[med-svn] [freebayes] 06/06: Commit as freebayes was uploaded
Andreas Tille
tille at debian.org
Sat Sep 2 05:46:08 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to tag debian/1.0.2-1
in repository freebayes.
commit a06c13fadadb4c48eec0795deb4d33c776a9d151
Author: Andreas Tille <tille at debian.org>
Date: Sat Sep 2 07:44:44 2017 +0200
Commit as freebayes was uploaded
---
debian/README.source | 11 ---
debian/changelog | 6 --
debian/control | 9 +-
.../patches/use_debian_packaged_libjsoncpp.patch | 17 ----
debian/patches/use_debian_packaged_seqlib.patch | 87 ----------------
debian/patches/vcffirstheader.patch | 29 ------
debian/rules | 6 +-
debian/test-simple-bash/lib/test-simple.bash | 110 ---------------------
debian/test-simple-bash/test/basics.t | 26 -----
debian/test-simple-bash/test/doc.t | 15 ---
debian/test-simple-bash/test/no-label.t | 25 -----
11 files changed, 3 insertions(+), 338 deletions(-)
diff --git a/debian/README.source b/debian/README.source
deleted file mode 100644
index 26e4dc4..0000000
--- a/debian/README.source
+++ /dev/null
@@ -1,11 +0,0 @@
-To run the test suite some bash testing framework was used
-bu upstream as Git submodules. For the Git packaging these
-were downloaded separately
-
-Files: debian/bash-tap/*
- Obtained from
- https://github.com/illusori/bash-tap
-
-Files: debian/test-simple-bash/*
- Obtained from
- https://github.com/ingydotnet/test-simple-bash/tree/master/lib
diff --git a/debian/changelog b/debian/changelog
index 4fec7a2..eaeaad5 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,9 +1,3 @@
-freebayes (1.1.0-1) UNRELEASED; urgency=medium
-
- * New upstream version
-
- -- Andreas Tille <tille at debian.org> Sun, 18 Jun 2017 14:47:55 +0200
-
freebayes (1.0.2-1) unstable; urgency=low
* Initial packaging (Closes: #851306)
diff --git a/debian/control b/debian/control
index 99d8397..301577b 100644
--- a/debian/control
+++ b/debian/control
@@ -7,16 +7,12 @@ Priority: optional
Build-Depends: debhelper (>= 9),
cmake,
pkg-config,
- python,
zlib1g-dev,
libbamtools-dev,
- libvcflib-dev (>= 1.0.0~rc1+dfsg1-4),
+ libvcflib-dev,
libtabixpp-dev,
- libseqlib-dev,
bc,
- samtools,
- parallel,
- libvcflib-tools
+ samtools
Standards-Version: 3.9.8
Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/freebayes.git
Vcs-Git: https://anonscm.debian.org/git/debian-med/freebayes.git
@@ -26,7 +22,6 @@ Package: freebayes
Architecture: any
Depends: ${shlibs:Depends},
${misc:Depends}
-Recommends: parallel
Description: Bayesian haplotype-based polymorphism discovery and genotyping
FreeBayes is a Bayesian genetic variant detector designed to find
small polymorphisms, specifically SNPs (single-nucleotide
diff --git a/debian/patches/use_debian_packaged_libjsoncpp.patch b/debian/patches/use_debian_packaged_libjsoncpp.patch
deleted file mode 100644
index 5ded25a..0000000
--- a/debian/patches/use_debian_packaged_libjsoncpp.patch
+++ /dev/null
@@ -1,17 +0,0 @@
-Author: Andreas Tille <tille at debian.org>
-Last-Update: Wed, 28 May 2014 21:23:38 +0200
-Description: Use Debian packaged libjsoncpp
