[med-svn] [wgs-assembler] 06/12: Merge tag 'upstream/8.3rc2+ds1'
Afif Elghraoui
afif-guest at moszumanska.debian.org
Sat Aug 8 07:38:08 UTC 2015
This is an automated email from the git hooks/post-receive script.
afif-guest pushed a commit to branch master
in repository wgs-assembler.
commit 947f95401211172dcfb9abd9f27a6c818287f47f
Merge: 4494394 7cbc871
Author: Afif Elghraoui <afif at ghraoui.name>
Date: Fri Aug 7 22:37:48 2015 -0700
Merge tag 'upstream/8.3rc2+ds1'
Upstream version 8.3rc2+ds1
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src/AS_PBR/boost/config/stdlib/._vacpp.hpp | Bin 0 -> 280 bytes
src/AS_PBR/boost/detail/._dynamic_bitset.hpp | Bin 0 -> 280 bytes
src/AS_PBR/boost/detail/._iterator.hpp | Bin 0 -> 280 bytes
src/AS_PBR/boost/detail/._workaround.hpp | Bin 0 -> 280 bytes
src/AS_PBR/boost/dynamic_bitset/._config.hpp | Bin 0 -> 280 bytes
.../boost/dynamic_bitset/._dynamic_bitset.hpp | Bin 0 -> 280 bytes
src/AS_PBR/boost/pending/._integer_log2.hpp | Bin 0 -> 280 bytes
src/AS_PBR/boost/pending/._lowest_bit.hpp | Bin 0 -> 280 bytes
src/AS_PBR/convertToPBCNS.pl | 381 +-
src/AS_PBR/falcon_sense.Darwin-amd64.bin | Bin 0 -> 5470817 bytes
src/AS_PBR/falcon_sense.Linux-amd64.bin | Bin 0 -> 7521743 bytes
src/AS_PBR/jellyfish.Darwin-amd64.bin | Bin 0 -> 851752 bytes
src/AS_PBR/jellyfish.Linux-amd64.bin | Bin 0 -> 989208 bytes
src/AS_PBR/libgcc_s.1.dylib | Bin 0 -> 82640 bytes
src/AS_PBR/libstdc++.6.dylib | Bin 0 -> 906176 bytes
src/AS_PBR/mhap.tar.gz | Bin 0 -> 2289816 bytes
src/AS_PBR/pacBioToCA.pl | 2056 -------
src/AS_PBR/pbdagcon.Linux-amd64.bin | Bin 0 -> 2956633 bytes
src/AS_PBR/pbutgcns.Darwin-amd64.bin | Bin 0 -> 1607332 bytes
src/AS_PBR/pbutgcns.Linux-amd64.bin | Bin 0 -> 1975552 bytes
src/AS_PER/._AS_PER_encodeSequenceQuality.C | Bin 0 -> 280 bytes
src/AS_PER/._AS_PER_encodeSequenceQuality.H | Bin 0 -> 280 bytes
src/AS_PER/._AS_PER_genericStore.C | Bin 0 -> 280 bytes
src/AS_PER/._AS_PER_genericStore.H | Bin 0 -> 280 bytes
src/AS_PER/._AS_PER_genericStore.doc.txt | Bin 0 -> 280 bytes
src/AS_PER/._AS_PER_gkLibrary.C | Bin 0 -> 280 bytes
src/AS_PER/._AS_PER_gkStore.C | Bin 0 -> 280 bytes
src/AS_PER/._AS_PER_gkStore_IID.C | Bin 0 -> 280 bytes
src/AS_PER/._AS_PER_gkStore_PLC.C | Bin 0 -> 280 bytes
src/AS_PER/._AS_PER_gkStore_UID.C | Bin 0 -> 280 bytes
src/AS_PER/._AS_PER_gkStore_clearRange.C | Bin 0 -> 280 bytes
src/AS_PER/._AS_PER_gkStore_fragments.C | Bin 0 -> 280 bytes
src/AS_PER/._AS_PER_gkStore_load.C | Bin 0 -> 280 bytes
src/AS_PER/._AS_PER_gkStore_partition.C | Bin 0 -> 280 bytes
src/AS_PER/._AS_PER_gkStore_stats.C | Bin 0 -> 280 bytes
