[med-svn] [Git][med-team/pbseqlib][upstream] New upstream version 5.3.5+dfsg
Andreas Tille (@tille)
gitlab at salsa.debian.org
Fri Oct 8 14:49:19 BST 2021
Andreas Tille pushed to branch upstream at Debian Med / pbseqlib
Commits:
0f0ab073 by Andreas Tille at 2021-09-30T14:20:08+02:00
New upstream version 5.3.5+dfsg
- - - - -
19 changed files:
- .gitignore
- alignment/files/ReaderAgglomerate.cpp
- hdf/BufferedHDFArrayImpl.hpp
- hdf/HDFAtom.hpp
- hdf/HDFAttributable.cpp
- hdf/HDFBasReader.hpp
- hdf/HDFBaseCallsWriter.cpp
- hdf/HDFCCSReader.hpp
- hdf/HDFFile.cpp
- hdf/HDFPlsReader.hpp
- hdf/HDFPulseCallsWriter.cpp
- meson.build
- pbdata/SMRTSequence.cpp
- pbdata/reads/RegionAnnotations.cpp
- subprojects/gtest.wrap
- subprojects/htslib.wrap
- + subprojects/pbcopper.wrap
- subprojects/zlib.wrap
- unittest/meson.build
Changes:
=====================================
.gitignore
=====================================
@@ -13,6 +13,5 @@ LibBlasrConfig.h
/build
# Meson WrapDB stuff
-subprojects/packagecache/
-subprojects/googletest*
-subprojects/pbbam*
+/subprojects/*
+!/subprojects/*.wrap
=====================================
alignment/files/ReaderAgglomerate.cpp
=====================================
@@ -264,7 +264,7 @@ int ReaderAgglomerate::Initialize(bool unrolled_mode, bool polymerase_mode)
// create dataset , common for both unrolled and regular modes
try {
dataSetPtr = new PacBio::BAM::DataSet(fileName);
- } catch (std::exception e) {
+ } catch (const std::exception &e) {
std::cout << "ERROR! Failed to open " << fileName << ": " << e.what() << std::endl;
return 0;
}
@@ -623,6 +623,7 @@ int ReaderAgglomerate::GetNextBases(SMRTSequence &seq, bool readQVs)
#ifdef USE_PBBAM
std::cout << "ERROR! Can not GetNextBases from a BAM File." << std::endl;
#endif
+ break;
case FileType::Fourbit:
case FileType::None:
UNREACHABLE();
@@ -668,6 +669,7 @@ int ReaderAgglomerate::GetNext(CCSSequence &seq)
#ifdef USE_PBBAM
std::cout << "ERROR! Could not read BamRecord as CCSSequence" << std::endl;
#endif
+ break;
case FileType::Fourbit:
case FileType::None:
UNREACHABLE();
=====================================
hdf/BufferedHDFArrayImpl.hpp
=====================================
@@ -143,7 +143,7 @@ void BufferedHDFArray<T>::Flush(bool append, DSLength writePos)
//
try {
TypedWrite(this->writeBuffer, memorySpace, extendedSpace);
- } catch (H5::DataSetIException e) {
+ } catch (const H5::DataSetIException &e) {
std::cout << "ERROR! Could not write HDF5 data." << std::endl;
e.printErrorStack();
std::exit(EXIT_FAILURE);
=====================================
hdf/HDFAtom.hpp
=====================================
@@ -49,7 +49,7 @@ public:
{
try {
attribute = object.openAttribute(attributeName.c_str());
- } catch (H5::Exception e) {
+ } catch (const H5::Exception &e) {
std::cout << "ERROR. Could not open attribute " << attributeName << std::endl;
std::exit(EXIT_FAILURE);
}
=====================================
hdf/HDFAttributable.cpp
=====================================
@@ -45,7 +45,7 @@ int HDFAttributable::ContainsAttribute(const std::string &attributeName)
for (i = 0; i < tmpAttributeNames.size(); i++) {
if (tmpAttributeNames[i] == attributeName) return true;
