[med-svn] [soapdenovo2] 03/09: Imported Upstream version 223+dfsg
Sascha Steinbiss
sascha at steinbiss.name
Fri May 27 22:37:08 UTC 2016
This is an automated email from the git hooks/post-receive script.
sascha-guest pushed a commit to branch master
in repository soapdenovo2.
commit 4422d01c23cc44b5e6103eb5209074cecd69b6d1
Author: Sascha Steinbiss <sascha at steinbiss.name>
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 b/standardPregraph/inc/knetfile.h
old mode 100755
new mode 100644
diff --git a/standardPregraph/inc/kstring.h b/standardPregraph/inc/kstring.h
old mode 100755
new mode 100644
diff --git a/standardPregraph/inc/libbam.a b/standardPregraph/inc/libbam.a
deleted file mode 100755
index d86ebe0..0000000
Binary files a/standardPregraph/inc/libbam.a and /dev/null differ
diff --git a/standardPregraph/inc/libbammac.a b/standardPregraph/inc/libbammac.a
deleted file mode 100755
index e3ef7a4..0000000
Binary files a/standardPregraph/inc/libbammac.a and /dev/null differ
diff --git a/standardPregraph/inc/newhash.h b/standardPregraph/inc/newhash.h
old mode 100755
new mode 100644
diff --git a/standardPregraph/inc/nuc.h b/standardPregraph/inc/nuc.h
old mode 100755
new mode 100644
diff --git a/standardPregraph/inc/razf.h b/standardPregraph/inc/razf.h
old mode 100755
new mode 100644
diff --git a/standardPregraph/inc/sam.h b/standardPregraph/inc/sam.h
old mode 100755
new mode 100644
diff --git 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
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diff --git a/standardPregraph/prlReadFillGap.c b/standardPregraph/prlReadFillGap.c
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diff --git a/standardPregraph/read2edge.c b/standardPregraph/read2edge.c
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diff --git a/standardPregraph/read2scaf.c b/standardPregraph/read2scaf.c
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diff --git a/standardPregraph/readInterval.c b/standardPregraph/readInterval.c
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diff --git a/standardPregraph/readseq1by1.c b/standardPregraph/readseq1by1.c
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diff --git a/standardPregraph/scaffold.c b/standardPregraph/scaffold.c
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diff --git a/standardPregraph/searchPath.c b/standardPregraph/searchPath.c
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diff --git a/standardPregraph/seperateScaff.pl b/standardPregraph/seperateScaff.pl
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diff --git a/standardPregraph/seq.c b/standardPregraph/seq.c
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diff --git a/standardPregraph/splitReps.c b/standardPregraph/splitReps.c
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diff --git a/standardPregraph/stack.c b/standardPregraph/stack.c
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diff --git a/update.log b/update.log
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--
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