[med-svn] [blasr] 01/02: Merge branch 'master' into debian/jessie-backports
Afif Elghraoui
afif-guest at moszumanska.debian.org
Mon Dec 21 21:56:54 UTC 2015
This is an automated email from the git hooks/post-receive script.
afif-guest pushed a commit to branch debian/jessie-backports
in repository blasr.
commit 07294d21cafd0281440968d0ed7fc4b62774c930
Merge: 464f3d6 11817b4
Author: Afif Elghraoui <afif at ghraoui.name>
Date: Mon Dec 21 13:05:14 2015 -0800
Merge branch 'master' into debian/jessie-backports
Conflicts:
debian/changelog
.gitignore | 4 +
Blasr.cpp | 4333 +-
MANUAL.md | 84 -
Makefile | 59 -
MappingSemaphores.h | 45 -
README.INSTALL.md | 86 +
README.MANUAL.md | 38 +
README.md | 52 +-
blasr_git_common.mk | 15 -
blasr_gitp4.mk | 24 -
common.mk | 139 -
configure.py | 125 +-
ctest/affineAlign.t | 2 +-
ctest/hitpolicy.t | 14 +-
ctest/useccsallLargeGenome.t | 3 +-
debian/changelog | 13 +
debian/control | 20 +-
debian/copyright | 61 -
debian/docs | 3 +-
debian/get-orig-source | 39 -
debian/lintian-overrides | 6 +
debian/patches/selective-static-linking | 31 -
debian/patches/series | 1 -
debian/rules | 28 +-
extrautils/GNUmakefile | 45 -
extrautils/Makefile | 78 -
extrautils/makefile | 49 +
extrautils/p4.mk | 79 -
include/BlasrAlign.hpp | 122 +
include/BlasrAlignImpl.hpp | 1564 +
include/BlasrHeaders.h | 149 +
include/BlasrMiscs.hpp | 100 +
include/BlasrMiscsImpl.hpp | 223 +
include/BlasrUtils.hpp | 199 +
include/BlasrUtilsImpl.hpp | 1225 +
include/MappingBuffers.hpp | 116 +
MappingIPC.h => include/MappingIPC.h | 4 +-
MappingParameters.h => include/MappingParameters.h | 40 +-
include/MappingSemaphores.h | 45 +
include/ReadAlignments.hpp | 199 +
.../RegisterBlasrOptions.h | 62 +-
.../RegisterFilterOptions.h | 30 +-
libcpp.makefile | 9 -
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libcpp/alignment/anchoring/AnchorParameters.hpp | 35 -
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libcpp/alignment/datastructures/alignment/Path.h | 23 -
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libcpp/alignment/files/BaseSequenceIO.cpp | 77 -
libcpp/alignment/files/BaseSequenceIO.hpp | 26 -
libcpp/alignment/files/CCSIterator.cpp | 28 -
libcpp/alignment/files/CCSIterator.hpp | 21 -
libcpp/alignment/files/FragmentCCSIterator.cpp | 109 -
libcpp/alignment/files/FragmentCCSIterator.hpp | 23 -
libcpp/alignment/files/ReaderAgglomerate.cpp | 505 -
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libcpp/alignment/format/BAMPrinter.hpp | 29 -
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libcpp/alignment/format/IntervalPrinter.cpp | 70 -
libcpp/alignment/format/IntervalPrinter.hpp | 21 -
libcpp/alignment/format/SAMHeaderPrinter.cpp | 432 -
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libcpp/alignment/qvs/QualityValueProfile.cpp | 41 -
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libcpp/pbdata/utils/SMRTReadUtils.cpp | 45 -
libcpp/pbdata/utils/SMRTReadUtils.hpp | 18 -
libcpp/pbdata/utils/SMRTTitle.cpp | 52 -
libcpp/pbdata/utils/SMRTTitle.hpp | 24 -
libcpp/pbdata/utilsImpl.hpp | 32 -
libcpp/rules.mk | 17 -
libcpp/simple.mk | 16 -
libcpp/unittest/.gitignore | 1 -
libcpp/unittest/Makefile | 151 -
libcpp/unittest/alignment/Makefile | 35 -
.../alignment/AlignmentMap_gtest.cpp | 63 -
.../alignment/CmpIndexedStringTable_gtest.cpp | 143 -
.../unittest/alignment/files/CCSIterator_gtest.cpp | 66 -
.../alignment/files/FragmentCCSIterator_gtest.cpp | 104 -
