[med-svn] [Git][med-team/pbdagcon][upstream] New upstream version 0.3+git20161121.0000000+ds
Andreas Tille
gitlab at salsa.debian.org
Mon Feb 4 14:44:31 GMT 2019
Andreas Tille pushed to branch upstream at Debian Med / pbdagcon
Commits:
578071e0 by Andreas Tille at 2019-02-04T14:33:28Z
New upstream version 0.3+git20161121.0000000+ds
- - - - -
11 changed files:
- README.md
- − bamboo_build.sh
- − bamboo_test.sh
- configure.py
- src/cpp/DazAlnProvider.cpp
- src/cpp/DazAlnProvider.hpp
- src/cpp/makefile
- src/filterm4.py
- src/m4topre.py
- src/q-sense.py
- test/cpp/makefile
Changes:
=====================================
README.md
=====================================
@@ -130,7 +130,3 @@ ga('send', 'pageview');
src/filterm4.py 'code'
[pbdagcon_wf.sh]:
src/cpp/pbdagcon_wf.sh 'code'
-
-DISCLAIMER
-----------
-THIS WEBSITE AND CONTENT AND ALL SITE-RELATED SERVICES, INCLUDING ANY DATA, ARE PROVIDED "AS IS," WITH ALL FAULTS, WITH NO REPRESENTATIONS OR WARRANTIES OF ANY KIND, EITHER EXPRESS OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, ANY WARRANTIES OF MERCHANTABILITY, SATISFACTORY QUALITY, NON-INFRINGEMENT OR FITNESS FOR A PARTICULAR PURPOSE. YOU ASSUME TOTAL RESPONSIBILITY AND RISK FOR YOUR USE OF THIS SITE, ALL SITE-RELATED SERVICES, AND ANY THIRD PARTY WEBSITES OR APPLICATIONS. NO ORAL OR WRITTEN INFORMATION OR ADVICE SHALL CREATE A WARRANTY OF ANY KIND. ANY REFERENCES TO SPECIFIC PRODUCTS OR SERVICES ON THE WEBSITES DO NOT CONSTITUTE OR IMPLY A RECOMMENDATION OR ENDORSEMENT BY PACIFIC BIOSCIENCES.
=====================================
bamboo_build.sh deleted
=====================================
@@ -1,75 +0,0 @@
-#!/bin/bash
-set -e
-NEXUS_BASEURL=http://ossnexus.pacificbiosciences.com/repository
-#NEXUS_URL=$NEXUS_BASEURL/unsupported/gcc-4.9.2
-if [ ! -e .distfiles/gtest/release-1.7.0.tar.gz ]; then
- mkdir -p .distfiles/gtest
- curl -sL $NEXUS_BASEURL/unsupported/distfiles/googletest/release-1.7.0.tar.gz \
- -o .distfiles/gtest/release-1.7.0.tar.gz
-fi
-tar zxf .distfiles/gtest/release-1.7.0.tar.gz -C repos/
-ln -sfn googletest-release-1.7.0 repos/gtest
-
-rm -rf deployment
-mkdir -p deployment
-/bin/ls -t tarballs/pbbam-*.tgz | head -1 | xargs -r -n 1 cat | tar zxv --strip-components 3 -C deployment
-/bin/ls -t tarballs/blasr_libcpp-*.tgz | head -1 | xargs -r -n 1 cat | tar zxv --strip-components 3 -C deployment
-/bin/ls -t tarballs/blasr-*.tgz | head -1 | xargs -r -n 1 cat | tar zxv --strip-components 2 -C deployment
-DEPLOYMENT=$PWD/deployment
-
-export PATH=$PWD/deployment/bin:$PATH
-export LD_LIBRARY_PATH=$PWD/deployment/lib:$LD_LIBRARY_PATH
-
-type module >& /dev/null || . /mnt/software/Modules/current/init/bash
-module load git
-module load gcc
-module load ccache
-if [[ $USER == bamboo ]]; then
- export CCACHE_DIR=/mnt/secondary/Share/tmp/bamboo.mobs.ccachedir
-fi
-module load boost
-if [[ $BOOST_ROOT =~ /include ]]; then
- set -x
