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commit 6a0b6c23eee5508419e0710d00c66753856a9dcb Merge: fb6c745 98dff73 Author: Andreas Tille <[email protected]> Date: Wed Sep 6 10:04:08 2017 +0200 Updated version 241+dfsg from 'upstream/241+dfsg' with Debian dir fa43c6daeceb1cdf7d31d32e7df4fa55fc533805 Makefile | 31 +- README.md | 18 +- VERSION | 2 +- fusion/Makefile | 46 + fusion/attachPEinfo.c | 634 ++ fusion/bundle.c | 517 ++ fusion/check.c | 69 + fusion/connect.c | 194 + fusion/darray.c | 60 + fusion/fib.c | 691 ++ fusion/fibHeap.c | 77 + fusion/finalFusion | Bin 0 -> 316190 bytes fusion/hashFunction.c | 86 + fusion/inc/check.h | 5 + fusion/inc/darray.h | 23 + fusion/inc/def.h | 299 + fusion/inc/def2.h | 44 + {standardPregraph => fusion}/inc/dfib.h | 47 +- fusion/inc/dfibHeap.h | 43 + fusion/inc/dfibpriv.h | 97 + fusion/inc/extfunc.h | 209 + fusion/inc/extfunc2.h | 7 + fusion/inc/extvab.h | 92 + fusion/inc/fib.h | 81 + fusion/inc/fibHeap.h | 43 + fusion/inc/fibpriv.h | 112 + fusion/inc/general.h | 89 + fusion/inc/global.h | 74 + fusion/inc/newhash.h | 122 + fusion/inc/nuc.h | 14 + fusion/inc/stack.h | 35 + fusion/inc/stdinc.h | 40 + fusion/inc/types.h | 14 + fusion/kmer.c | 145 + fusion/lib.c | 438 + fusion/loadGraph.c | 494 + fusion/localAsm.c | 1976 ++++ fusion/main.c | 210 + fusion/map.c | 42 + fusion/mem_manager.c | 95 + fusion/newhash.c | 630 ++ fusion/orderContig.c | 4426 +++++++++ fusion/output_scaffold.c | 76 + fusion/potential.c | 268 + fusion/prepare.c | 254 + fusion/prlHashCtg.c | 387 + fusion/prlRead2Ctg.c | 1090 +++ fusion/prlReadFillGap.c | 1234 +++ fusion/read2scaf.c | 294 + fusion/readseq1by1.c | 591 ++ fusion/scaffold.c | 62 + fusion/searchPath.c | 205 + fusion/seq.c | 195 + fusion/stack.c | 132 + sparsePregraph/Makefile | 40 +- sparsePregraph/build_edge.cpp | 2504 +++--- sparsePregraph/build_graph.cpp | 1124 +-- sparsePregraph/build_preArc.cpp | 2019 ++--- sparsePregraph/change.log | 24 - sparsePregraph/convert_soapdenovo.cpp | 700 +- sparsePregraph/global.cpp | 24 +- sparsePregraph/inc/build_edge.h | 70 +- sparsePregraph/inc/build_graph.h | 10 +- sparsePregraph/inc/build_preArc.h | 152 +- sparsePregraph/inc/convert_soapdenovo.h | 6 +- sparsePregraph/inc/core.h | 164 +- sparsePregraph/inc/faidx.h | 104 +- sparsePregraph/inc/glf.h | 48 +- sparsePregraph/inc/global.h | 24 +- sparsePregraph/inc/io_func.h | 14 +- sparsePregraph/inc/knetfile.h | 66 +- sparsePregraph/inc/kstring.h | 66 +- sparsePregraph/inc/multi_threads.h | 28 +- sparsePregraph/inc/razf.h | 84 +- sparsePregraph/inc/sam_header.h | 18 +- sparsePregraph/inc/sam_view.h | 75 +- sparsePregraph/inc/seq_util.h | 891 +- sparsePregraph/inc/sparse_kmer.h | 447 +- sparsePregraph/inc/stdinc.h | 2 +- sparsePregraph/inc/xcurses.h | 1326 +-- sparsePregraph/inc/xcurses.h.gch | Bin 3154808 -> 0 bytes sparsePregraph/io_func.cpp | 1565 ++-- sparsePregraph/main.cpp | 8 +- sparsePregraph/multi_threads.cpp | 176 +- sparsePregraph/pregraph_sparse.cpp | 1197 +-- standardPregraph/Makefile | 32 +- standardPregraph/arc.c | 396 +- standardPregraph/attachPEinfo.c | 1028 +-- standardPregraph/bubble.c | 3440 +++---- standardPregraph/check.c | 172 +- standardPregraph/compactEdge.c | 182 +- standardPregraph/concatenateEdge.c | 526 +- standardPregraph/connect.c | 258 +- standardPregraph/contig.c | 492 +- standardPregraph/cutTipPreGraph.c | 1084 +-- standardPregraph/cutTip_graph.c | 810 +- standardPregraph/cutTip_graph2.c | 770 +- standardPregraph/darray.c | 88 +- standardPregraph/dfib.c | 866 +- standardPregraph/dfibHeap.c | 50 +- standardPregraph/fib.c | 1002 +-- standardPregraph/fibHeap.c | 38 +- standardPregraph/hashFunction.c | 190 +- standardPregraph/inc/check.h | 8 +- standardPregraph/inc/darray.h | 20 +- standardPregraph/inc/def.h | 340 +- standardPregraph/inc/def2.h | 34 +- standardPregraph/inc/dfib.h | 4 +- standardPregraph/inc/dfibHeap.h | 22 +- standardPregraph/inc/dfibpriv.h | 34 +- standardPregraph/inc/extfunc.h | 222 +- standardPregraph/inc/extfunc2.h | 10 +- standardPregraph/inc/extvab.h | 56 +- standardPregraph/inc/faidx.h | 104 +- standardPregraph/inc/fib.h | 10 +- standardPregraph/inc/fibHeap.h | 22 +- standardPregraph/inc/fibpriv.h | 58 +- standardPregraph/inc/glf.h | 48 +- standardPregraph/inc/global.h | 56 +- standardPregraph/inc/kmerhash.h | 48 +- standardPregraph/inc/knetfile.h | 66 +- standardPregraph/inc/kstring.h | 66 +- standardPregraph/inc/newhash.h | 68 +- standardPregraph/inc/nuc.h | 2 +- standardPregraph/inc/razf.h | 84 +- standardPregraph/inc/sam_header.h | 18 +- standardPregraph/inc/sam_view.h | 75 +- standardPregraph/inc/stack.h | 36 +- standardPregraph/inc/stdinc.h | 2 +- standardPregraph/inc/types.h | 2 +- standardPregraph/inc/xcurses.h | 1326 +-- standardPregraph/iterate.c | 4180 ++++----- standardPregraph/kmer.c | 921 +- standardPregraph/kmerhash.c | 678 +- standardPregraph/lib.c | 1128 +-- standardPregraph/linearEdge.c | 598 +- standardPregraph/loadGraph.c | 1042 +-- standardPregraph/loadPath.c | 522 +- standardPregraph/loadPreGraph.c | 1014 +-- standardPregraph/localAsm.c | 3997 ++++----- standardPregraph/main.c | 1008 ++- standardPregraph/map.c | 276 +- standardPregraph/mem_manager.c | 110 +- standardPregraph/newhash.c | 844 +- standardPregraph/node2edge.c | 1010 +-- standardPregraph/orderContig.c | 14376 ++++++++++++++++-------------- standardPregraph/output_contig.c | 691 +- standardPregraph/output_pregraph.c | 128 +- standardPregraph/output_scaffold.c | 120 +- standardPregraph/pregraph.c | 309 +- standardPregraph/prlHashCtg.c | 682 +- standardPregraph/prlHashReads.c | 1905 ++-- standardPregraph/prlRead2Ctg.c | 2178 ++--- standardPregraph/prlRead2path.c | 2312 ++--- standardPregraph/prlReadFillGap.c | 3516 ++++---- standardPregraph/read2edge.c | 2757 +++--- standardPregraph/read2scaf.c | 526 +- standardPregraph/readInterval.c | 46 +- standardPregraph/readseq1by1.c | 2350 ++--- standardPregraph/scaffold.c | 343 +- standardPregraph/searchPath.c | 416 +- standardPregraph/seq.c | 204 +- standardPregraph/splitReps.c | 868 +- standardPregraph/stack.c | 236 +- update.log | 91 - 165 files changed, 57227 insertions(+), 38555 deletions(-) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/soapdenovo2.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