-
---- a/src/Makefile
-+++ b/src/Makefile
-@@ -12,8 +12,8 @@ C=gcc
- CFLAGS=-O3 -D_FILE_OFFSET_BITS=64 -g
- #CFLAGS=-O3 -static -D VERBOSE_DEBUG # enables verbose debugging via --debug2
-
--LIBS = -lbamtools -ltabixpp -lz -lm -lpthread `pkg-config --libs libvcflib` `pkg-config --libs htslib` `pkg-config --libs libseqlib`
--INCLUDE = -I../ttmath -I/usr/include/bamtools `pkg-config --cflags libvcflib` `pkg-config --cflags libseqlib` `pkg-config --cflags htslib`
-+LIBS = -lbamtools -ltabixpp -lz -lm -lpthread `pkg-config --libs libvcflib` `pkg-config --libs htslib` `pkg-config --libs libseqlib` `pkg-config --libs jsoncpp`
-+INCLUDE = -I../ttmath -I/usr/include/bamtools `pkg-config --cflags libvcflib` `pkg-config --cflags libseqlib` `pkg-config --cflags htslib` `pkg-config --cflags jsoncpp`
-
- all: autoversion ../bin/freebayes ../bin/bamleftalign
-
diff --git a/debian/patches/use_debian_packaged_seqlib.patch b/debian/patches/use_debian_packaged_seqlib.patch
deleted file mode 100644
index 9e7a35b..0000000
--- a/debian/patches/use_debian_packaged_seqlib.patch
+++ /dev/null
@@ -1,87 +0,0 @@
-Author: Andreas Tille <tille at debian.org>
-Last-Update: Wed, 28 May 2014 21:23:38 +0200
-Description: Use Debian packaged htslib and seqlib
- seqlib carries another copy of htslib - we replace both
-
---- a/src/Makefile
-+++ b/src/Makefile
-@@ -12,10 +12,8 @@ C=gcc
- CFLAGS=-O3 -D_FILE_OFFSET_BITS=64 -g
- #CFLAGS=-O3 -static -D VERBOSE_DEBUG # enables verbose debugging via --debug2
-
--SEQLIB_ROOT=../SeqLib
--
--LIBS = -lbamtools -ltabixpp -lz -lm -lpthread `pkg-config --libs libvcflib`
--INCLUDE = -I../ttmath -I/usr/include/bamtools `pkg-config --cflags libvcflib` -I$(SEQLIB_ROOT) -I$(SEQLIB_ROOT)/htslib
-+LIBS = -lbamtools -ltabixpp -lz -lm -lpthread `pkg-config --libs libvcflib` `pkg-config --libs htslib` `pkg-config --libs libseqlib`
-+INCLUDE = -I../ttmath -I/usr/include/bamtools `pkg-config --cflags libvcflib` `pkg-config --cflags libseqlib` `pkg-config --cflags htslib`
-
- all: autoversion ../bin/freebayes ../bin/bamleftalign
-
-@@ -33,12 +31,6 @@ gprof:
-
- .PHONY: all static debug profiling gprof
-
--$(HTSLIB_ROOT)/libhts.a:
-- cd $(HTSLIB_ROOT) && make
--
--$(SEQLIB_ROOT)/src/libseqlib.a:
-- cd $(SEQLIB_ROOT) && ./configure && make
--
- OBJECTS=BedReader.o \
- CNV.o \
- fastlz.o \
-@@ -62,11 +54,7 @@ OBJECTS=BedReader.o \
- Bias.o \
- Contamination.o \
- NonCall.o \
-- SegfaultHandler.o \
-- $(SEQLIB_ROOT)/src/libseqlib.a \
-- $(SEQLIB_ROOT)/bwa/libbwa.a \
-- $(SEQLIB_ROOT)/fermi-lite/libfml.a \
-- $(SEQLIB_ROOT)/htslib/libhts.a
-+ SegfaultHandler.o
-
- HEADERS=multichoose.h version_git.h
-
-@@ -81,10 +69,10 @@ alleles ../bin/alleles: alleles.o $(OBJE
- dummy ../bin/dummy: dummy.o $(OBJECTS) $(HEADERS)
- $(CXX) $(CFLAGS) $(INCLUDE) dummy.o $(OBJECTS) -o ../bin/dummy $(LIBS)
-
--bamleftalign ../bin/bamleftalign: $(SEQLIB_ROOT)/src/libseqlib.a $(SEQLIB_ROOT)/htslib/libhts.a bamleftalign.o Fasta.o LeftAlign.o IndelAllele.o split.o