}
- } catch (H5::Exception e) {
+ } catch (const H5::Exception &e) {
//Failed to read attribute // e.printError();
}
return false;
=====================================
hdf/HDFBasReader.hpp
=====================================
@@ -599,7 +599,7 @@ public:
DNALength seqLength;
try {
seqLength = GetNextWithoutPosAdvance(seq);
- } catch (H5::DataSetIException e) {
+ } catch (const H5::DataSetIException &e) {
std::cout << "ERROR, could not read base calls for FASTA Sequence " << seq.GetName()
<< std::endl;
std::exit(EXIT_FAILURE);
@@ -644,7 +644,7 @@ public:
}
seq.SetQVScale(qvScale);
curBasePos += seqLength;
- } catch (H5::DataSetIException e) {
+ } catch (const H5::DataSetIException &e) {
std::cout << "ERROR, could not read quality metrics for FASTQ Sequence "
<< seq.GetName() << std::endl;
std::exit(EXIT_FAILURE);
@@ -688,7 +688,7 @@ public:
seq.SubreadStart(0).SubreadEnd(seq.length);
zmwReader.GetNext(seq.zmwData);
- } catch (H5::DataSetIException e) {
+ } catch (const H5::DataSetIException &e) {
std::cout << "ERROR, could not read bases or QVs for SMRTSequence " << seq.GetName()
<< std::endl;
std::exit(EXIT_FAILURE);
@@ -757,7 +757,7 @@ public:
//
seq.SubreadStart(0).SubreadEnd(seq.length);
zmwReader.GetNext(seq.zmwData);
- } catch (H5::DataSetIException e) {
+ } catch (const H5::DataSetIException &e) {
std::cout << "ERROR, could not read pulse metrics for SMRTSequence " << seq.GetName()
<< std::endl;
std::exit(EXIT_FAILURE);
=====================================
hdf/HDFBaseCallsWriter.cpp
=====================================
@@ -361,7 +361,7 @@ void HDFBaseCallsWriter::Close(void)
try {
_WriteAttributes();
- } catch (H5::Exception e) {
+ } catch (const H5::Exception& e) {
AddErrorMessage("Failed to write attributes to " + PacBio::GroupNames::basecalls);
}
=====================================
hdf/HDFCCSReader.hpp
=====================================
@@ -49,7 +49,7 @@ public:
try {
H5::Exception::dontPrint();
this->hdfBasFile.openFile(ccsBasFileName.c_str(), H5F_ACC_RDONLY, H5P_DEFAULT);
- } catch (H5::Exception &e) {
+ } catch (const H5::Exception &e) {
std::cout << "ERROR, could not open hdf file " << ccsBasFileName << " Stopping."
<< std::endl;
std::exit(EXIT_FAILURE);
@@ -267,7 +267,7 @@ public:
ccsSequence.CopyTitle(ccsSequence.unrolledRead.title);
std::string newTitle = std::string(ccsSequence.title) + "/ccs";
ccsSequence.CopyTitle(newTitle.c_str());
- } catch (H5::DataSetIException e) {
+ } catch (const H5::DataSetIException &e) {
std::cout << "ERROR, could not read ccs data for CCS Sequence "
<< ccsSequence.unrolledRead.title << std::endl;
std::exit(EXIT_FAILURE);
=====================================
hdf/HDFFile.cpp
=====================================
@@ -20,7 +20,7 @@ void HDFFile::Open(std::string fileName, unsigned int flags, const FileAccPropLi
if (fileExists and H5File::isHdf5(fileName.c_str()) and flagsIsNotTrunc) {
try {
hdfFile.openFile(fileName.c_str(), flags, fileAccPropList);
- } catch (FileIException e) {
+ } catch (const FileIException& e) {
std::cout << "Error opening file " << fileName << std::endl;
std::exit(EXIT_FAILURE);
}
