diff -Nru velvet-1.1.06~nozlibcopy/ChangeLog velvet-1.1.07~nozlibcopy/ChangeLog --- velvet-1.1.06~nozlibcopy/ChangeLog 2011-09-15 13:06:39.000000000 +0000 +++ velvet-1.1.07~nozlibcopy/ChangeLog 2011-12-05 17:53:32.000000000 +0000 @@ -402,3 +402,12 @@ - Added gap mask in Columbus - Offsets used in kmerOccurenceTable to accelerate searches - Some memory leaks + +V 1.1.07 +- Concurrency issues in Columbus +- Pairing bug for odd number of reads +- Variable size in reading sequence lengths +- Ubuntu patch to Makefile + +V 1.1.08 +- Added conserveLong option diff -Nru velvet-1.1.06~nozlibcopy/debian/changelog velvet-1.1.07~nozlibcopy/debian/changelog --- velvet-1.1.06~nozlibcopy/debian/changelog 2011-11-02 12:57:12.000000000 +0000 +++ velvet-1.1.07~nozlibcopy/debian/changelog 2011-12-09 05:08:03.000000000 +0000 @@ -1,20 +1,11 @@ -velvet (1.1.06~nozlibcopy-1ubuntu3) precise; urgency=low +velvet (1.1.07~nozlibcopy-1) unstable; urgency=low - * Add Pre-Depends for xz compression to *all* binaries. + * New upstream release (Closes: #647415). + * debian/contol: + - Pre-Depends on dpkg (>= 1.15.6) for Ubuntu LTS. + - Removed Multi-Arch: foreign. - -- Ilya Barygin Wed, 02 Nov 2011 16:56:51 +0400 - -velvet (1.1.06~nozlibcopy-1ubuntu2) precise; urgency=low - - * Add Pre-Depends for xz compression. - - -- Ilya Barygin Wed, 02 Nov 2011 16:39:02 +0400 - -velvet (1.1.06~nozlibcopy-1ubuntu1) precise; urgency=low - - * Fix FTBFS with --as-needed linker option. - - -- Ilya Barygin Wed, 02 Nov 2011 16:20:35 +0400 + -- Charles Plessy Fri, 09 Dec 2011 14:07:58 +0900 velvet (1.1.06~nozlibcopy-1) unstable; urgency=low diff -Nru velvet-1.1.06~nozlibcopy/debian/control velvet-1.1.07~nozlibcopy/debian/control --- velvet-1.1.06~nozlibcopy/debian/control 2011-11-02 12:56:45.000000000 +0000 +++ velvet-1.1.07~nozlibcopy/debian/control 2011-12-09 05:07:30.000000000 +0000 @@ -1,8 +1,7 @@ Source: velvet Section: science Priority: optional -Maintainer: Ubuntu Developers -XSBC-Original-Maintainer: Debian Med Packaging Team +Maintainer: Debian Med Packaging Team DM-Upload-Allowed: yes Uploaders: Charles Plessy , Andreas Tille @@ -14,7 +13,6 @@ Package: velvet Architecture: any -Multi-Arch: foreign Pre-Depends: dpkg (>= 1.15.6) Depends: ${shlibs:Depends}, ${misc:Depends} Recommends: python diff -Nru velvet-1.1.06~nozlibcopy/debian/patches/as-needed.patch velvet-1.1.07~nozlibcopy/debian/patches/as-needed.patch --- velvet-1.1.06~nozlibcopy/debian/patches/as-needed.patch 2011-11-02 12:21:32.000000000 +0000 +++ velvet-1.1.07~nozlibcopy/debian/patches/as-needed.patch 1970-01-01 00:00:00.000000000 +0000 @@ -1,49 +0,0 @@ -Description: fix FTBFS with --as-needed linker option -Author: Ilya Barygin - ---- velvet-1.1.06~nozlibcopy.orig/Makefile -+++ velvet-1.1.06~nozlibcopy/Makefile -@@ -1,7 +1,7 @@ - CC = gcc - CFLAGS = -Wall - DEBUG = -g --LDFLAGS = -lm -+LIBS = -lm - OPT = -O3 - MAXKMERLENGTH=31 - CATEGORIES=2 -@@ -67,26 +67,26 @@ clean-zlib : - endif - - velveth : obj -- $(CC) $(CFLAGS) $(OPT) $(LDFLAGS) -o velveth obj/tightString.o obj/run.o obj/recycleBin.o obj/splay.o obj/splayTable.o obj/readSet.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o $(Z_LIB_FILES) -+ $(CC) $(CFLAGS) $(OPT) $(LDFLAGS) -o velveth obj/tightString.o obj/run.o obj/recycleBin.o obj/splay.o obj/splayTable.o obj/readSet.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o $(Z_LIB_FILES) $(LIBS) - - - velvetg : obj -- $(CC) $(CFLAGS) $(OPT) $(LDFLAGS) -o velvetg obj/tightString.o obj/graph.o obj/run2.o obj/fibHeap.o obj/fib.o obj/concatenatedGraph.o obj/passageMarker.o obj/graphStats.o obj/correctedGraph.o obj/dfib.o obj/dfibHeap.o obj/recycleBin.o obj/readSet.o obj/shortReadPairs.o obj/scaffold.o obj/locallyCorrectedGraph.o obj/graphReConstruction.o obj/roadMap.o obj/preGraph.o obj/preGraphConstruction.o obj/concatenatedPreGraph.o obj/readCoherentGraph.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/allocArray.o $(Z_LIB_FILES) -+ $(CC) $(CFLAGS) $(OPT) $(LDFLAGS) -o velvetg obj/tightString.o obj/graph.o obj/run2.o obj/fibHeap.o obj/fib.o obj/concatenatedGraph.o obj/passageMarker.o obj/graphStats.o obj/correctedGraph.o obj/dfib.o obj/dfibHeap.o obj/recycleBin.o obj/readSet.o obj/shortReadPairs.o obj/scaffold.o obj/locallyCorrectedGraph.o obj/graphReConstruction.o obj/roadMap.o obj/preGraph.o obj/preGraphConstruction.o obj/concatenatedPreGraph.o obj/readCoherentGraph.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/allocArray.o $(Z_LIB_FILES) $(LIBS) - - debug : override DEF := $(DEF) -D DEBUG - debug : cleanobj obj/dbg -- $(CC) $(CFLAGS) $(LDFLAGS) $(DEBUG) -o velveth obj/dbg/tightString.o obj/dbg/run.o obj/dbg/recycleBin.o obj/dbg/splay.o obj/dbg/splayTable.o obj/dbg/readSet.o obj/dbg/utility.o obj/dbg/kmer.o obj/dbg/kmerOccurenceTable.o obj/dbg/allocArray.o $(Z_LIB_FILES) -- $(CC) $(CFLAGS) $(LDFLAGS) $(DEBUG) -o velvetg obj/dbg/tightString.o obj/dbg/graph.o obj/dbg/run2.o obj/dbg/fibHeap.o obj/dbg/fib.o obj/dbg/concatenatedGraph.o obj/dbg/passageMarker.o obj/dbg/graphStats.o obj/dbg/correctedGraph.o obj/dbg/dfib.o obj/dbg/dfibHeap.o obj/dbg/recycleBin.o obj/dbg/readSet.o obj/dbg/shortReadPairs.o obj/dbg/scaffold.o obj/dbg/locallyCorrectedGraph.o obj/dbg/graphReConstruction.o