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commit 4422d01c23cc44b5e6103eb5209074cecd69b6d1 Author: Sascha Steinbiss <[email protected]> Date: Fri May 27 20:23:28 2016 +0000 Imported Upstream version 223+dfsg --- LICENSE | 0 MANUAL | 0 sparsePregraph/Makefile | 4 ++-- sparsePregraph/build_edge.cpp | 0 sparsePregraph/build_graph.cpp | 0 sparsePregraph/build_preArc.cpp | 0 sparsePregraph/convert_soapdenovo.cpp | 0 sparsePregraph/global.cpp | 0 sparsePregraph/inc/bam.h | 0 sparsePregraph/inc/bgzf.h | 0 sparsePregraph/inc/build_edge.h | 0 sparsePregraph/inc/build_graph.h | 0 sparsePregraph/inc/build_preArc.h | 0 sparsePregraph/inc/convert_soapdenovo.h | 0 sparsePregraph/inc/core.h | 0 sparsePregraph/inc/faidx.h | 0 sparsePregraph/inc/glf.h | 0 sparsePregraph/inc/global.h | 0 sparsePregraph/inc/io_func.h | 0 sparsePregraph/inc/knetfile.h | 0 sparsePregraph/inc/kstring.h | 0 sparsePregraph/inc/libbam.a | Bin 872084 -> 0 bytes sparsePregraph/inc/libbammac.a | Bin 636664 -> 0 bytes sparsePregraph/inc/multi_threads.h | 0 sparsePregraph/inc/razf.h | 0 sparsePregraph/inc/sam.h | 0 sparsePregraph/inc/sam_header.h | 0 sparsePregraph/inc/sam_view.h | 0 sparsePregraph/inc/seq_util.h | 0 sparsePregraph/inc/sparse_kmer.h | 0 sparsePregraph/inc/spinLock.h | 0 sparsePregraph/inc/stdinc.h | 0 sparsePregraph/inc/xcurses.h | 0 sparsePregraph/inc/zconf.h | 0 sparsePregraph/inc/zlib.h | 0 sparsePregraph/io_func.cpp | 0 sparsePregraph/make.sh | 0 sparsePregraph/multi_threads.cpp | 0 sparsePregraph/pregraph_sparse.cpp | 0 standardPregraph/INSTALL | 0 standardPregraph/Makefile | 12 ++++++------ standardPregraph/VERSION | 0 standardPregraph/arc.c | 0 standardPregraph/attachPEinfo.c | 0 standardPregraph/bubble.c | 0 standardPregraph/change.log | 0 standardPregraph/check.c | 0 standardPregraph/compactEdge.c | 0 standardPregraph/concatenateEdge.c | 0 standardPregraph/connect.c | 0 standardPregraph/contig.c | 0 standardPregraph/cutTipPreGraph.c | 0 standardPregraph/cutTip_graph.c | 0 standardPregraph/cutTip_graph2.c | 0 standardPregraph/darray.c | 0 standardPregraph/dfib.c | 0 standardPregraph/dfibHeap.c | 0 standardPregraph/fib.c | 0 standardPregraph/fibHeap.c | 0 standardPregraph/hashFunction.c | 0 standardPregraph/inc/bam.h | 0 standardPregraph/inc/bgzf.h | 0 standardPregraph/inc/check.h | 0 standardPregraph/inc/darray.h | 0 standardPregraph/inc/def.h | 0 standardPregraph/inc/def2.h | 0 standardPregraph/inc/dfib.h | 0 standardPregraph/inc/dfibHeap.h | 0 standardPregraph/inc/dfibpriv.h | 0 standardPregraph/inc/extfunc.h | 0 standardPregraph/inc/extfunc2.h | 0 standardPregraph/inc/extvab.h | 0 standardPregraph/inc/faidx.h | 0 standardPregraph/inc/fib.h | 0 standardPregraph/inc/fibHeap.h | 0 standardPregraph/inc/fibpriv.h | 0 standardPregraph/inc/glf.h | 0 standardPregraph/inc/global.h | 0 standardPregraph/inc/kmerhash.h | 0 standardPregraph/inc/knetfile.h | 0 standardPregraph/inc/kstring.h | 0 standardPregraph/inc/libbam.a | Bin 872084 -> 0 bytes standardPregraph/inc/libbammac.a | Bin 636664 -> 0 bytes standardPregraph/inc/newhash.h | 0 standardPregraph/inc/nuc.h | 0 standardPregraph/inc/razf.h | 0 standardPregraph/inc/sam.h | 0 standardPregraph/inc/sam_header.h | 0 standardPregraph/inc/sam_view.h | 0 standardPregraph/inc/stack.h | 0 standardPregraph/inc/stdinc.h | 