,18 @@ see
and
[commits](https://github.com/freebayes/freebayes/commits/master).
+## ChangeLog v1.3.8 (20240423)
+
+This is a maintenance release of Freebayes:
+
++ fixes for Debian https://github.com/freebayes/freebayes/issues/786, thanks Hrithik Mangla and Nilesh Patra for reporting
++ unbundled vcflib and vendored back in the much smaller fastahack and smithwaterman modules until Debian provides the include files
+
+Note:
+
++ quality scores in test/regression/NA12878.chr22.tiny.vcf changed with recent builds. Probably caused by gcc-13 and we should look into that
++ github-CI won't build until wfa2lib is included from Debian (WIP)
+
## ChangeLog v1.3.7 (20230212)
+ sanitizing git submodules
=====================================
guix.scm
=====================================
@@ -10,7 +10,7 @@
;;
;; mkdir -p /usr/bin ; ln -s $GUIX_ENVIRONMENT/bin/env /usr/bin/env
;;
-;; meson build/ --buildtype debug
+;; meson setup build/ --buildtype debug
;; cd build
;; ninja
;; ninja test
@@ -22,12 +22,14 @@
(guix git-download)
(guix build-system meson)
(gnu packages algebra)
+ (gnu packages assembly)
(gnu packages base)
(gnu packages compression)
(gnu packages bioinformatics)
(gnu packages build-tools)
(gnu packages curl)
(gnu packages gcc)
+ (gnu packages gdb)
(gnu packages llvm)
(gnu packages ninja)
(gnu packages parallel)
@@ -51,28 +53,35 @@
(source (local-file %source-dir #:recursive? #t))
(build-system meson-build-system)
(propagated-inputs
- `(("perl" ,perl) ; for testing
- ("python" ,python) ; for testing
+ `(
+ ("bzip2-static" ,bzip2 "static") ; libz2 part of htslib for static builds
+ ;; ("fastahack" ,fastahack) ; bundle for Debian
("grep" ,grep) ; for testing
+ ("htslib" ,htslib) ; does work, but lacks codecs
+ ("intervaltree" ,intervaltree)
+ ("perl" ,perl) ; for testing
+ ("python" ,python) ; for testing
("samtools" ,samtools) ; for testing
+ ("simde" ,simde)
+ ;; ("smithwaterman" ,smithwaterman) ; bundle for Debian
+ ("tabixpp" ,tabixpp) ; for htslib
("vcflib" ,vcflib) ; for testing freebayes-parallel
+ ("wfa2-lib" ,wfa2-lib) ; vcflib dependency
("which" ,which) ; for version
- ; ("htslib" ,htslib) ; does work, but lacks codecs
- ; ("tabixpp" ,tabixpp) ; for htslib
- ("bzip2-static" ,bzip2 "static") ; libz2 part of htslib for static builds
("xz-static" ,xz "static") ; for static builds
("zlib-static" ,zlib "static")))
(native-inputs
`(
("meson" ,meson)
("ninja" ,ninja)
+ ("gdb" ,gdb)
("pkg-config" ,pkg-config)
))
(inputs
`(
;; ("clang" ,clang) ; add this to test clang builds
;; ("lld" ,lld) ; add this to test clang builds
- ("gcc" ,gcc-11)
+ ;; ("gcc" ,gcc-13)
("bc" ,bc) ; for tests
("coreutils" ,coreutils) ; for echo and env in tests
("curl" ,curl)
=====================================
meson.build
=====================================
@@ -15,25 +15,29 @@
# meson build -Dstatic=true -Dprefer_system_deps=false --buildtype release
project('freebayes', ['cpp', 'c'],
- version : '1.3.6',
+ version : '1.3.8',
default_options : ['warning_level=1', 'cpp_std=c++17', 'optimization=3'])
static_build = get_option('static')
+# used by Debian: add_global_arguments('-D_GLIBCXX_ASSERTIONS=1', language : 'cpp')
+
cc = meson.get_compiler('cpp')
-zlib_dep = dependency('zlib', static: static_build)
+# fastahack_dep = cc.find_library('libfastahack')
lzma_dep = dependency('liblzma', static: static_build)
-thread_dep = dependency('threads', static: static_build)
+seqlib_dep = dependency('libseqlib', static: static_build, required: false)
+# smithwaterman_dep = cc.find_library('libsmithwaterman')
tabixpp_dep = cc.find_library('tabixpp', required: false, static: static_build)