- BOOST_ROOT=$(dirname $BOOST_ROOT)
- set +x
-fi
-module load htslib
-module load hdf5-tools
-module load zlib
-
-DAZZDB=$PWD/repos/dazzdb
-DALIGNER=$PWD/repos/daligner
-cd repos/pbdagcon
-export CCACHE_BASEDIR=$PWD
-rm -rf build
-set -x
-mkdir -p build
- BOOST_INCLUDE=$BOOST_ROOT/include \
-LIBPBDATA_INCLUDE=$DEPLOYMENT/include/pbdata \
- LIBPBDATA_LIB=$DEPLOYMENT/lib \
- LIBBLASR_INCLUDE=$DEPLOYMENT/include/alignment \
- LIBBLASR_LIB=$DEPLOYMENT/lib \
-LIBPBIHDF_INCLUDE=$DEPLOYMENT/include/hdf \
- LIBPBIHDF_LIB=$DEPLOYMENT/lib \
- PBBAM_INCLUDE=$DEPLOYMENT/include \
- PBBAM_LIB=$DEPLOYMENT/lib \
- HTSLIB_CFLAGS=$(pkg-config --cflags htslib) \
- HTSLIB_LIBS=$(pkg-config --libs htslib) \
- HDF5_INCLUDE=$(pkg-config --cflags-only-I hdf5|awk '{print $1}'|sed -e 's/^-I//') \
- HDF5_LIB=$(pkg-config --libs-only-L hdf5|awk '{print $1}'|sed -e 's/^-L//') \
- DALIGNER_SRC=$DALIGNER \
- DAZZ_DB_SRC=$DAZZDB \
- GTEST_SRC=$PWD/../gtest/src \
- GTEST_INCLUDE=$PWD/../gtest/include \
- ZLIB_LIBFLAGS="$(pkg-config --libs zlib)" \
-./configure.py --build-dir=$PWD/build
-sed -i -e 's/-lpbihdf/-llibcpp/;s/-lblasr//;s/-lpbdata//' build/defines.mk
-make -C build
-cp -a build/src/cpp/pbdagcon $DEPLOYMENT/bin/
-cp -a build/src/cpp/dazcon $DEPLOYMENT/bin/
-cd ../..
-
-myVERSION=`pbdagcon --version|awk '/version/{print $3}'`
-#rm -rf tarballs && mkdir -p tarballs
-cd deployment
-tar zcf ../tarballs/pbdagcon-${myVERSION}.tgz bin/pbdagcon bin/dazcon
=====================================
bamboo_test.sh deleted
=====================================
@@ -1,12 +0,0 @@
-#!/bin/bash
-export PATH=$PWD/deployment/bin:$PATH
-export LD_LIBRARY_PATH=$PWD/deployment/lib:$LD_LIBRARY_PATH
-type module >& /dev/null \
-|| . /mnt/software/Modules/current/init/bash
-module load gcc
-module load htslib
-module load hdf5-tools
-module load zlib
-
-make -C repos/pbdagcon/build check
-chmod +w -R repos/pbdagcon
=====================================
configure.py
=====================================
@@ -152,8 +152,8 @@ def compose_defines_pacbio(envin):
'LIBPBIHDF_INCLUDE', 'LIBPBIHDF_LIB', 'LIBPBIHDF_LIBFLAGS',
'HDF5_INCLUDE', 'HDF5_LIB', 'HDF5_LIBFLAGS',
'PBBAM_INCLUDE', 'PBBAM_LIB', 'PBBAM_LIBFLAGS',
- 'HTSLIB_CFLAGS', 'HTSLIB_LIBS',
- 'BOOST_INCLUDE', 'PTHREAD_LIBFLAGS',
+ 'HTSLIB_INCLUDE', 'HTSLIB_LIB', 'HTSLIB_LIBFLAGS',
+ 'BOOST_INCLUDE','PTHREAD_LIBFLAGS',
'ZLIB_LIB', 'ZLIB_LIBFLAGS',
'GCC_LIB',
'DAZZ_DB_SRC', 'DAZZ_DB_INCLUDE',
@@ -244,7 +244,7 @@ def set_defs_defaults(env, nopbbam):
pbbam_defaults = {
'LIBPBIHDF_LIBFLAGS': '-lpbihdf',
'PBBAM_LIBFLAGS': '-lpbbam',
- 'HTSLIB_LIBS': '-lhts',
+ 'HTSLIB_LIBFLAGS': '-lhts',
'HDF5_LIBFLAGS': '-lhdf5_cpp -lhdf5',
'ZLIB_LIBFLAGS': '-lz',
'PTHREAD_LIBFLAGS': '-lpthread',
=====================================
src/cpp/DazAlnProvider.cpp
=====================================
@@ -222,7 +222,7 @@ int TargetHit::aend() {
// daligner structures.