0 standardPregraph/inc/types.h | 0 standardPregraph/inc/xcurses.h | 0 standardPregraph/inc/zconf.h | 0 standardPregraph/inc/zlib.h | 0 standardPregraph/iterate.c | 0 standardPregraph/kmer.c | 0 standardPregraph/kmerhash.c | 0 standardPregraph/lib.c | 0 standardPregraph/linearEdge.c | 0 standardPregraph/loadGraph.c | 0 standardPregraph/loadPath.c | 0 standardPregraph/loadPreGraph.c | 0 standardPregraph/localAsm.c | 0 standardPregraph/main.c | 0 standardPregraph/make.sh | 0 standardPregraph/makeclean.sh | 0 standardPregraph/map.c | 0 standardPregraph/mem_manager.c | 0 standardPregraph/newhash.c | 0 standardPregraph/node2edge.c | 0 standardPregraph/orderContig.c | 0 standardPregraph/output_contig.c | 0 standardPregraph/output_pregraph.c | 0 standardPregraph/output_scaffold.c | 0 standardPregraph/pregraph.c | 0 standardPregraph/prlHashCtg.c | 0 standardPregraph/prlHashReads.c | 0 standardPregraph/prlRead2Ctg.c | 0 standardPregraph/prlRead2path.c | 0 standardPregraph/prlReadFillGap.c | 0 standardPregraph/read2edge.c | 0 standardPregraph/read2scaf.c | 0 standardPregraph/readInterval.c | 0 standardPregraph/readseq1by1.c | 0 standardPregraph/scaffold.c | 0 standardPregraph/searchPath.c | 0 standardPregraph/seperateScaff.pl | 0 standardPregraph/seq.c | 0 standardPregraph/splitReps.c | 0 standardPregraph/stack.c | 0 update.log | 0 132 files changed, 8 insertions(+), 8 deletions(-) diff --git a/LICENSE b/LICENSE old mode 100755 new mode 100644 diff --git a/MANUAL b/MANUAL old mode 100755 new mode 100644 diff --git a/sparsePregraph/Makefile b/sparsePregraph/Makefile old mode 100755 new mode 100644 index 243c5f0..da6a391 --- a/sparsePregraph/Makefile +++ b/sparsePregraph/Makefile @@ -1,4 +1,4 @@ -CC= /opt/blc/gcc-4.5.0/bin/gcc #gcc +CC= gcc CFLAGS= -O4 -fomit-frame-pointer #-static #-mcrc32 -march=core2 -msse4.1 -msse4.2 DFLAGS= OBJS= build_graph.o build_edge.o multi_threads.o \ @@ -76,5 +76,5 @@ clean: @printf "$(PROG) cleaning done.\n"; install: - @cp $(PROG) ../bin/ + @mkdir -p ../bin; cp $(PROG) ../bin/ @printf "$(PROG) installed at ../bin/$(PROG)\n" diff --git a/sparsePregraph/build_edge.cpp b/sparsePregraph/build_edge.cpp old mode 100755 new mode 100644 diff --git a/sparsePregraph/build_graph.cpp b/sparsePregraph/build_graph.cpp old mode 100755 new mode 100644 diff --git a/sparsePregraph/build_preArc.cpp b/sparsePregraph/build_preArc.cpp old mode 100755 new mode 100644 diff --git a/sparsePregraph/convert_soapdenovo.cpp b/sparsePregraph/convert_soapdenovo.cpp old mode 100755 new mode 100644 diff --git a/sparsePregraph/global.cpp b/sparsePregraph/global.cpp old mode 100755 new mode 100644 diff --git a/sparsePregraph/inc/bam.h b/sparsePregraph/inc/bam.h old mode 100755 new mode 100644 diff --git a/sparsePregraph/inc/bgzf.h b/sparsePregraph/inc/bgzf.h old mode 100755 new mode 100644 diff --git a/sparsePregraph/inc/build_edge.h b/sparsePregraph/inc/build_edge.h old mode 100755 new mode 100644 diff --git a/sparsePregraph/inc/build_graph.h b/sparsePregraph/inc/build_graph.h old mode 100755 new mode 100644 diff --git a/sparsePregraph/inc/build_preArc.h b/sparsePregraph/inc/build_preArc.h old mode 100755 new mode 100644 diff --git a/sparsePregraph/inc/convert_soapdenovo.h b/sparsePregraph/inc/convert_soapdenovo.h old mode 100755 new mode 100644 diff --git