[med-svn] [soapdenovo2] 02/03: Updated version 241+dfsg from 'upstream/241+dfsg'
Andreas Tille
tille at debian.org
Wed Sep 6 08:50:54 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository soapdenovo2.
commit 6a0b6c23eee5508419e0710d00c66753856a9dcb
Merge: fb6c745 98dff73
Author: Andreas Tille <tille at debian.org>
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(-)
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