src/AS_PER/._AS_PER_gkStream.C | Bin 0 -> 280 bytes
src/AS_PER/._AS_PER_gkpStore.H | Bin 0 -> 280 bytes
src/AS_PER/._Makefile | Bin 0 -> 280 bytes
src/AS_PER/._gkClearRange.H | Bin 0 -> 280 bytes
src/AS_PER/._gkFragment.H | Bin 0 -> 280 bytes
src/AS_PER/._gkLibrary.H | Bin 0 -> 280 bytes
src/AS_PER/._gkPlacement.H | Bin 0 -> 280 bytes
src/AS_PER/._gkStore.H | Bin 0 -> 280 bytes
src/AS_PER/._gkStream.H | Bin 0 -> 280 bytes
src/AS_PER/._size.C | Bin 0 -> 280 bytes
src/AS_PL5/._AS_MSG | Bin 0 -> 311 bytes
src/AS_PL5/._AS_PER | Bin 0 -> 311 bytes
src/AS_PL5/._README | Bin 0 -> 280 bytes
src/AS_PL5/._caqc.pl | Bin 0 -> 280 bytes
src/AS_PL5/AS_MSG/._MSG.C | Bin 0 -> 280 bytes
src/AS_PL5/AS_MSG/._MSG.h | Bin 0 -> 280 bytes
src/AS_PL5/AS_MSG/._MSG.swig | Bin 0 -> 280 bytes
src/AS_PL5/AS_MSG/._Makefile.PL | Bin 0 -> 280 bytes
src/AS_PL5/AS_MSG/._Parser.pm | Bin 0 -> 280 bytes
src/AS_PL5/AS_MSG/._acronyms.h | Bin 0 -> 280 bytes
src/AS_PL5/AS_MSG/._parser.h | Bin 0 -> 280 bytes
src/AS_PL5/AS_MSG/._pmesg.h | Bin 0 -> 280 bytes
src/AS_PL5/AS_MSG/._test.pl | Bin 0 -> 280 bytes
src/AS_PL5/AS_PER/._GateKeeperStore.pm | Bin 0 -> 280 bytes
src/AS_PL5/AS_PER/._Makefile.PL | Bin 0 -> 280 bytes
src/AS_PL5/AS_PER/._PER.swig | Bin 0 -> 280 bytes
src/AS_REF/._Makefile | Bin 0 -> 280 bytes
src/AS_REF/._NOTES | Bin 0 -> 280 bytes
src/AS_REF/._buildRefContigs.C | Bin 0 -> 280 bytes
src/AS_REF/._buildRefOverlaps.C | Bin 0 -> 280 bytes
src/AS_REF/._frg-to-fasta.pl | Bin 0 -> 280 bytes
src/AS_REF/._refAlignment.H | Bin 0 -> 280 bytes
src/AS_REF/buildRefContigs.C | 8 +-
src/AS_REF/buildRefOverlaps.C | 4 +-
src/AS_REZ/._CommonREZ.H | Bin 0 -> 280 bytes
src/AS_REZ/._ConsistencyChecksREZ.C | Bin 0 -> 280 bytes
src/AS_REZ/._ConsistencyChecksREZ.H | Bin 0 -> 280 bytes
src/AS_REZ/._DataTypesREZ.H | Bin 0 -> 280 bytes
src/AS_REZ/._GapFillREZ.C | Bin 0 -> 280 bytes
src/AS_REZ/._GapWalkerREZ.C | Bin 0 -> 280 bytes
src/AS_REZ/._GapWalkerREZ.H | Bin 0 -> 280 bytes
src/AS_REZ/._Makefile | Bin 0 -> 280 bytes
src/AS_REZ/._MicroHetREZ.C | Bin 0 -> 280 bytes
src/AS_REZ/._MicroHetREZ.H | Bin 0 -> 280 bytes
src/AS_REZ/._PartitionsREZ.H | Bin 0 -> 280 bytes
src/AS_REZ/._RepeatRez.H | Bin 0 -> 280 bytes
src/AS_REZ/._SUBDELREZ.H | Bin 0 -> 280 bytes
src/AS_REZ/._StatisticsREZ.C | Bin 0 -> 280 bytes
src/AS_REZ/._StatisticsREZ.H | Bin 0 -> 280 bytes
src/AS_REZ/._UpdateREZ.C | Bin 0 -> 280 bytes
src/AS_REZ/._UpdateREZ.H | Bin 0 -> 280 bytes
src/AS_REZ/._UtilsREZ.C | Bin 0 -> 280 bytes
src/AS_REZ/._UtilsREZ.H | Bin 0 -> 280 bytes
src/AS_RUN/._Makefile | Bin 0 -> 280 bytes
src/AS_RUN/._README | Bin 0 -> 280 bytes