@@ -32,7 +32,7 @@ void HDFFile::Open(std::string fileName, unsigned int flags, const FileAccPropLi
FileCreatPropList filePropList;
filePropList.setUserblock(512);
hdfFile = H5File(fileName.c_str(), H5F_ACC_TRUNC, filePropList);
- } catch (FileIException fileException) {
+ } catch (const FileIException& fileException) {
std::cout << "Error creating file " << fileName << std::endl;
std::exit(EXIT_FAILURE);
}
=====================================
hdf/HDFPlsReader.hpp
=====================================
@@ -546,7 +546,7 @@ public:
curRead++;
curPos += seqLength;
- } catch (DataSetIException e) {
+ } catch (const DataSetIException &e) {
std::cout << "ERROR, could not read pulse metrics for SMRTSequence " << read.GetName()
<< std::endl;
std::exit(EXIT_FAILURE);
=====================================
hdf/HDFPulseCallsWriter.cpp
=====================================
@@ -510,7 +510,7 @@ void HDFPulseCallsWriter::Close(void)
// Write attributes to pulsecallsGroup
try {
_WriteAttributes();
- } catch (H5::Exception e) {
+ } catch (const H5::Exception& e) {
AddErrorMessage("Failed to write attributes to " + PacBio::GroupNames::pulsecalls);
}
=====================================
meson.build
=====================================
@@ -1,14 +1,14 @@
project(
'libblasr',
'cpp',
- version : '5.3.4',
+ version : '5.3.5',
default_options : [
'buildtype=release',
'warning_level=3',
- 'cpp_std=c++14',
+ 'cpp_std=c++17',
'b_ndebug=false'],
license : 'BSD-3',
- meson_version : '>= 0.46.0')
+ meson_version : '>= 0.52.0')
# TODO:
# try to reenable 'b_ndebug=true'
@@ -46,7 +46,7 @@ endif
################
# boost
-libblasr_boost_dep = dependency('boost', required : true)
+libblasr_boost_dep = dependency('boost', include_type : 'system', required : true)
# pbbam
libblasr_pbbam_dep = dependency('pbbam', fallback : ['pbbam', 'pbbam_dep'])
=====================================
pbdata/SMRTSequence.cpp
=====================================
@@ -325,8 +325,9 @@ float SMRTSequence::HQRegionSnr(const char base) const
return hqRegionSnr_[SMRTSequence::SnrIndex4Base::G];
else if (::toupper(base) == 'T')
return hqRegionSnr_[SMRTSequence::SnrIndex4Base::T];
- else
+ else {
BLASR_THROW("Base must be in A, C, G, T");
+ }
}
SMRTSequence &SMRTSequence::HQRegionSnr(const char base, float v)
=====================================
pbdata/reads/RegionAnnotations.cpp
=====================================
@@ -63,8 +63,9 @@ RegionAnnotation RegionAnnotations::TheHQRegion() const
return RegionAnnotation(holeNumber_, RegionTypeMap::ToIndex(HQRegion, types_), 0, 0, 0);
else if (hqs_.size() == 1)
return hqs_[0];
- else
+ else {
BLASR_THROW("Zmw has more than one HQRegion");
+ }
}
DNALength RegionAnnotations::HQStart() const { return TheHQRegion().GetStart(); }
=====================================
subprojects/gtest.wrap
=====================================
@@ -1,10 +1,10 @@
[wrap-file]
-directory = googletest-release-1.8.0
+directory = googletest-release-1.10.0
-source_url = https://github.com/google/googletest/archive/release-1.8.0.zip
-source_filename = gtest-1.8.0.zip
-source_hash = f3ed3b58511efd272eb074a3a6d6fb79d7c2e6a0e374323d1e6bcbcc1ef141bf
+source_url = https://github.com/google/googletest/archive/release-1.10.0.zip
