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afif pushed a commit to branch debian/jessie-backports
in repository blasr.
commit eb92ed223d3e63ac632f90f4ada467546f849215
Merge: 7fbf228 c6a674f
Author: Afif Elghraoui <a...@debian.org>
Date: Wed Apr 26 01:25:32 2017 -0400
Merge tag 'debian/5.3+0-1' into debian/jessie-backports
tagging package blasr version debian/5.3+0-1
.gitignore | 9 +
Blasr.cpp | 292 +++---
LICENSE | 34 +
README.INSTALL.md | 24 +-
configure.py | 10 +-
cram.mk | 48 +
ctest/.gitignore | 1 +
ctest/affineAlign.t | 6 +-
ctest/aggressiveIntervalCut.t | 8 +-
ctest/alignScore.t | 2 +-
ctest/bamConcordant.t | 33 +
ctest/bamIn.t | 39 +-
ctest/bamOut.t | 4 +-
ctest/bug25328.t | 2 +-
ctest/bug25741.t | 9 -
ctest/bug25766.t | 4 +-
ctest/ccsH5.t | 4 +-
ctest/cigarAdjecentIndels.t | 22 +
ctest/concordant.t | 44 +-
ctest/dataset.t | 64 ++
ctest/deterministic.t | 47 +
ctest/ecoli.t | 13 +-
ctest/fastMaxInterval.t | 8 +-
ctest/filtercriteria.t | 8 +-
ctest/fofn.t | 4 +-
ctest/hitpolicy.t | 18 +-
ctest/holeNumbers.t | 4 +-
ctest/m0-5.t | 10 +-
ctest/multipart.t | 6 +-
ctest/noSplitSubreads.t | 40 +-
ctest/open_fail.t | 2 +-
ctest/samNM.t | 13 -
ctest/setup.sh | 8 +-
ctest/unaligned.t | 25 +
ctest/useccsallBestN1.t | 9 +-
ctest/useccsallLargeGenome.t | 4 +-
ctest/verbose.t | 2 +-
debian/NEWS | 6 +
debian/TODO | 5 +-
debian/changelog | 31 +
debian/control | 20 +-
debian/copyright | 4 +-
debian/install | 2 +
debian/lintian-overrides | 4 -
debian/patches/cmake-utils.patch | 25 +
debian/patches/disable-gtest.patch | 28 +
debian/patches/series | 2 +
debian/rules | 50 +-
extrautils/BasH5Simulator.cpp | 524 ----------
extrautils/CCSH5ToBam.cpp | 135 ---
extrautils/SimpleShredder.cpp | 2 +-
extrautils/ctest/alchemy.t | 20 -
extrautils/ctest/ccsh5tobam.t | 10 -
extrautils/ctest/printTupleCountTable.t | 2 +-
extrautils/makefile | 12 +-
{include => iblasr}/BlasrAlign.hpp | 39 +-
{include => iblasr}/BlasrAlignImpl.hpp | 157 ++-
iblasr/BlasrHeaders.h | 114 +++
iblasr/BlasrMiscs.hpp | 62 ++
{include => iblasr}/BlasrMiscsImpl.hpp | 100 +-
{include => iblasr}/BlasrUtils.hpp | 57 +-
{include => iblasr}/BlasrUtilsImpl.hpp | 111 +--
{include => iblasr}/MappingBuffers.hpp | 52 +-
{include => iblasr}/MappingIPC.h | 30 +-
{include => iblasr}/MappingParameters.h | 160 ++-
{include => iblasr}/MappingSemaphores.h | 15 +-
{include => iblasr}/ReadAlignments.hpp | 45 +-
{include => iblasr}/RegisterBlasrOptions.h | 415 ++++----
{include => iblasr}/RegisterFilterOptions.h | 41 +-
include/BlasrHeaders.h | 149 ---
include/BlasrMiscs.hpp | 100 --
makefile | 40 +-
rules.mk | 9 +-
sub.mk | 9 +
utils/.gitignore | 2 +
utils/LoadPulses.cpp | 145 ++-
utils/PulseToFasta.cpp | 37 +-
utils/SAWriter.cpp | 358 +++----
utils/SDPMatcher.cpp | 39 +-
utils/SamFilter.cpp | 56 +-
utils/SamToCmpH5.cpp | 29 +-
utils/SamToM4.cpp | 26 +-
utils/ToAfg.cpp | 42 +-
utils/bam2bax/BUILD.txt | 68 ++
utils/bam2bax/CMakeLists.txt | 139 +++
utils/bam2bax/README.md | 11 +
utils/bam2bax/makefile | 52 +
utils/bam2bax/src/Bam2Bax.cpp | 29 +