a/sparsePregraph/inc/core.h b/sparsePregraph/inc/core.h old mode 100755 new mode 100644 diff --git a/sparsePregraph/inc/faidx.h b/sparsePregraph/inc/faidx.h old mode 100755 new mode 100644 diff --git a/sparsePregraph/inc/glf.h b/sparsePregraph/inc/glf.h old mode 100755 new mode 100644 diff --git a/sparsePregraph/inc/global.h b/sparsePregraph/inc/global.h old mode 100755 new mode 100644 diff --git a/sparsePregraph/inc/io_func.h b/sparsePregraph/inc/io_func.h old mode 100755 new mode 100644 diff --git a/sparsePregraph/inc/knetfile.h b/sparsePregraph/inc/knetfile.h old mode 100755 new mode 100644 diff --git a/sparsePregraph/inc/kstring.h b/sparsePregraph/inc/kstring.h old mode 100755 new mode 100644 diff --git a/sparsePregraph/inc/libbam.a b/sparsePregraph/inc/libbam.a deleted file mode 100755 index d86ebe0..0000000 Binary files a/sparsePregraph/inc/libbam.a and /dev/null differ diff --git a/sparsePregraph/inc/libbammac.a b/sparsePregraph/inc/libbammac.a deleted file mode 100755 index e3ef7a4..0000000 Binary files a/sparsePregraph/inc/libbammac.a and /dev/null differ diff --git a/sparsePregraph/inc/multi_threads.h b/sparsePregraph/inc/multi_threads.h old mode 100755 new mode 100644 diff --git a/sparsePregraph/inc/razf.h b/sparsePregraph/inc/razf.h old mode 100755 new mode 100644 diff --git a/sparsePregraph/inc/sam.h b/sparsePregraph/inc/sam.h old mode 100755 new mode 100644 diff --git a/sparsePregraph/inc/sam_header.h b/sparsePregraph/inc/sam_header.h old mode 100755 new mode 100644 diff --git a/sparsePregraph/inc/sam_view.h b/sparsePregraph/inc/sam_view.h old mode 100755 new mode 100644 diff --git a/sparsePregraph/inc/seq_util.h b/sparsePregraph/inc/seq_util.h old mode 100755 new mode 100644 diff --git a/sparsePregraph/inc/sparse_kmer.h b/sparsePregraph/inc/sparse_kmer.h old mode 100755 new mode 100644 diff --git a/sparsePregraph/inc/spinLock.h b/sparsePregraph/inc/spinLock.h old mode 100755 new mode 100644 diff --git a/sparsePregraph/inc/stdinc.h b/sparsePregraph/inc/stdinc.h old mode 100755 new mode 100644 diff --git a/sparsePregraph/inc/xcurses.h b/sparsePregraph/inc/xcurses.h old mode 100755 new mode 100644 diff --git a/sparsePregraph/inc/zconf.h b/sparsePregraph/inc/zconf.h old mode 100755 new mode 100644 diff --git a/sparsePregraph/inc/zlib.h b/sparsePregraph/inc/zlib.h old mode 100755 new mode 100644 diff --git a/sparsePregraph/io_func.cpp b/sparsePregraph/io_func.cpp old mode 100755 new mode 100644 diff --git a/sparsePregraph/make.sh b/sparsePregraph/make.sh old mode 100755 new mode 100644 diff --git a/sparsePregraph/multi_threads.cpp b/sparsePregraph/multi_threads.cpp old mode 100755 new mode 100644 diff --git a/sparsePregraph/pregraph_sparse.cpp b/sparsePregraph/pregraph_sparse.cpp old mode 100755 new mode 100644 diff --git a/standardPregraph/INSTALL b/standardPregraph/INSTALL old mode 100755 new mode 100644 diff --git a/standardPregraph/Makefile b/standardPregraph/Makefile old mode 100755 new mode 100644 index ab21d62..a8affc8 --- a/standardPregraph/Makefile +++ b/standardPregraph/Makefile @@ -5,9 +5,9 @@ # ################################### -CC= /opt/blc/gcc-4.5.0/bin/gcc #gcc -GCCVERSIONMAJOR := $(shell expr `$(CC) -dumpversion | cut -f1 -d.` \>= 4) -GCCVERSIONMINOR := $(shell expr `$(CC) -dumpversion | cut -f2 -d.