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

-#!/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

-#!/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

@@ -152,7 +152,7 @@ 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',
+            'HTSLIB_INCLUDE', 'HTSLIB_LIB', 'HTSLIB_LIBFLAGS',
             'BOOST_INCLUDE','PTHREAD_LIBFLAGS',
             'ZLIB_LIB', 'ZLIB_LIBFLAGS',
             'GCC_LIB',
@@ -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',

debian/changelog

-pbdagcon (0.3+git20180411.c14c422+ds-1) UNRELEASED; urgency=low
+pbdagcon (0.3+git20161121.0000000+ds-1) unstable; urgency=low
 
   * Team upload
 
@@ -7,6 +7,7 @@ pbdagcon (0.3+git20180411.c14c422+ds-1) UNRELEASED; urgency=low
 
   [ Andreas Tille ]
   * d/watch: use git mode to detect new upstream commit
+  * Reimport old source with version number fitting git mode
   * d/get-orig-source: checkout submodules for code copy of DALIGNER and
     DAZZ_DB which are specific adaptations to pbdagcon
   * debhelper 12
@@ -16,7 +17,7 @@ pbdagcon (0.3+git20180411.c14c422+ds-1) UNRELEASED; urgency=low
     Closes: #916576
   * Secure URI in copyright format
 
- -- Andreas Tille <tille@debian.org>  Thu, 19 Jul 2018 11:25:43 +0200
+ -- Andreas Tille <tille@debian.org>  Mon, 04 Feb 2019 15:36:14 +0100
 
 pbdagcon (0.3+20161121+ds-1) unstable; urgency=medium
 

debian/patches/compiler-flags.patch

@@ -2,15 +2,15 @@ Description: Prevent override of dpkg-buildflags
 Author: Afif Elghraoui <afif@debian.org>
 Forwarded: no
 Last-Update: 2016-10-23
---- a/src/cpp/makefile
-+++ b/src/cpp/makefile
-@@ -8,8 +8,8 @@ PBDAGCON_OBJECTS := BlasrM5AlnProvider.o
+--- pbdagcon.orig/src/cpp/makefile
++++ pbdagcon/src/cpp/makefile
+@@ -8,8 +8,8 @@
  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
-+CXXFLAGS += -O3 -std=c++14 -Wall -Wuninitialized -pedantic
++CXXFLAGS += -O3 -std=c++11 -Wall -Wuninitialized -pedantic
 +CFLAGS += -O3 -Wall -Wextra -fno-strict-aliasing
  
  INCDIRS := \

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

 #!/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 \