Target::Target(): needsFree_(false) { }
-Target::Target(DAZZ_DB& db, int tspace, int small) :
+Target::Target(HITS_DB& db, int tspace, int small) :
db_(db),
tspace_(tspace),
small_(small),
=====================================
src/cpp/DazAlnProvider.hpp
=====================================
@@ -94,7 +94,7 @@ std::ostream& operator<<(std::ostream& ostrm, TargetHit& hit);
class Target {
public:
Target();
- Target(DAZZ_DB& db, int tspace, int small);
+ Target(HITS_DB& db, int tspace, int small);
~Target();
// Initializes this target based on the given record, possibly scoring as
@@ -119,7 +119,7 @@ public:
std::vector<TargetHit> hits;
private:
- DAZZ_DB db_;
+ HITS_DB db_;
char* abuffer_, *bbuffer_;
Work_Data* work_;
int tspace_, small_;
@@ -158,7 +158,7 @@ private:
const ProgramOpts popts_;
// Dazzler-related data
- DAZZ_DB db_;
+ HITS_DB db_;
int64 novl_, covl_;
int tbytes_;
FILE* input_;
=====================================
src/cpp/makefile
=====================================
@@ -8,7 +8,7 @@ PBDAGCON_OBJECTS := BlasrM5AlnProvider.o main.o SimpleAligner.o
DAZCON_OBJECTS := DB.o QV.o align.o DazAlnProvider.o dazcon.o
CPPFLAGS += -MMD -MP
-CXXFLAGS = -O3 -std=c++14 -Wall -Wuninitialized -pedantic
+CXXFLAGS = -O3 -std=c++11 -Wall -Wuninitialized -pedantic
CFLAGS = -O3 -Wall -Wextra -fno-strict-aliasing
INCDIRS := \
@@ -18,7 +18,8 @@ INCDIRS := \
${LIBPBDATA_INCLUDE} \
${LIBPBIHDF_INCLUDE} \
${PBBAM_INCLUDE} \
- ${HDF5_INCLUDE}
+ ${HDF5_INCLUDE} \
+ ${HTSLIB_INCLUDE}
SYS_INCDIRS := \
${BOOST_INCLUDE} \
${THISDIR}/third-party
@@ -28,6 +29,7 @@ LIBDIRS := \
${LIBPBIHDF_LIB} \
${PBBAM_LIB} \
${HDF5_LIB} \
+ ${HTSLIB_LIB} \
${GCC_LIB} \
${ZLIB_LIB}
LDLIBS+= \
@@ -36,11 +38,11 @@ LDLIBS+= \
${LIBPBIHDF_LIBFLAGS} \
${PBBAM_LIBFLAGS} \
${HDF5_LIBFLAGS} \
- ${HTSLIB_LIBS} \
+ ${HTSLIB_LIBFLAGS} \
${ZLIB_LIBFLAGS} \
${PTHREAD_LIBFLAGS} \
${DL_LIBFLAGS}
-CPPFLAGS+=$(patsubst %,-I%,${INCDIRS}) $(patsubst %,-isystem%,${SYS_INCDIRS}) $(HTSLIB_CFLAGS)
+CPPFLAGS+=$(patsubst %,-I%,${INCDIRS}) $(patsubst %,-isystem%,${SYS_INCDIRS})
LDFLAGS+=$(patsubst %,-L %,${LIBDIRS})
LDFLAGS += ${EXTRA_LDFLAGS}
=====================================
src/filterm4.py
=====================================
@@ -3,7 +3,6 @@
# Filters for unique, highest scoring subread query/target pairs from an m4
# file. Helps get rid of chimeras, at the cost of some yield.
-from __future__ import print_function
import sys
from collections import namedtuple
@@ -37,7 +36,7 @@ def printUniq(qgroup, count):
for r in top.values():
count.filt += 1
- print(r, end=' ')
+ print r,
qgroup[:] = []
=====================================
src/m4topre.py
=====================================
@@ -2,7 +2,6 @@
"""Super-simple converter from blasr m4 alignments to pbdagcon 'pre'
alignments. For use in the pre-assembler dagcon workflow.
