[med-svn] [soapdenovo2] branch upstream updated (932cad1 -> 98dff73)
Andreas Tille
tille at debian.org
Wed Sep 6 08:50:55 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch upstream
in repository soapdenovo2.
from 932cad1 New upstream version 240+dfsg1
new 98dff73 New upstream version 241+dfsg
The 1 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails. The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.
Summary of changes:
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(-)
create mode 100755 fusion/Makefile
create mode 100644 fusion/attachPEinfo.c
create mode 100644 fusion/bundle.c
create mode 100644 fusion/check.c
create mode 100644 fusion/connect.c
create mode 100644 fusion/darray.c
create mode 100644 fusion/fib.c
create mode 100644 fusion/fibHeap.c
create mode 100755 fusion/finalFusion
create mode 100644 fusion/hashFunction.c
create mode 100755 fusion/inc/check.h
create mode 100644 fusion/inc/darray.h
create mode 100644 fusion/inc/def.h
create mode 100644 fusion/inc/def2.h
copy {standardPregraph => fusion}/inc/dfib.h (52%)
mode change 100644 => 100755
create mode 100644 fusion/inc/dfibHeap.h
create mode 100644 fusion/inc/dfibpriv.h
create mode 100644 fusion/inc/extfunc.h
create mode 100644 fusion/inc/extfunc2.h
create mode 100644 fusion/inc/extvab.h
create mode 100755 fusion/inc/fib.h
create mode 100644 fusion/inc/fibHeap.h
create mode 100644 fusion/inc/fibpriv.h
create mode 100644 fusion/inc/general.h
create mode 100644 fusion/inc/global.h
create mode 100644 fusion/inc/newhash.h
create mode 100644 fusion/inc/nuc.h
create mode 100644 fusion/inc/stack.h
create mode 100755 fusion/inc/stdinc.h
create mode 100755 fusion/inc/types.h
create mode 100644 fusion/kmer.c
create mode 100644 fusion/lib.c
create mode 100644 fusion/loadGraph.c
create mode 100644 fusion/localAsm.c
create mode 100644 fusion/main.c
create mode 100644 fusion/map.c
create mode 100644 fusion/mem_manager.c
create mode 100644 fusion/newhash.c
create mode 100644 fusion/orderContig.c
create mode 100644 fusion/output_scaffold.c
create mode 100644 fusion/potential.c
create mode 100644 fusion/prepare.c
create mode 100644 fusion/prlHashCtg.c
create mode 100644 fusion/prlRead2Ctg.c
create mode 100644 fusion/prlReadFillGap.c
create mode 100644 fusion/read2scaf.c
create mode 100644 fusion/readseq1by1.c
create mode 100644 fusion/scaffold.c
create mode 100644 fusion/searchPath.c
create mode 100644 fusion/seq.c
create mode 100644 fusion/stack.c
delete mode 100644 sparsePregraph/change.log
delete mode 100644 sparsePregraph/inc/xcurses.h.gch
delete mode 100644 update.log
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