+thread_dep = dependency('threads', static: static_build)
+vcflib_dep = cc.find_library('libvcflib')
+wfa2lib_dep = cc.find_library('libwfa2')
+zlib_dep = dependency('zlib', static: static_build)
# to compile htslib use
# meson build -Dprefer_system_deps=false
# otherwise it tries to pick up the local system libs
if get_option('prefer_system_deps')
htslib_dep = dependency('htslib', static: static_build, required: false)
- tabixpp_dep = cc.find_library('tabixpp', static: static_build, required: false)
- vcflib_dep = dependency('libvcflib', static: static_build, required: false)
- seqlib_dep = dependency('libseqlib', static: static_build, required: false)
else
# uses the local git submodules
htslib_dep = dependency('', required : false)
@@ -45,7 +49,27 @@ endif
# for setting a warning_level on the external code in custom_* targets below
warn_quiet = ['warning_level=0']
-# optionally build from source
+# We pull in the include files because they are currently not packaged in Debian, note that we expect
+# the share libs nevertheless
+fastahack_inc = include_directories('contrib/fastahack')
+fastahack_src = files(
+ 'contrib/fastahack/Fasta.cpp',
+ )
+
+multichoose_inc = include_directories('contrib/multichoose')
+multichoose_src = files(
+ )
+
+smithwaterman_inc = include_directories('contrib/smithwaterman')
+smithwaterman_src = files(
+ 'contrib/smithwaterman/SmithWatermanGotoh.cpp',
+ 'contrib/smithwaterman/disorder.cpp',
+ 'contrib/smithwaterman/Repeats.cpp',
+ 'contrib/smithwaterman/LeftAlign.cpp',
+ 'contrib/smithwaterman/IndelAllele.cpp',
+ )
+
+# optionally build from source. As we unbundled just check out the vcflib repo in contrib.
# note that the build version adds support for lzma and bzip2 in CRAM
if not htslib_dep.found()
htslib_inc = include_directories(
@@ -116,6 +140,9 @@ else
tabixpp_inc = []
endif
+vcflib_inc = include_directories()
+
+# optionally build from source. As we unbundled just check out the vcflib repo in contrib.
if not vcflib_dep.found()
vcflib_inc = include_directories(
'contrib/vcflib/src',
@@ -129,12 +156,6 @@ if not vcflib_dep.found()
'contrib/vcflib/src/allele.cpp',
'contrib/vcflib/src/cigar.cpp',
'contrib/vcflib/src/split.cpp',
- 'contrib/vcflib/contrib/fastahack/Fasta.cpp',
- 'contrib/vcflib/contrib/smithwaterman/SmithWatermanGotoh.cpp',
- 'contrib/vcflib/contrib/smithwaterman/disorder.cpp',
- 'contrib/vcflib/contrib/smithwaterman/Repeats.cpp',
- 'contrib/vcflib/contrib/smithwaterman/LeftAlign.cpp',
- 'contrib/vcflib/contrib/smithwaterman/IndelAllele.cpp',
)
vcflib_lib = static_library('custom_vcflib',
vcflib_src,
@@ -217,10 +238,10 @@ extra_cpp_args = cc.get_supported_arguments(
freebayes_lib = static_library(
'freebayes_common',
freebayes_common_src,
- include_directories : incdir,
+ include_directories : [multichoose_inc, fastahack_inc, smithwaterman_inc, incdir],
cpp_args : extra_cpp_args,
dependencies : [zlib_dep, lzma_dep, thread_dep, htslib_dep, tabixpp_dep,
- vcflib_dep, seqlib_dep],
+ vcflib_dep, wfa2lib_dep, seqlib_dep],
install : false,
)
@@ -231,23 +252,38 @@ else
endif
executable('freebayes',
- freebayes_src,
- include_directories : incdir,
+ [freebayes_src,multichoose_src,fastahack_src,smithwaterman_src],
+ include_directories : [multichoose_inc, fastahack_inc, smithwaterman_inc, incdir],
cpp_args : extra_cpp_args,
link_args: link_arguments,
- dependencies: [zlib_dep, lzma_dep, thread_dep,
- htslib_dep, tabixpp_dep, vcflib_dep, seqlib_dep],
+ dependencies: [zlib_dep,
+ lzma_dep,
+ thread_dep,
+ htslib_dep,
+ tabixpp_dep,
+ vcflib_dep,
+ seqlib_dep,
+ # fastahack_dep,
+ # smithwaterman_dep,
+ wfa2lib_dep],
link_with : freebayes_lib,