src/AS_RUN/._asmQC | Bin 0 -> 311 bytes
src/AS_RUN/._fragmentDepth.C | Bin 0 -> 280 bytes
src/AS_RUN/._get-commit-logs.pl | Bin 0 -> 280 bytes
src/AS_RUN/._markUniqueUnique.C | Bin 0 -> 280 bytes
src/AS_RUN/._new.pl | Bin 0 -> 280 bytes
src/AS_RUN/._replaceIIDwithName-overlapDump.pl | Bin 0 -> 280 bytes
src/AS_RUN/._replaceUIDwithName-fastq.pl | Bin 0 -> 280 bytes
src/AS_RUN/._replaceUIDwithName-posmap.pl | Bin 0 -> 280 bytes
src/AS_RUN/._runCA-dedupe.pl | Bin 0 -> 280 bytes
src/AS_RUN/._runCA-overlapStoreBuild.pl | Bin 0 -> 280 bytes
src/AS_RUN/._runCA.pl | Bin 0 -> 280 bytes
src/AS_RUN/._sanity | Bin 0 -> 311 bytes
src/AS_RUN/Makefile | 13 +-
src/AS_RUN/asmQC/._TIGR | Bin 0 -> 311 bytes
src/AS_RUN/asmQC/._asmToAGP.pl | Bin 0 -> 280 bytes
src/AS_RUN/asmQC/._asmToFasta.pl | Bin 0 -> 280 bytes
src/AS_RUN/asmQC/._ca2ace.pl | Bin 0 -> 280 bytes
src/AS_RUN/asmQC/._caqc-diff.pl | Bin 0 -> 280 bytes
src/AS_RUN/asmQC/._caqc.pl | Bin 0 -> 280 bytes
src/AS_RUN/asmQC/._caqc_help.ini | Bin 0 -> 280 bytes
src/AS_RUN/asmQC/._checkMates.rb | Bin 0 -> 280 bytes
src/AS_RUN/asmQC/._compare-asm.sh | Bin 0 -> 280 bytes
src/AS_RUN/asmQC/._compare-qc.pl | Bin 0 -> 280 bytes
src/AS_RUN/asmQC/._compare-trim-against-map.pl | Bin 0 -> 280 bytes
src/AS_RUN/asmQC/._find-chimeric-contigs.pl | Bin 0 -> 280 bytes
src/AS_RUN/asmQC/._find-chimeric-reads.pl | Bin 0 -> 280 bytes
src/AS_RUN/asmQC/._mergeqc.pl | Bin 0 -> 280 bytes
src/AS_RUN/asmQC/._statsFromAGP.rb | Bin 0 -> 280 bytes
src/AS_RUN/asmQC/._unitigGraph.rb | Bin 0 -> 280 bytes
src/AS_RUN/asmQC/._utgCoverageGaps.rb | Bin 0 -> 280 bytes
src/AS_RUN/asmQC/TIGR/._AsmLib.pm | Bin 0 -> 280 bytes
src/AS_RUN/asmQC/TIGR/._Foundation.pm | Bin 0 -> 280 bytes
src/AS_RUN/markUniqueUnique.C | 7 +-
src/AS_RUN/new.pl | 6325 ++++++++++++++++++++
src/AS_RUN/replaceUIDwithName-fastq.pl | 117 +
src/AS_RUN/replaceUIDwithName-posmap.pl | 62 +
src/AS_RUN/replaceUIDwithName-simple.pl | 67 -
src/AS_RUN/replaceUIDwithName.pl | 117 -
src/AS_RUN/runCA-overlapStoreBuild.pl | 98 +-
src/AS_RUN/runCA.pl | 1114 ++--
src/AS_RUN/sanity/._build-all-kmer-revisions.pl | Bin 0 -> 280 bytes
src/AS_RUN/sanity/._build-all-wgs-revisions.pl | Bin 0 -> 280 bytes
src/AS_RUN/sanity/._compile-all-wgs-revisions.pl | Bin 0 -> 280 bytes
src/AS_RUN/sanity/._sanity-all-done.pl | Bin 0 -> 280 bytes
src/AS_RUN/sanity/._sanity-asm-done.pl | Bin 0 -> 280 bytes
src/AS_RUN/sanity/._sanity-get-next-date.pl | Bin 0 -> 280 bytes
src/AS_RUN/sanity/._sanity-merge-qc.pl | Bin 0 -> 280 bytes
src/AS_RUN/sanity/._sanity-purge-old.pl | Bin 0 -> 280 bytes