-- $(CXX) $(CFLAGS) $(INCLUDE) bamleftalign.o Fasta.o Utility.o LeftAlign.o IndelAllele.o split.o $(SEQLIB_ROOT)/src/libseqlib.a $(SEQLIB_ROOT)/htslib/libhts.a -o ../bin/bamleftalign $(LIBS)
-+bamleftalign ../bin/bamleftalign: bamleftalign.o Fasta.o LeftAlign.o IndelAllele.o split.o
-+ $(CXX) $(CFLAGS) $(INCLUDE) bamleftalign.o Fasta.o Utility.o LeftAlign.o IndelAllele.o split.o -o ../bin/bamleftalign $(LIBS)
-
--bamfiltertech ../bin/bamfiltertech: $(SEQLIB_ROOT)/src/libseqlib.a $(SEQLIB_ROOT)/htslib/libhts.a bamfiltertech.o $(OBJECTS) $(HEADERS)
-+bamfiltertech ../bin/bamfiltertech: bamfiltertech.o $(OBJECTS) $(HEADERS)
- $(CXX) $(CFLAGS) $(INCLUDE) bamfiltertech.o $(OBJECTS) -o ../bin/bamfiltertech $(LIBS)
-
-
-@@ -99,7 +87,7 @@ alleles.o: alleles.cpp AlleleParser.o Al
- dummy.o: dummy.cpp AlleleParser.o Allele.o
- $(CXX) $(CFLAGS) $(INCLUDE) -c dummy.cpp
-
--freebayes.o: freebayes.cpp TryCatch.h $(HTSLIB_ROOT)/libhts.a
-+freebayes.o: freebayes.cpp TryCatch.h
- $(CXX) $(CFLAGS) $(INCLUDE) -c freebayes.cpp
-
- fastlz.o: fastlz.c fastlz.h
-@@ -120,7 +108,7 @@ Genotype.o: Genotype.cpp Genotype.h Alle
- Ewens.o: Ewens.cpp Ewens.h
- $(CXX) $(CFLAGS) $(INCLUDE) -c Ewens.cpp
-
--AlleleParser.o: AlleleParser.cpp AlleleParser.h multichoose.h Parameters.h $(HTSLIB_ROOT)/libhts.a
-+AlleleParser.o: AlleleParser.cpp AlleleParser.h multichoose.h Parameters.h
- $(CXX) $(CFLAGS) $(INCLUDE) -c AlleleParser.cpp
-
- Utility.o: Utility.cpp Utility.h Sum.h Product.h
-@@ -168,7 +156,7 @@ bamleftalign.o: bamleftalign.cpp LeftAli
- bamfiltertech.o: bamfiltertech.cpp
- $(CXX) $(CFLAGS) $(INCLUDE) -c bamfiltertech.cpp
-
--LeftAlign.o: LeftAlign.h LeftAlign.cpp $(HTSLIB_ROOT)/libhts.a
-+LeftAlign.o: LeftAlign.h LeftAlign.cpp
- $(CXX) $(CFLAGS) $(INCLUDE) -c LeftAlign.cpp
-
- IndelAllele.o: IndelAllele.cpp IndelAllele.h
diff --git a/debian/patches/vcffirstheader.patch b/debian/patches/vcffirstheader.patch
deleted file mode 100644
index 070fcd0..0000000
--- a/debian/patches/vcffirstheader.patch
+++ /dev/null
@@ -1,29 +0,0 @@
-Author: Andreas Tille <tille at debian.org>
-Last-Update: Fri, 10 Feb 2017 09:09:35 +0100
-Description: This script was not part of the vcflib release
- tarball but is available in Git
- https://github.com/vcflib/vcflib/blob/master/scripts/vcffirstheader
- Since it is used in the test suite of freebayes 1.1 it is installed
- here as quilt patch. Once vcflib might be release including the
- scripts directory the patch can be dropped and replaced by an according
- symlink inside rules or by setting PATH accordingly
-
---- /dev/null
-+++ b/vcflib/scripts/vcffirstheader
-@@ -0,0 +1,16 @@
-+#!/usr/bin/env python
-+
-+import sys
-+
-+header=True
-+for line in sys.stdin:
-+ if line.startswith('##'):
-+ if header:
-+ print line.strip()
-+ continue
-+ elif line.startswith('#'):
-+ if header:
-+ print line.strip()
-+ header=False
-+ continue
-+ print line.strip()
diff --git a/debian/rules b/debian/rules
index 666b949..8045fdf 100755
--- a/debian/rules
+++ b/debian/rules
@@ -9,9 +9,5 @@ override_dh_auto_install:
override_dh_auto_test:
mkdir -p $(CURDIR)/test/bash-tap/