obj/dbg/roadMap.o obj/dbg/preGraph.o obj/dbg/preGraphConstruction.o obj/dbg/concatenatedPreGraph.o obj/dbg/readCoherentGraph.o obj/dbg/utility.o obj/dbg/kmer.o obj/dbg/kmerOccurenceTable.o obj/dbg/allocArray.o $(Z_LIB_FILES) -+ $(CC) $(CFLAGS) $(LDFLAGS) $(DEBUG) -o velveth obj/dbg/tightString.o obj/dbg/run.o obj/dbg/recycleBin.o obj/dbg/splay.o obj/dbg/splayTable.o obj/dbg/readSet.o obj/dbg/utility.o obj/dbg/kmer.o obj/dbg/kmerOccurenceTable.o obj/dbg/allocArray.o $(Z_LIB_FILES) $(LIBS) -+ $(CC) $(CFLAGS) $(LDFLAGS) $(DEBUG) -o velvetg obj/dbg/tightString.o obj/dbg/graph.o obj/dbg/run2.o obj/dbg/fibHeap.o obj/dbg/fib.o obj/dbg/concatenatedGraph.o obj/dbg/passageMarker.o obj/dbg/graphStats.o obj/dbg/correctedGraph.o obj/dbg/dfib.o obj/dbg/dfibHeap.o obj/dbg/recycleBin.o obj/dbg/readSet.o obj/dbg/shortReadPairs.o obj/dbg/scaffold.o obj/dbg/locallyCorrectedGraph.o obj/dbg/graphReConstruction.o obj/dbg/roadMap.o obj/dbg/preGraph.o obj/dbg/preGraphConstruction.o obj/dbg/concatenatedPreGraph.o obj/dbg/readCoherentGraph.o obj/dbg/utility.o obj/dbg/kmer.o obj/dbg/kmerOccurenceTable.o obj/dbg/allocArray.o $(Z_LIB_FILES) $(LIBS) - - color : override DEF := $(DEF) -D COLOR - color : cleanobj obj_de -- $(CC) $(CFLAGS) $(OPT) $(LDFLAGS) -o velveth_de obj/tightString.o obj/run.o obj/recycleBin.o obj/splay.o obj/splayTable.o obj/readSet.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/allocArray.o $(Z_LIB_FILES) -- $(CC) $(CFLAGS) $(OPT) $(LDFLAGS) -o velvetg_de obj/tightString.o obj/graph.o obj/run2.o obj/fibHeap.o obj/fib.o obj/concatenatedGraph.o obj/passageMarker.o obj/graphStats.o obj/correctedGraph.o obj/dfib.o obj/dfibHeap.o obj/recycleBin.o obj/readSet.o obj/shortReadPairs.o obj/scaffold.o obj/locallyCorrectedGraph.o obj/graphReConstruction.o obj/roadMap.o obj/preGraph.o obj/preGraphConstruction.o obj/concatenatedPreGraph.o obj/readCoherentGraph.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/allocArray.o $(Z_LIB_FILES) -+ $(CC) $(CFLAGS) $(OPT) $(LDFLAGS) -o velveth_de obj/tightString.o obj/run.o obj/recycleBin.o obj/splay.o obj/splayTable.o obj/readSet.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/allocArray.o $(Z_LIB_FILES) $(LIBS) -+ $(CC) $(CFLAGS) $(OPT) $(LDFLAGS) -o velvetg_de obj/tightString.o obj/graph.o obj/run2.o obj/fibHeap.o obj/fib.o obj/concatenatedGraph.o obj/passageMarker.o obj/graphStats.o obj/correctedGraph.o obj/dfib.o obj/dfibHeap.o obj/recycleBin.o obj/readSet.o obj/shortReadPairs.o obj/scaffold.o obj/locallyCorrectedGraph.o obj/graphReConstruction.o obj/roadMap.o obj/preGraph.o obj/preGraphConstruction.o obj/concatenatedPreGraph.o obj/readCoherentGraph.