src/AS_RUN/sanity/._sanity-update-reference.pl | Bin 0 -> 280 bytes
src/AS_RUN/sanity/._sanity.pl | Bin 0 -> 280 bytes
src/AS_RUN/sanity/._sanity.sh | Bin 0 -> 280 bytes
src/AS_RUN/sanity/build-all-kmer-revisions.pl | 26 +
src/AS_RUN/sanity/build-all-wgs-revisions.pl | 153 +
src/AS_RUN/sanity/compile-all-wgs-revisions.pl | 177 +
src/AS_RUN/sanity/sanity.pl | 163 +-
src/AS_TER/._Makefile | Bin 0 -> 280 bytes
src/AS_TER/._analyzePosMap-gapFillProbability.C | Bin 0 -> 280 bytes
src/AS_TER/._analyzePosMap-libraryFate.C | Bin 0 -> 280 bytes
src/AS_TER/._analyzePosMap-load.C | Bin 0 -> 280 bytes
src/AS_TER/._analyzePosMap.C | Bin 0 -> 280 bytes
src/AS_TER/._analyzePosMap.H | Bin 0 -> 280 bytes
src/AS_TER/._asmOutputFasta.C | Bin 0 -> 280 bytes
src/AS_TER/._asmOutputStatistics.C | Bin 0 -> 280 bytes
src/AS_TER/._buildPosMap.C | Bin 0 -> 280 bytes
src/AS_TER/._demotePosMap.C | Bin 0 -> 280 bytes
src/AS_TER/._fragsInVars.C | Bin 0 -> 280 bytes
src/AS_TER/._posmap-to-gff3.pl | Bin 0 -> 280 bytes
src/AS_TER/._terminator.C | Bin 0 -> 280 bytes
src/AS_TER/analyzePosMap.H | 6 +-
src/AS_TER/buildPosMap.C | 13 +-
src/AS_TER/demotePosMap.C | 4 +-
src/AS_TER/posmap-to-gff3.pl | 109 +
src/AS_UID/._Makefile | Bin 0 -> 280 bytes
src/AS_UID/._SYS_UIDclient.H | Bin 0 -> 280 bytes
src/AS_UID/._SYS_UIDclient_JTC.C | Bin 0 -> 280 bytes
src/AS_UID/._SYS_UIDclient_LOCAL.C | Bin 0 -> 280 bytes
src/AS_UID/._SYS_UIDclient_SERVER.C | Bin 0 -> 280 bytes
src/AS_UID/._uidclient.C | Bin 0 -> 280 bytes
src/AS_UID/._uidserver.C | Bin 0 -> 280 bytes
src/AS_UID/._uidserver_common.H | Bin 0 -> 280 bytes
src/AS_UTL/._AS_UTL_GPL.C | Bin 0 -> 280 bytes
src/AS_UTL/._AS_UTL_GPL.H | Bin 0 -> 280 bytes
src/AS_UTL/._AS_UTL_Hash.C | Bin 0 -> 280 bytes
src/AS_UTL/._AS_UTL_Hash.H | Bin 0 -> 280 bytes
src/AS_UTL/._AS_UTL_IID.H | Bin 0 -> 280 bytes
src/AS_UTL/._AS_UTL_UID.C | Bin 0 -> 280 bytes
src/AS_UTL/._AS_UTL_UID.H | Bin 0 -> 280 bytes
src/AS_UTL/._AS_UTL_Var.C | Bin 0 -> 280 bytes
src/AS_UTL/._AS_UTL_Var.H | Bin 0 -> 280 bytes
src/AS_UTL/._AS_UTL_alloc.C | Bin 0 -> 280 bytes
src/AS_UTL/._AS_UTL_alloc.H | Bin 0 -> 280 bytes
src/AS_UTL/._AS_UTL_decodeRange.C | Bin 0 -> 280 bytes
src/AS_UTL/._AS_UTL_decodeRange.H | Bin 0 -> 280 bytes
src/AS_UTL/._AS_UTL_extractMSG | Bin 0 -> 280 bytes
src/AS_UTL/._AS_UTL_extractMSG.awk | Bin 0 -> 280 bytes
src/AS_UTL/._AS_UTL_fasta.C | Bin 0 -> 280 bytes
src/AS_UTL/._AS_UTL_fasta.H | Bin 0 -> 280 bytes
src/AS_UTL/._AS_UTL_fileIO.C | Bin 0 -> 280 bytes
src/AS_UTL/._AS_UTL_fileIO.H | Bin 0 -> 280 bytes
src/AS_UTL/._AS_UTL_heap.C | Bin 0 -> 280 bytes
src/AS_UTL/._AS_UTL_heap.H | Bin 0 -> 280 bytes