for bt in $(CURDIR)/debian/bash-tap/* ; do ln -s $${bt} $(CURDIR)/test/bash-tap/`basename $${bt}` ; done
- ln -s $(CURDIR)/debian/test-simple-bash/lib test/test-simple-bash
- chmod +x vcflib/scripts/vcffirstheader
- # export PATH=/usr/lib/vcflib/binaries/:$(PATH) dh_auto_test
- echo "Tests should be run" && PATH=/usr/lib/vcflib/binaries/:$(PATH) dh_auto_test && echo "Tests were running successfully"
+ export PATH=/usr/lib/vcflib/binaries/:$(PATH) dh_auto_test && echo "Tests were running successfully"
rm -rf $(CURDIR)/test/bash-tap
- rm test/test-simple-bash/lib
diff --git a/debian/test-simple-bash/lib/test-simple.bash b/debian/test-simple-bash/lib/test-simple.bash
deleted file mode 100644
index dab44e7..0000000
--- a/debian/test-simple-bash/lib/test-simple.bash
+++ /dev/null
@@ -1,110 +0,0 @@
-# test-simple.bash - Simple TAP test framework for Bash
-#
-# Copyright (c) 2013 Ingy döt Net
-
-TestSimple_VERSION='0.0.1'
-
-TestSimple.init() {
- TestSimple_plan=0
- TestSimple_run=0
- TestSimple_failed=0
- TestSimple_usage='Usage: source test-simple.bash tests <number>'
-
- if [ $# -gt 0 ]; then
- [[ $# -eq 2 ]] && [[ "$1" == 'tests' ]] ||
- TestSimple.die "$TestSimple_usage"
- [[ "$2" =~ ^-?[0-9]+$ ]] ||
- TestSimple.die 'Plan must be a number'
- [[ $2 -gt 0 ]] ||
- TestSimple.die 'Plan must greater then 0'
- TestSimple_plan=$2
- printf "1..%d\n" $TestSimple_plan
- fi
-
- trap TestSimple.END EXIT
-}
-
-ok() {
- local args=("$@")
- local last=$((${#args[@]} - 1))
- local label=''
- local ending_re='^]]?$'
- let TestSimple_run=TestSimple_run+1
- (
- set +e
- local rc=
- if [[ $last -gt 0 ]] && [[ ! "${args[$last]}" =~ $ending_re ]]; then
- label="${args[$last]}"
- unset args[$last]
- fi
- if [[ ${#args[@]} -eq 1 ]] && [[ "${args[0]}" =~ ^[0-9]+$ ]]; then
- rc=${args[0]}
- elif [ ${args[0]} == '[[' ]; then
- # XXX Currently need eval to support [[. Is there another way?
- # Is [[ overkill? So many questons!
- eval "${args[@]}" &> /dev/null
- rc=$?
- else
- "${args[@]}" &> /dev/null
- rc=$?
- fi
- if [ $rc -eq 0 ]; then
- if [ -n "$label" ]; then
- echo "ok $TestSimple_run - $label"
- else
- echo "ok $TestSimple_run"
- fi
- else
- let TestSimple_failed=TestSimple_failed+1
- if [ -n "$label" ]; then
- echo "not ok $TestSimple_run - $label"
- TestSimple.failure "$label"
- else
- echo "not ok $TestSimple_run"
- TestSimple.failure "$label"
- fi
- fi
- return $rc
- )
-}
-
-TestSimple_CALL_STACK_LEVEL=1
-TestSimple.failure() {
- local c=( $(caller $TestSimple_CALL_STACK_LEVEL) )
- local file=${c[2]}
- local line=${c[0]}
- local label="$1"
- label=${label:+"'$label'\n# at $file line $line."}
- label=${label:-"at $file line $line."}
- echo -e "# Failed test $label" >&2
-}
-
-TestSimple.END() {
- for v in plan run failed; do eval local $v=\$TestSimple_$v; done
- if [ $plan -eq 0 ]; then
- if [ $run -gt 0 ]; then
- echo "# Tests were run but no plan was declared." >&2
- fi
- else
- if [ $run -eq 0 ]; then
- echo "# No tests run!" >&2
- elif [ $run -ne $plan ]; then
- local msg="# Looks like you planned $plan tests but ran $run."