"""
-from __future__ import print_function
import sys
import heapq
@@ -202,8 +201,8 @@ def main(): # pylint: disable=R0914
else:
tseq = seqs[rec.tname].translate(__rc__)[::-1][tst:tnd]
- print(' '.join([rec.qname, rec.tname, strand,
- rec.tseqlength, str(tst), str(tnd), qseq, tseq]))
+ print ' '.join([rec.qname, rec.tname, strand,
+ rec.tseqlength, str(tst), str(tnd), qseq, tseq])
if __name__ == '__main__':
sys.exit(main())
=====================================
src/q-sense.py
=====================================
@@ -1,5 +1,4 @@
#!/usr/bin/env python
-from __future__ import print_function
import sys
import os
import logging
@@ -86,8 +85,8 @@ class Consensus(PBMultiToolRunner):
prefix = ".".join(prefix)
full_prefix = os.path.join(self.args.out_dir_name, prefix)
with open("%s_ref.fa" % full_prefix, "w") as f:
- print(">%s_ref" % self.args.consensus_seq_name, file=f)
- print(s, file=f)
+ print >>f ,">%s_ref" % self.args.consensus_seq_name
+ print >>f, s
hp_corr = True if self.args.enable_hp_corr else False
mark_lower_case = True if self.args.mark_lower_case else False
generate_consensus(input_fasta_name, "%s_ref.fa" % full_prefix, full_prefix, self.args.consensus_seq_name,
=====================================
test/cpp/makefile
=====================================
@@ -15,6 +15,7 @@ INCDIRS := . \
${LIBPBIHDF_INCLUDE} \
${PBBAM_INCLUDE} \
${HDF5_INCLUDE} \
+ ${HTSLIB_INCLUDE} \
${BOOST_INCLUDE} \
${GTEST_INCLUDE} \
third-party
@@ -25,6 +26,7 @@ LIBDIRS := \
${LIBPBIHDF_LIB} \
${PBBAM_LIB} \
${HDF5_LIB} \
+ ${HTSLIB_LIB} \
${GCC_LIB} \
${ZLIB_LIB}
@@ -35,11 +37,11 @@ LDLIBS+= \
${LIBPBIHDF_LIBFLAGS} \
${PBBAM_LIBFLAGS} \
${HDF5_LIBFLAGS} \
- ${HTSLIB_LIBS} \
+ ${HTSLIB_LIBFLAGS} \
${ZLIB_LIBFLAGS} \
${PTHREAD_LIBFLAGS} \
${DL_LIBFLAGS}
-CPPFLAGS+=$(patsubst %,-I%,${INCDIRS}) $(HTSLIB_CFLAGS)
+CPPFLAGS+=$(patsubst %,-I%,${INCDIRS})
LDFLAGS+=$(patsubst %,-L %,${LIBDIRS})
# For fused-src, gtest-all.cc includes gtest/*.
@@ -48,7 +50,7 @@ LDFLAGS+=$(patsubst %,-L %,${LIBDIRS})
GTEST_CPPFLAGS += -isystem $(GTEST_INCLUDE) -isystem ${GTEST_SRC}/..
GTEST_CXXFLAGS += -g -Wall -Wextra -pthread
-CXXFLAGS := -O3 -std=c++14
+CXXFLAGS := -O3 -std=c++11
GTEST_OBJECTS := gtest-all.o gtest_main.o
DAZCON_OBJECTS := DB.o QV.o align.o Alignment.o \
View it on GitLab: https://salsa.debian.org/med-team/pbdagcon/commit/578071e0934f74f9a8fce1f559e3cc542d0a7fc1
--
View it on GitLab: https://salsa.debian.org/med-team/pbdagcon/commit/578071e0934f74f9a8fce1f559e3cc542d0a7fc1
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