src/AS_UTL/._AS_UTL_histo.C | Bin 0 -> 280 bytes
src/AS_UTL/._AS_UTL_histo.H | Bin 0 -> 280 bytes
src/AS_UTL/._AS_UTL_interval.C | Bin 0 -> 280 bytes
src/AS_UTL/._AS_UTL_interval.H | Bin 0 -> 280 bytes
src/AS_UTL/._AS_UTL_param_proc.C | Bin 0 -> 280 bytes
src/AS_UTL/._AS_UTL_param_proc.H | Bin 0 -> 280 bytes
src/AS_UTL/._AS_UTL_rand.C | Bin 0 -> 280 bytes
src/AS_UTL/._AS_UTL_rand.H | Bin 0 -> 280 bytes
src/AS_UTL/._AS_UTL_reverseComplement.C | Bin 0 -> 280 bytes
src/AS_UTL/._AS_UTL_reverseComplement.H | Bin 0 -> 280 bytes
src/AS_UTL/._AS_UTL_skiplist.C | Bin 0 -> 280 bytes
src/AS_UTL/._AS_UTL_skiplist.H | Bin 0 -> 280 bytes
src/AS_UTL/._AS_UTL_skiplist_test.C | Bin 0 -> 280 bytes
src/AS_UTL/._AS_UTL_stackTrace.C | Bin 0 -> 280 bytes
src/AS_UTL/._AS_UTL_stackTrace.H | Bin 0 -> 280 bytes
src/AS_UTL/._AS_UTL_stackTraceTest.C | Bin 0 -> 280 bytes
src/AS_UTL/._AS_UTL_testhisto.C | Bin 0 -> 280 bytes
src/AS_UTL/._Makefile | Bin 0 -> 280 bytes
src/AS_UTL/._UnionFind_AS.C | Bin 0 -> 280 bytes
src/AS_UTL/._UnionFind_AS.H | Bin 0 -> 280 bytes
src/AS_UTL/._extractMSG | Bin 0 -> 280 bytes
src/AS_UTL/._testHashTable.C | Bin 0 -> 280 bytes
src/AS_UTL/._testRand.C | Bin 0 -> 280 bytes
src/AS_UTL/._testVar.C | Bin 0 -> 280 bytes
src/AS_UTL/AS_UTL_alloc.H | 6 +-
src/AS_UTL/AS_UTL_fileIO.C | 3 +-
src/AS_UTL/AS_UTL_intervalList.C | 510 --
src/AS_UTL/AS_UTL_intervalList.H | 173 -
src/AS_UTL/AS_UTL_intervalListTest.C | 63 -
src/AS_UTL/AS_UTL_splitToWords.H | 139 -
src/AS_UTL/Makefile | 1 -
src/AS_VWR/._Makefile | Bin 0 -> 280 bytes
src/AS_VWR/._agrep.c | Bin 0 -> 280 bytes
src/AS_VWR/._agrep.h | Bin 0 -> 280 bytes
src/AS_VWR/._button.c | Bin 0 -> 280 bytes
src/AS_VWR/._button.h | Bin 0 -> 280 bytes
src/AS_VWR/._celagram.c | Bin 0 -> 280 bytes
src/AS_VWR/._celamy.c | Bin 0 -> 280 bytes
src/AS_VWR/._gendata.c | Bin 0 -> 280 bytes
src/AS_VWR/._hash.c | Bin 0 -> 280 bytes
src/AS_VWR/._hash.h | Bin 0 -> 280 bytes
src/AS_VWR/._layout.c | Bin 0 -> 280 bytes
src/AS_VWR/._layout.h | Bin 0 -> 280 bytes
src/AS_VWR/._layout_uint.c | Bin 0 -> 280 bytes
src/AS_VWR/._nata1 | Bin 0 -> 280 bytes
src/AS_VWR/._nata2.5 | Bin 0 -> 280 bytes
src/AS_VWR/._nata2.7 | Bin 0 -> 280 bytes
src/AS_VWR/._nata3 | Bin 0 -> 280 bytes
src/AS_VWR/._nata4 | Bin 0 -> 280 bytes
src/AS_VWR/._query_celamy.c | Bin 0 -> 280 bytes
src/AS_VWR/._wpack.c | Bin 0 -> 280 bytes
src/AS_VWR/._wpack.h | Bin 0 -> 280 bytes
src/AS_global.C | 2 +-
src/AS_global.H | 64 +-
src/c_make.as | 72 +-
1360 files changed, 27870 insertions(+), 90786 deletions(-)
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