install: true
)
executable('bamleftalign',
- bamleftalign_src,
- include_directories : incdir,
+ [bamleftalign_src,fastahack_src,smithwaterman_src],
+ include_directories : [multichoose_inc, fastahack_inc, smithwaterman_inc, incdir],
cpp_args : extra_cpp_args,
link_args: link_arguments,
- dependencies: [zlib_dep, lzma_dep, thread_dep,
- htslib_dep, vcflib_dep, seqlib_dep],
+ dependencies: [zlib_dep,
+ lzma_dep,
+ thread_dep,
+ htslib_dep,
+ vcflib_dep,
+ seqlib_dep,
+ # fastahack_dep,
+ # smithwaterman_dep,
+ wfa2lib_dep],
link_with : freebayes_lib,
install: true
)
=====================================
src/BedReader.cpp
=====================================
@@ -11,7 +11,7 @@
#include "Utility.h"
#include "BedReader.h"
#include "Logging.h"
-#include "../intervaltree/IntervalTree.h"
+#include <IntervalTree.h>
using namespace std;
=====================================
src/BedReader.h
=====================================
@@ -9,7 +9,7 @@
#include <map>
#include <iterator>
#include <algorithm>
-#include "../intervaltree/IntervalTree.h"
+#include <IntervalTree.h>
#include "split.h"
using namespace std;
=====================================
src/version_git.h
=====================================
@@ -1,4 +1,4 @@
#ifndef VERSION_GIT_H
#define VERSION_GIT_H
-#define VERSION_GIT "v1.3.7"
+#define VERSION_GIT "v1.3.8"
#endif /* VERSION_GIT_H */
=====================================
test/t/01_call_variants.t
=====================================
@@ -78,29 +78,30 @@ is $(samtools view tiny/NA12878.chr22.tiny.bam | wc -l) $(freebayes -f tiny/q.fa
is $(freebayes -f tiny/q.fa tiny/NA12878.chr22.tiny.bam -d 2>&1 | grep ^alignment: | wc -l) $(freebayes -f tiny/q.fa tiny/NA12878.chr22.tiny.cram -d 2>&1 | grep ^alignment: | wc -l) "freebayes processes all alignments in CRAM input"
# Add a regression test
-$(freebayes -f tiny/q.fa tiny/NA12878.chr22.tiny.bam 2>&1 |egrep -vi "source|filedate|RPPR=7.64277|11126|10515" > regression/NA12878.chr22.tiny.vcf)
+$(freebayes -f tiny/q.fa tiny/NA12878.chr22.tiny.bam 2>&1 |grep -vEi "source|filedate|RPPR=7.64277|11126|10515" > regression/NA12878.chr22.tiny.vcf)
# ensure targeting works even when there are no reads
is $(freebayes -f tiny/q.fa -l@ tiny/q.vcf.gz tiny/NA12878.chr22.tiny.bam | grep -v "^#" | wc -l) 16 "freebayes correctly handles variant input"
# ensure that positions at which no variants exist get put in the out vcf
-is $(freebayes -f tiny/q.fa -@ tiny/q_spiked.vcf.gz tiny/NA12878.chr22.tiny.bam | grep -v "^#" | cut -f1,2 | grep -P "(\t500$|\t11000$|\t1000$)" | wc -l) 3 "freebayes puts required variants in output"
+is $(freebayes -f tiny/q.fa -@ tiny/q_spiked.vcf.gz tiny/NA12878.chr22.tiny.bam | grep -v "^#" | cut -f1,2 | grep $'\t500$\|\t11000$\|\t1000$' | wc -l) 3 "freebayes puts required variants in output"
+
+is $(freebayes -f tiny/q.fa -@ tiny/q_spiked.vcf.gz tiny/NA12878.chr22.tiny.bam -l | grep -v "^#" | cut -f1,2 | grep $'\t500$\|\t11000$\|\t1000$' | wc -l) 3 "freebayes limits calls to input variants correctly"
-is $(freebayes -f tiny/q.fa -@ tiny/q_spiked.vcf.gz tiny/NA12878.chr22.tiny.bam -l | grep -v "^#" | cut -f1,2 | grep -P "(\t500$|\t11000$|\t1000$)" | wc -l) 3 "freebayes limits calls to input variants correctly"
is $(freebayes -f tiny/q.fa -@ tiny/q.vcf.gz -l tiny/1read.bam | grep -v "^#" | wc -l) 16 "freebayes reports all input variants even when there is no input data"
# check variant input with region specified
-is $(freebayes -f tiny/q.fa -@ tiny/q_spiked.vcf.gz -r q:1-10000 tiny/NA12878.chr22.tiny.bam | grep -v "^#" | cut -f1,2 | grep -P "(\t500$|\t11000$|\t1000$)" | wc -l) 2 "freebayes handles region and variant input"