.../alignment/files/ReaderAgglomerate_gtest.cpp | 129 -
.../alignment/format/SAMHeaderPrinter_gtest.cpp | 138 -
.../unittest/alignment/format/SAMPrinter_gtest.cpp | 45 -
.../unittest/alignment/utils/FileUtils_gtest.cpp | 54 -
.../unittest/alignment/utils/RangeUtils_gtest.cpp | 63 -
.../unittest/alignment/utils/RegionUtils_gtest.cpp | 236 -
libcpp/unittest/build.mk | 27 -
libcpp/unittest/common.mk | 64 -
libcpp/unittest/hdf/HDF2DArray_gtest.cpp | 96 -
libcpp/unittest/hdf/HDFBasReader_gtest.cpp | 56 -
libcpp/unittest/hdf/HDFCCSReader_gtest.cpp | 68 -
libcpp/unittest/hdf/HDFPlsReader_gtest.cpp | 49 -
libcpp/unittest/hdf/HDFScanDataReader_gtest.cpp | 52 -
libcpp/unittest/hdf/HDFScanDataWriter_gtest.cpp | 36 -
libcpp/unittest/hdf/HDFUtils_gtest.cpp | 38 -
libcpp/unittest/hdf/HDFZMWReader_gtest.cpp | 125 -
libcpp/unittest/hdf/Makefile | 26 -
libcpp/unittest/normal.Makefile | 9 -
libcpp/unittest/normal.defines.mk | 54 -
libcpp/unittest/pbdata/CCSSequence_gtest.cpp | 117 -
libcpp/unittest/pbdata/ChangeListID_gtest.cpp | 34 -
libcpp/unittest/pbdata/DNASequence_gtest.cpp | 279 -
libcpp/unittest/pbdata/FASTAReader_gtest.cpp | 65 -
libcpp/unittest/pbdata/FASTASequence_gtest.cpp | 143 -
libcpp/unittest/pbdata/FASTQReader_gtest.cpp | 90 -
libcpp/unittest/pbdata/Makefile | 31 -
libcpp/unittest/pbdata/NucConversion_gtest.cpp | 105 -
libcpp/unittest/pbdata/SMRTSequence_gtest.cpp | 62 -
libcpp/unittest/pbdata/ScanData_gtest.cpp | 31 -
libcpp/unittest/pbdata/SeqUtils_gtest.cpp | 50 -
libcpp/unittest/pbdata/StringUtils_gtest.cpp | 80 -
libcpp/unittest/pbdata/VectorUtils_gtest.cpp | 38 -
libcpp/unittest/pbdata/defs_gtest.cpp | 44 -
.../pbdata/metagenome/TitleTable_gtest.cpp | 32 -
.../pbdata/qvs/QualityValueVector_gtest.cpp | 50 -
libcpp/unittest/pbdata/reads/ReadType_gtest.cpp | 57 -
libcpp/unittest/pbdata/saf/AlnGroup_gtest.cpp | 44 -
libcpp/unittest/pbdata/saf/MovieInfo_gtest.cpp | 43 -
libcpp/unittest/pbdata/saf/RefInfo_gtest.cpp | 45 -
libcpp/unittest/pbdata/testdata.h | 71 -
libcpp/unittest/pbdata/utils/SMRTTitle_gtest.cpp | 28 -
libcpp/unittest/pbdata/utils_gtest.cpp | 37 -
GNUmakefile => makefile | 37 +-
p4.common.mk | 147 -
p4.fetch.tmpmk | 10 -
p4.mk | 76 -
rules.mk | 19 +-
travis.sh | 2 +-
utils/.gitignore | 8 +
utils/Makefile | 64 -
utils/PulseToFasta.cpp | 106 +-
utils/SamFilter.cpp | 2 +-
utils/ToAfg.cpp | 15 +-
utils/{GNUmakefile => makefile} | 28 +-
utils/p4.mk | 65 -
yli.common.mk | 94 -
yli.makefile | 80 -
534 files changed, 5150 insertions(+), 100072 deletions(-)
diff --cc debian/changelog
index a96a363,d298ead..4ade97a
--- a/debian/changelog
+++ b/debian/changelog
@@@ -1,9 -1,16 +1,22 @@@
+ blasr (0~20151014+git8e668be-1) unstable; urgency=high
+
+ * Don't install LICENSES.txt file
+ * Imported Upstream version 0~20151014+git8e668be
+ * Use externally packaged pbseqlib and dynamically link to it
+ (Closes: #807985)
+ * Adjust for renamed upstream documentation
+ * Minor clean-ups
+ * Update comment about why tests can't be run
+ * Allow building in parallel
+
+ -- Afif Elghraoui <afif at ghraoui.name> Mon, 14 Dec 2015 19:51:57 -0800
+
+blasr (0~20150724+git3ca7fe8-1~bpo8+1) jessie-backports; urgency=medium
+
+ * Rebuild for jessie-backports.
+
+ -- Afif Elghraoui <afif at ghraoui.name> Sun, 06 Sep 2015 02:20:55 -0700
+
blasr (0~20150724+git3ca7fe8-1) unstable; urgency=low
* Initial release (Closes: #793763)
--
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