- [ $plan -eq 1 ] && msg=${msg/tests/test}
- echo "$msg" >&2
- fi
- fi
- local exit_code=0
- if [ $TestSimple_failed -gt 0 ]; then
- exit_code=$TestSimple_failed
- [ $exit_code -gt 254 ] && exit_code=254
- local msg="# Looks like you failed $failed tests of $run run."
- [ $TestSimple_failed -eq 1 ] && msg=${msg/tests/test}
- echo "$msg" >&2
- fi
- exit $exit_code
-}
-
-TestSimple.die() { echo "$@" >&2; trap EXIT; exit 255; }
-
-[[ "${BASH_SOURCE[0]}" != "${0}" ]] && TestSimple.init "$@"
diff --git a/debian/test-simple-bash/test/basics.t b/debian/test-simple-bash/test/basics.t
deleted file mode 100644
index 61949ea..0000000
--- a/debian/test-simple-bash/test/basics.t
+++ /dev/null
@@ -1,26 +0,0 @@
-#!/bin/bash
-
-PATH=lib:$PATH
-source test-simple.bash tests 14
-
-ok 0 '0 is true'
-ok $((6 * 7 -42)) 'Math result is 0'
-ok true 'true is ok'
-ok $(false || true; echo $?) 'Expression expansion'
-
-ls &> /dev/null
-ok $? '$? is success'
-ls --qqq &> /dev/null
-ok $((! $?)) 'Negate $? failure'
-
-fruit=apple
-
-ok [ $fruit = apple ] '[ … ] testing works'
-ok [ "0" == "0" -a 1 -eq 1 ] '[ … -a … ] (AND) testing works'
-ok [ ${fruit/a/A} = Apple ] 'Substitution expansion works'
-ok [ "${fruit}s" = 'app''les' ] 'Quote removal works'
-ok [[ $fruit = apple ]] '[[ … ]] works'
-ok [[ $fruit == apple ]] '== works'
-ok [[ $((6 * 7)) -eq 42 ]] '-eq works with math expression'
-ok $(ls | grep lib &> /dev/null; echo $?) \
- 'Testing a grep command works'
diff --git a/debian/test-simple-bash/test/doc.t b/debian/test-simple-bash/test/doc.t
deleted file mode 100644
index 7d77db7..0000000
--- a/debian/test-simple-bash/test/doc.t
+++ /dev/null
@@ -1,15 +0,0 @@
-#!/bin/bash
-
-question() { echo yes; }
-
-PATH=lib:$PATH
-source test-simple.bash tests 5
-
-ok 0 '0 is true (other numbers are false)'
-
-answer=$(question "...?")
-ok [ $answer == yes ] 'The answer is yes!'
-ok [[ $answer =~ ^y ]] 'The answer begins with y'
-
-ok true 'true is ok'
-ok '! false' '! false is true'
diff --git a/debian/test-simple-bash/test/no-label.t b/debian/test-simple-bash/test/no-label.t
deleted file mode 100644
index 9b58eb4..0000000
--- a/debian/test-simple-bash/test/no-label.t
+++ /dev/null
@@ -1,25 +0,0 @@
-#!/bin/bash
-
-PATH=lib:$PATH
-source test-simple.bash tests 14
-
-ok 0
-ok $((6 * 7 -42))
-ok true
-ok $(false || true; echo $?)
-
-ls &> /dev/null
-ok $?
-ls --qqq &> /dev/null
-ok $((! $?))
-
-fruit=apple
-
-ok [ $fruit = apple ]
-ok [ "0" == "0" -a 1 -eq 1 ]
-ok [ ${fruit/a/A} = Apple ]
-ok [ "${fruit}s" = 'app''les' ]
-ok [[ $fruit = apple ]]
-ok [[ $fruit == apple ]]
-ok [[ $((6 * 7)) -eq 42 ]]
-ok $(ls | grep lib &> /dev/null; echo $?)
--
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