utils/bam2bax/src/Bam2Bax.h | 13 +
utils/bam2bax/src/Bam2BaxConverter.h | 38 +
utils/bam2bax/src/Bam2BaxConverterImpl.hpp | 57 ++
utils/bam2bax/src/Bam2BaxInternal.h | 78 ++
utils/bam2bax/src/Bam2BaxMain.cpp | 75 ++
utils/bam2bax/src/Bam2PlxMain.cpp | 65 ++
utils/bam2bax/src/CMakeLists.txt | 81 ++
utils/bam2bax/src/Converter.cpp | 130 +++
utils/bam2bax/src/Converter.h | 77 ++
utils/bam2bax/src/MetadataWriter.cpp | 42 +
utils/bam2bax/src/MetadataWriter.h | 38 +
utils/bam2bax/src/OptionParser.cpp | 562 +++++++++++
utils/bam2bax/src/OptionParser.h | 306 ++++++
utils/bam2bax/src/RegionTypeAdapter.h | 129 +++
utils/bam2bax/src/RegionsAdapter.h | 118 +++
utils/bam2bax/src/Settings.cpp | 224 +++++
utils/bam2bax/src/Settings.h | 80 ++
utils/bam2bax/tests/CMakeLists.txt | 94 ++
utils/bam2bax/tests/cram/bam2bax.t | 84 ++
utils/bam2bax/tests/cram/bam2plx.t | 230 +++++
...4852550000001823085912221377_s1_X0.1.scraps.bam | Bin 0 -> 644642 bytes
...52550000001823085912221377_s1_X0.1.subreads.bam | Bin 0 -> 220556 bytes
utils/bam2bax/tests/data/tiny.scraps.sam | 18 +
utils/bam2bax/tests/data/tiny.subreads.sam | 27 +
.../bam2bax/tests/data/tiny_bam2plx.polymerase.sam | 4 +
utils/bam2bax/tests/example/end-to-end.sh | 66 ++
utils/bam2bax/tests/files.cmake | 64 ++
.../tests/resequencing/bam2bax_resequencing.py | 179 ++++
utils/bam2bax/tests/resequencing/one_bax_test.sh | 5 +
utils/bam2bax/tests/resequencing/settings.xml | 201 ++++
utils/bam2bax/tests/resequencing/tiny_test.sh | 5 +
utils/bam2bax/tests/src/TestConstants.h | 195 ++++
utils/bam2bax/tests/src/TestData.h.in | 18 +
utils/bam2bax/tests/src/TestUtils.cpp | 42 +
utils/bam2bax/tests/src/TestUtils.h | 13 +
utils/bam2bax/tests/src/test.cpp | 23 +
utils/bam2bax/tests/src/test_Bam2BaxConverter.cpp | 94 ++
.../bam2bax/tests/src/test_HDFBaseCallsWriter.cpp | 56 ++
utils/bam2bax/tests/src/test_HDFBaxWriter.cpp | 100 ++
utils/bam2bax/tests/src/test_HDFScanDataWriter.cpp | 76 ++
.../bam2bax/tests/src/test_HDFZMWMetricsWriter.cpp | 51 +
utils/bam2bax/tests/src/test_HDFZMWWriter.cpp | 40 +
utils/bax2bam/BUILD.txt | 10 +
utils/bax2bam/CMakeLists.txt | 137 +++
utils/bax2bam/README.md | 62 ++
utils/bax2bam/makefile | 34 +
utils/bax2bam/src/Bax2Bam.cpp | 251 +++++
utils/bax2bam/src/Bax2Bam.h | 13 +
utils/bax2bam/src/CMakeLists.txt | 60 ++
utils/bax2bam/src/CcsConverter.cpp | 117 +++
utils/bax2bam/src/CcsConverter.h | 47 +
utils/bax2bam/src/ConverterBase.h | 1023 ++++++++++++++++++++
utils/bax2bam/src/HqRegionConverter.cpp | 192 ++++
utils/bax2bam/src/HqRegionConverter.h | 26 +
utils/bax2bam/src/IConverter.cpp | 78 ++
utils/bax2bam/src/IConverter.h | 53 +
utils/bax2bam/src/OptionParser.cpp | 562 +++++++++++
utils/bax2bam/src/OptionParser.h | 306 ++++++
utils/bax2bam/src/PolymeraseReadConverter.cpp | 60 ++
utils/bax2bam/src/PolymeraseReadConverter.h | 26 +
utils/bax2bam/src/Settings.cpp | 271 ++++++
utils/bax2bam/src/Settings.h | 91 ++
utils/bax2bam/src/SubreadConverter.cpp | 395 ++++++++
utils/bax2bam/src/SubreadConverter.h | 26 +
utils/bax2bam/src/main.cpp | 131 +++