` \>= 4) +CC= gcc +#GCCVERSIONMAJOR := $(shell expr `$(CC) -dumpversion | cut -f1 -d.` \>= 4) +#GCCVERSIONMINOR := $(shell expr `$(CC) -dumpversion | cut -f2 -d.` \>= 4) CFLAGS= -O4 -fomit-frame-pointer #-static #-mcrc32 -march=core2 -msse4.1 -msse4.2 DFLAGS= OBJS= arc.o attachPEinfo.o bubble.o check.o compactEdge.o \ @@ -78,8 +78,8 @@ all: clean SOAPdenovo envTest: @test $(BIT_ERR) != 1 || sh -c 'echo "Fatal: 64bit CPU and Operating System required!";false;' - @test $(GCCVERSIONMAJOR) == 1 || sh -c 'echo "GCC version lower than 4.4.0";false;' - @test $(GCCVERSIONMINOR) == 1 || sh -c 'echo "GCC version lower than 4.4.0";false;' +# @test $(GCCVERSIONMAJOR) == 1 || sh -c 'echo "GCC version lower than 4.4.0";false;' +# @test $(GCCVERSIONMINOR) == 1 || sh -c 'echo "GCC version lower than 4.4.0";false;' SOAPdenovo: envTest $(OBJS) @printf "Linking... \r" @@ -91,5 +91,5 @@ clean: @printf "$(PROG) cleaning done.\n"; install: - @cp $(PROG) ../bin/ + @mkdir -p ../bin; cp $(PROG) ../bin/ @printf "$(PROG) installed at ../bin/$(PROG)\n" diff --git a/standardPregraph/VERSION b/standardPregraph/VERSION old mode 100755 new mode 100644 diff --git a/standardPregraph/arc.c b/standardPregraph/arc.c old mode 100755 new mode 100644 diff --git a/standardPregraph/attachPEinfo.c b/standardPregraph/attachPEinfo.c old mode 100755 new mode 100644 diff --git a/standardPregraph/bubble.c b/standardPregraph/bubble.c old mode 100755 new mode 100644 diff --git a/standardPregraph/change.log b/standardPregraph/change.log old mode 100755 new mode 100644 diff --git a/standardPregraph/check.c b/standardPregraph/check.c old mode 100755 new mode 100644 diff --git a/standardPregraph/compactEdge.c b/standardPregraph/compactEdge.c old mode 100755 new mode 100644 diff --git a/standardPregraph/concatenateEdge.c b/standardPregraph/concatenateEdge.c old mode 100755 new mode 100644 diff --git a/standardPregraph/connect.c b/standardPregraph/connect.c old mode 100755 new mode 100644 diff --git a/standardPregraph/contig.c b/standardPregraph/contig.c old mode 100755 new mode 100644 diff --git a/standardPregraph/cutTipPreGraph.c b/standardPregraph/cutTipPreGraph.c old mode 100755 new mode 100644 diff --git a/standardPregraph/cutTip_graph.c b/standardPregraph/cutTip_graph.c old mode 100755 new mode 100644 diff --git a/standardPregraph/cutTip_graph2.c b/standardPregraph/cutTip_graph2.c old mode 100755 new mode 100644 diff --git a/standardPregraph/darray.c b/standardPregraph/darray.c old mode 100755 new mode 100644 diff --git a/standardPregraph/dfib.c b/standardPregraph/dfib.c old mode 100755 new mode 100644 diff --git a/standardPregraph/dfibHeap.c b/standardPregraph/dfibHeap.c old mode 100755 new mode 100644 diff --git a/standardPregraph/fib.c b/standardPregraph/fib.c old mode 100755 new mode 100644 diff --git a/standardPregraph/fibHeap.c b/standardPregraph/fibHeap.c old mode 100755 new mode 100644 diff --git a/standardPregraph/hashFunction.c b/standardPregraph/hashFunction.c old mode 100755 new mode 100644 diff --git a/standardPregraph/inc/bam.h b/standardPregraph/inc/bam.h old mode 100755 new mode 100644 diff --git a/standardPregraph/inc/bgzf.h b/standardPregraph/inc/bgzf.h old mode 100755 new mode 100644 diff --git a/standardPregraph/inc/check.h b/standardPregraph/inc/check.h old mode 100755 new mode 100644 diff --git