+source_filename = gtest-1.10.0.zip
+source_hash = 94c634d499558a76fa649edb13721dce6e98fb1e7018dfaeba3cd7a083945e91
-patch_url = https://wrapdb.mesonbuild.com/v1/projects/gtest/1.8.0/5/get_zip
-patch_filename = gtest-1.8.0-5-wrap.zip
-patch_hash = 7eeaede4aa2610a403313b74e04baf91ccfbaef03203d8f56312e22df1834ec5
+patch_url = https://wrapdb.mesonbuild.com/v1/projects/gtest/1.10.0/1/get_zip
+patch_filename = gtest-1.10.0-1-wrap.zip
+patch_hash = 04ff14e8880e4e465f6260221e9dfd56fea6bc7cce4c4aff0dc528e4a2c8f514
=====================================
subprojects/htslib.wrap
=====================================
@@ -1,10 +1,12 @@
[wrap-file]
-directory = htslib-1.9
+directory = htslib-1.10.2
+source_url = https://github.com/samtools/htslib/archive/1.10.2.zip
+source_filename = htslib-1.10.2.zip
+source_hash = f7994e9636f8a4032dea477a8613f5f73b330c23b5538e45666ce7306240ac14
+patch_url = https://wrapdb.mesonbuild.com/v1/projects/htslib/1.10.2/1/get_zip
+patch_filename = htslib-1.10.2-1-wrap.zip
+patch_hash = 7e8a0bfef2fb17e78ba1a8fd78e152bfbcfcb941b555d88c75b6d818a07d49d1
-source_url = https://github.com/samtools/htslib/archive/1.9.zip
-source_filename = htslib-1.9.zip
-source_hash = c4d3ae84014f8a80f5011521f391e917bc3b4f6ebd78e97f238472e95849ec14
+[provide]
+htslib = htslib_dep
-patch_url = https://wrapdb.mesonbuild.com/v1/projects/htslib/1.9/1/get_zip
-patch_filename = htslib-1.9-1-wrap.zip
-patch_hash = 02f4a3c64d668d4d09f8bb0f57eb33398e90e6901989f257be6a6716a15bdcdd
=====================================
subprojects/pbcopper.wrap
=====================================
@@ -0,0 +1,4 @@
+[wrap-git]
+directory=pbcopper
+url=https://github.com/PacificBiosciences/pbcopper.git
+revision=develop
=====================================
subprojects/zlib.wrap
=====================================
@@ -1,10 +1,12 @@
[wrap-file]
directory = zlib-1.2.11
-
source_url = http://zlib.net/fossils/zlib-1.2.11.tar.gz
source_filename = zlib-1.2.11.tar.gz
source_hash = c3e5e9fdd5004dcb542feda5ee4f0ff0744628baf8ed2dd5d66f8ca1197cb1a1
+patch_url = https://wrapdb.mesonbuild.com/v1/projects/zlib/1.2.11/5/get_zip
+patch_filename = zlib-1.2.11-5-wrap.zip
+patch_hash = 728c8e24acbc2e6682fbd950fec39e2fc77528af361adb87259f8a8511434004
+
+[provide]
+zlib = zlib_dep
-patch_url = https://wrapdb.mesonbuild.com/v1/projects/zlib/1.2.11/4/get_zip
-patch_filename = zlib-1.2.11-4-wrap.zip
-patch_hash = f733976fbfc59e0bcde01aa9469a24eeb16faf0a4280b17e9eaa60a301d75657
=====================================
unittest/meson.build
=====================================
@@ -11,7 +11,11 @@ subdir('pbdata')
# Sources #
###########
-libblasr_gtest_dep = dependency('gtest_main', fallback : ['gtest', 'gtest_main_dep'])
+# find GoogleTest
+libblasr_gtest_dep = dependency(
+ 'gtest',
+ main : true,
+ fallback : ['gtest', 'gtest_main_dep'])
libblasr_unittest = executable(
'libblasr_unittest', [
View it on GitLab: https://salsa.debian.org/med-team/pbseqlib/-/commit/0f0ab0737117b7db8c8637f8c785f12c5d63c03e
--
View it on GitLab: https://salsa.debian.org/med-team/pbseqlib/-/commit/0f0ab0737117b7db8c8637f8c785f12c5d63c03e
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