utils/bax2bam/tests/CMakeLists.txt | 90 ++
utils/bax2bam/tests/bax2bam.t | 7 +
utils/bax2bam/tests/files.cmake | 52 +
utils/bax2bam/tests/src/TestData.h.in | 19 +
utils/bax2bam/tests/src/TestUtils.cpp | 43 +
utils/bax2bam/tests/src/TestUtils.h | 13 +
utils/bax2bam/tests/src/test_ccs.cpp | 219 +++++
utils/bax2bam/tests/src/test_common.cpp | 16 +
utils/bax2bam/tests/src/test_hqregions.cpp | 422 ++++++++
utils/bax2bam/tests/src/test_polymerase.cpp | 238 +++++
utils/bax2bam/tests/src/test_subreads.cpp | 416 ++++++++
.../gtest/.deps/test_fused_gtest_test-gtest-all.Po | 1 +
.../.deps/test_fused_gtest_test-gtest_main.Po | 1 +
.../bax2bam/third-party/gtest-1.7.0/lib/.dirstamp | 0
.../gtest-1.7.0/samples/.deps/.dirstamp | 0
.../gtest-1.7.0/samples/.deps/sample1.Plo | 3 +
.../gtest-1.7.0/samples/.deps/sample10_unittest.Po | 1 +
.../gtest-1.7.0/samples/.deps/sample1_unittest.Po | 1 +
.../gtest-1.7.0/samples/.deps/sample2.Plo | 29 +
.../gtest-1.7.0/samples/.deps/sample4.Plo | 48 +
.../samples/.deps/test_fused_gtest_test-sample1.Po | 1 +
.../test_fused_gtest_test-sample1_unittest.Po | 1 +
.../third-party/gtest-1.7.0/samples/.dirstamp | 0
.../third-party/gtest-1.7.0/src/.deps/.dirstamp | 0
.../gtest-1.7.0/src/.deps/gtest-all.Plo | 617 ++++++++++++
.../gtest-1.7.0/src/.deps/gtest_main.Plo | 460 +++++++++
.../bax2bam/third-party/gtest-1.7.0/src/.dirstamp | 0
.../gtest-1.7.0/test/.deps/gtest_all_test.Po | 1 +
utils/ctest/.gitignore | 1 +
utils/ctest/samFilter.t | 24 +-
utils/makefile | 22 +-
184 files changed, 12667 insertions(+), 2348 deletions(-)
diff --cc debian/changelog
index 9a8c47a,5080cee..c068e72
--- a/debian/changelog
+++ b/debian/changelog
@@@ -1,9 -1,34 +1,40 @@@
+ blasr (5.3+0-1) unstable; urgency=medium
+
+ * Imported Upstream version 5.3+0 (corresponds to smrtanalysis-4.0.0 tag)
+ * Refresh patches
+
+ -- Afif Elghraoui <a...@debian.org> Fri, 23 Dec 2016 17:50:11 -0800
+
+ blasr (5.3-2) unstable; urgency=medium
+
+ * Use pbseqlib metapackage rather than depending on individual libraries
+ * Build with pbbam (Closes: #848751, #848541)
+ * Build bax2bam and bam2bax
+
+ -- Afif Elghraoui <a...@debian.org> Tue, 20 Dec 2016 02:02:51 -0800
+
+ blasr (5.3-1) unstable; urgency=medium
+
+ * Imported Upstream version 5.3
+ (upstream git revision 1baabc8 from 2016-09-12)
+ * Find PB libraries in the default LD path
+ * Bump Standards-Version to 3.9.8
+ * Use encrypted protocols for VCS
+ * Update email address and copyright year
+ * Update paths to pbseqlib headers
+ * Remove unused lintian overrides
+ * Update debian/TODO
+ * Add d/NEWS to explain interface change
+ * d/rules: Minor clean-ups
+
+ -- Afif Elghraoui <a...@debian.org> Sun, 23 Oct 2016 18:21:55 -0700
+
+blasr (0~20151014+git8e668be-1~bpo8+1) jessie-backports; urgency=high
+
+ * Rebuild for jessie-backports.
+
+ -- Afif Elghraoui <a...@ghraoui.name> Mon, 21 Dec 2015 13:05:44 -0800
+
blasr (0~20151014+git8e668be-1) unstable; urgency=high
* Don't install LICENSES.txt file
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