a/standardPregraph/inc/darray.h b/standardPregraph/inc/darray.h old mode 100755 new mode 100644 diff --git a/standardPregraph/inc/def.h b/standardPregraph/inc/def.h old mode 100755 new mode 100644 diff --git a/standardPregraph/inc/def2.h b/standardPregraph/inc/def2.h old mode 100755 new mode 100644 diff --git a/standardPregraph/inc/dfib.h b/standardPregraph/inc/dfib.h old mode 100755 new mode 100644 diff --git a/standardPregraph/inc/dfibHeap.h b/standardPregraph/inc/dfibHeap.h old mode 100755 new mode 100644 diff --git a/standardPregraph/inc/dfibpriv.h b/standardPregraph/inc/dfibpriv.h old mode 100755 new mode 100644 diff --git a/standardPregraph/inc/extfunc.h b/standardPregraph/inc/extfunc.h old mode 100755 new mode 100644 diff --git a/standardPregraph/inc/extfunc2.h b/standardPregraph/inc/extfunc2.h old mode 100755 new mode 100644 diff --git a/standardPregraph/inc/extvab.h b/standardPregraph/inc/extvab.h old mode 100755 new mode 100644 diff --git a/standardPregraph/inc/faidx.h b/standardPregraph/inc/faidx.h old mode 100755 new mode 100644 diff --git a/standardPregraph/inc/fib.h b/standardPregraph/inc/fib.h old mode 100755 new mode 100644 diff --git a/standardPregraph/inc/fibHeap.h b/standardPregraph/inc/fibHeap.h old mode 100755 new mode 100644 diff --git a/standardPregraph/inc/fibpriv.h b/standardPregraph/inc/fibpriv.h old mode 100755 new mode 100644 diff --git a/standardPregraph/inc/glf.h b/standardPregraph/inc/glf.h old mode 100755 new mode 100644 diff --git a/standardPregraph/inc/global.h b/standardPregraph/inc/global.h old mode 100755 new mode 100644 diff --git a/standardPregraph/inc/kmerhash.h b/standardPregraph/inc/kmerhash.h old mode 100755 new mode 100644 diff --git a/standardPregraph/inc/knetfile.h 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a/standardPregraph/inc/sam_header.h b/standardPregraph/inc/sam_header.h old mode 100755 new mode 100644 diff --git a/standardPregraph/inc/sam_view.h b/standardPregraph/inc/sam_view.h old mode 100755 new mode 100644 diff --git a/standardPregraph/inc/stack.h b/standardPregraph/inc/stack.h old mode 100755 new mode 100644 diff --git a/standardPregraph/inc/stdinc.h b/standardPregraph/inc/stdinc.h old mode 100755 new mode 100644 diff --git a/standardPregraph/inc/types.h b/standardPregraph/inc/types.h old mode 100755 new mode 100644 diff --git a/standardPregraph/inc/xcurses.h b/standardPregraph/inc/xcurses.h old mode 100755 new mode 100644 diff --git a/standardPregraph/inc/zconf.h b/standardPregraph/inc/zconf.h old mode 100755 new mode 100644 diff --git a/standardPregraph/inc/zlib.h b/standardPregraph/inc/zlib.h old mode 100755 new mode 100644 diff --git a/standardPregraph/iterate.c b/standardPregraph/iterate.c old mode 100755 new mode 100644 diff --git a/standardPregraph/kmer.c b/standardPregraph/kmer.c old mode 100755 new mode 100644 diff --git a/standardPregraph/kmerhash.c b/standardPregraph/kmerhash.c old mode 100755 new mode 100644 diff --git a/standardPregraph/lib.c b/standardPregraph/lib.c old mode 100755 new mode 100644 diff --git a/standardPregraph/linearEdge.c b/standardPregraph/linearEdge.c old mode 100755 new mode 100644 diff --git a/standardPregraph/loadGraph.c b/standardPregraph/loadGraph.c old mode 100755 new mode 100644 diff --git a/standardPregraph/loadPath.c b/standardPregraph/loadPath.c