+is $(freebayes -f tiny/q.fa -@ tiny/q_spiked.vcf.gz -r q:1-10000 tiny/NA12878.chr22.tiny.bam | grep -v "^#" | cut -f1,2 | grep $'\t500$\|\t11000$\|\t1000$' | wc -l) 2 "freebayes handles region and variant input"
-is $(freebayes -f tiny/q.fa -@ tiny/q_spiked.vcf.gz -r q:1-10000 tiny/NA12878.chr22.tiny.bam -l | grep -v "^#" | cut -f1,2 | grep -P "(\t500$|\t1000$)" | wc -l) 2 "freebayes limits to variant input correctly when region is given"
+is $(freebayes -f tiny/q.fa -@ tiny/q_spiked.vcf.gz -r q:1-10000 tiny/NA12878.chr22.tiny.bam -l | grep -v "^#" | cut -f1,2 | grep $'\t500$\|\t1000$' | wc -l) 2 "freebayes limits to variant input correctly when region is given"
# check variant input when reading from stdin
-is $(freebayes -f tiny/q.fa -@ tiny/q_spiked.vcf.gz --stdin < tiny/NA12878.chr22.tiny.bam | grep -v "^#" | cut -f1,2 | grep -P "(\t500$|\t11000$|\t1000$)" | wc -l) 3 "freebayes handles variant input and reading from stdin"
+is $(freebayes -f tiny/q.fa -@ tiny/q_spiked.vcf.gz --stdin < tiny/NA12878.chr22.tiny.bam | grep -v "^#" | cut -f1,2 | grep $'\t500$\|\t11000$\|\t1000$' | wc -l) 3 "freebayes handles variant input and reading from stdin"
-is $(freebayes -f tiny/q.fa -@ tiny/q_spiked.vcf.gz -l --stdin < tiny/NA12878.chr22.tiny.bam | grep -v "^#" | cut -f1,2 | grep -P "(\t500$|\t11000$|\t1000$)" | wc -l) 3 "freebayes limits to variant input when reading from stdin"
+is $(freebayes -f tiny/q.fa -@ tiny/q_spiked.vcf.gz -l --stdin < tiny/NA12878.chr22.tiny.bam | grep -v "^#" | cut -f1,2 | grep $'\t500$\|\t11000$\|\t1000$' | wc -l) 3 "freebayes limits to variant input when reading from stdin"
-is $(freebayes -f tiny/q.fa -@ tiny/q_spiked.vcf.gz -r q:1-10000 -l --stdin < tiny/NA12878.chr22.tiny.bam | grep -v "^#" | cut -f1,2 | grep -P "(\t500$|\t1000$)" | wc -l) 2 "freebayes handles region, stdin, and variant input"
+is $(freebayes -f tiny/q.fa -@ tiny/q_spiked.vcf.gz -r q:1-10000 -l --stdin < tiny/NA12878.chr22.tiny.bam | grep -v "^#" | cut -f1,2 | grep $'\t500$\|\t1000$' | wc -l) 2 "freebayes handles region, stdin, and variant input"
gzip -c tiny/q.fa >tiny/q.fa.gz
cp tiny/q.fa.fai tiny/q.fa.gz.fai
=====================================
test/t/01b_call_variants.t
=====================================
@@ -18,7 +18,7 @@ is $(freebayes -f tiny/q.fa tiny/NA12878.chr22.tiny.bam | grep -v "^#" | wc -l)
is $(freebayes -f 'tiny/q with spaces.fa' tiny/NA12878.chr22.tiny.bam | grep -v "^#" | wc -l) $(freebayes-parallel 'tiny/q with spaces.regions' 2 -f 'tiny/q\ with\ spaces.fa' tiny/NA12878.chr22.tiny.bam | grep -v "^#" | wc -l) "freebayes handles spaces in file names"
# check input can hand colons in name like the HLA contigs in GRCh38
-is $(freebayes -f tiny/hla.fa -@ tiny/hla.vcf.gz -r HLA-DRB1*16:02:01:1-10000 tiny/NA12878.chr22.tiny.hla.bam | grep -v "^#" | cut -f1,2 | grep -P "(\t500$|\t11000$|\t1000$)" | wc -l) 2 "freebayes handles region and variant input even with : in contig names"
+is $(freebayes -f tiny/hla.fa -@ tiny/hla.vcf.gz -r HLA-DRB1*16:02:01:1-10000 tiny/NA12878.chr22.tiny.hla.bam | grep -v "^#" | cut -f1,2 | grep $'\t500$\|\t11000$\|\t1000$' | wc -l) 2 "freebayes handles region and variant input even with : in contig names"
is $(freebayes -f splice/1:883884-887618.fa splice/1:883884-887618.bam -F 0.05 -C 1 | grep ^1 | wc -l) 3 "freebayes can handle spliced reads"
View it on GitLab: https://salsa.debian.org/med-team/freebayes/-/commit/96243c4d051a11617ba65f357f54e9379ff5b37a
--
View it on GitLab: https://salsa.debian.org/med-team/freebayes/-/commit/96243c4d051a11617ba65f357f54e9379ff5b37a
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