old mode 100755 new mode 100644 diff --git a/standardPregraph/loadPreGraph.c b/standardPregraph/loadPreGraph.c old mode 100755 new mode 100644 diff --git a/standardPregraph/localAsm.c b/standardPregraph/localAsm.c old mode 100755 new mode 100644 diff --git a/standardPregraph/main.c b/standardPregraph/main.c old mode 100755 new mode 100644 diff --git a/standardPregraph/make.sh b/standardPregraph/make.sh old mode 100755 new mode 100644 diff --git a/standardPregraph/makeclean.sh b/standardPregraph/makeclean.sh old mode 100755 new mode 100644 diff --git a/standardPregraph/map.c b/standardPregraph/map.c old mode 100755 new mode 100644 diff --git a/standardPregraph/mem_manager.c b/standardPregraph/mem_manager.c old mode 100755 new mode 100644 diff --git a/standardPregraph/newhash.c b/standardPregraph/newhash.c old mode 100755 new mode 100644 diff --git a/standardPregraph/node2edge.c b/standardPregraph/node2edge.c old mode 100755 new mode 100644 diff --git a/standardPregraph/orderContig.c b/standardPregraph/orderContig.c old mode 100755 new mode 100644 diff --git a/standardPregraph/output_contig.c b/standardPregraph/output_contig.c old mode 100755 new mode 100644 diff --git a/standardPregraph/output_pregraph.c b/standardPregraph/output_pregraph.c old mode 100755 new mode 100644 diff --git a/standardPregraph/output_scaffold.c b/standardPregraph/output_scaffold.c old mode 100755 new mode 100644 diff --git a/standardPregraph/pregraph.c b/standardPregraph/pregraph.c old mode 100755 new mode 100644 diff --git a/standardPregraph/prlHashCtg.c b/standardPregraph/prlHashCtg.c old mode 100755 new mode 100644 diff --git a/standardPregraph/prlHashReads.c b/standardPregraph/prlHashReads.c old mode 100755 new mode 100644 diff --git a/standardPregraph/prlRead2Ctg.c b/standardPregraph/prlRead2Ctg.c old mode 100755 new mode 100644 diff --git a/standardPregraph/prlRead2path.c b/standardPregraph/prlRead2path.c old mode 100755 new mode 100644 diff --git a/standardPregraph/prlReadFillGap.c b/standardPregraph/prlReadFillGap.c old mode 100755 new mode 100644 diff --git a/standardPregraph/read2edge.c b/standardPregraph/read2edge.c old mode 100755 new mode 100644 diff --git a/standardPregraph/read2scaf.c b/standardPregraph/read2scaf.c old mode 100755 new mode 100644 diff --git a/standardPregraph/readInterval.c b/standardPregraph/readInterval.c old mode 100755 new mode 100644 diff --git a/standardPregraph/readseq1by1.c b/standardPregraph/readseq1by1.c old mode 100755 new mode 100644 diff --git a/standardPregraph/scaffold.c b/standardPregraph/scaffold.c old mode 100755 new mode 100644 diff --git a/standardPregraph/searchPath.c b/standardPregraph/searchPath.c old mode 100755 new mode 100644 diff --git a/standardPregraph/seperateScaff.pl b/standardPregraph/seperateScaff.pl old mode 100755 new mode 100644 diff --git a/standardPregraph/seq.c b/standardPregraph/seq.c old mode 100755 new mode 100644 diff --git a/standardPregraph/splitReps.c b/standardPregraph/splitReps.c old mode 100755 new mode 100644 diff --git a/standardPregraph/stack.c b/standardPregraph/stack.c old mode 100755 new mode 100644 diff --git a/update.log b/update.log old mode 100755 new mode 100644 -- 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] 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