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/allocArray.o $(Z_LIB_FILES) $(LIBS) - - colordebug : override DEF := $(DEF) -D COLOR -D DEBUG - colordebug : cleanobj obj/dbg_de -- $(CC) $(CFLAGS) $(LDFLAGS) $(DEBUG) -o velveth_de obj/dbg/tightString.o obj/dbg/run.o obj/dbg/recycleBin.o obj/dbg/splay.o obj/dbg/splayTable.o obj/dbg/readSet.o obj/dbg/utility.o obj/dbg/kmer.o obj/dbg/kmerOccurenceTable.o obj/dbg/allocArray.o $(Z_LIB_FILES) -- $(CC) $(CFLAGS) $(LDFLAGS) $(DEBUG) -o velvetg_de obj/dbg/tightString.o obj/dbg/graph.o obj/dbg/run2.o obj/dbg/fibHeap.o obj/dbg/fib.o obj/dbg/concatenatedGraph.o obj/dbg/passageMarker.o obj/dbg/graphStats.o obj/dbg/correctedGraph.o obj/dbg/dfib.o obj/dbg/dfibHeap.o obj/dbg/recycleBin.o obj/dbg/readSet.o obj/dbg/shortReadPairs.o obj/dbg/scaffold.o obj/dbg/locallyCorrectedGraph.o obj/dbg/graphReConstruction.o obj/dbg/roadMap.o obj/dbg/preGraph.o obj/dbg/preGraphConstruction.o obj/dbg/concatenatedPreGraph.o obj/dbg/readCoherentGraph.o obj/dbg/utility.o obj/dbg/kmer.o obj/dbg/kmerOccurenceTable.o obj/dbg/allocArray.o $(Z_LIB_FILES) -+ $(CC) $(CFLAGS) $(LDFLAGS) $(DEBUG) -o velveth_de obj/dbg/tightString.o obj/dbg/run.o obj/dbg/recycleBin.o obj/dbg/splay.o obj/dbg/splayTable.o obj/dbg/readSet.o obj/dbg/utility.o obj/dbg/kmer.o obj/dbg/kmerOccurenceTable.o obj/dbg/allocArray.o $(Z_LIB_FILES) $(LIBS) -+ $(CC) $(CFLAGS) $(LDFLAGS) $(DEBUG) -o velvetg_de obj/dbg/tightString.o obj/dbg/graph.o obj/dbg/run2.o obj/dbg/fibHeap.o obj/dbg/fib.o obj/dbg/concatenatedGraph.o obj/dbg/passageMarker.o obj/dbg/graphStats.o obj/dbg/correctedGraph.o obj/dbg/dfib.o obj/dbg/dfibHeap.o obj/dbg/recycleBin.o obj/dbg/readSet.o obj/dbg/shortReadPairs.o obj/dbg/scaffold.o obj/dbg/locallyCorrectedGraph.o obj/dbg/graphReConstruction.o obj/dbg/roadMap.o obj/dbg/preGraph.o obj/dbg/preGraphConstruction.o obj/dbg/concatenatedPreGraph.o obj/dbg/readCoherentGraph.o obj/dbg/utility.o obj/dbg/kmer.o obj/dbg/kmerOccurenceTable.o obj/dbg/allocArray.o $(Z_LIB_FILES) $(LIBS) - - objdir: - mkdir -p obj diff -Nru velvet-1.1.06~nozlibcopy/debian/patches/series velvet-1.1.07~nozlibcopy/debian/patches/series --- velvet-1.1.06~nozlibcopy/debian/patches/series 2011-11-02 12:21:11.000000000 +0000 +++ velvet-1.1.07~nozlibcopy/debian/patches/series 2011-08-11 12:59:52.000000000 +0000 @@ -1,4 +1,3 @@ include_debians_zlib.patch shuffleSequences_fasta.patch fix-perl-path.patch -as-needed.patch diff -Nru velvet-1.1.06~nozlibcopy/Makefile velvet-1.1.07~nozlibcopy/Makefile --- velvet-1.1.06~nozlibcopy/Makefile 2011-07-28 20:38:46.000000000 +0000 +++ velvet-1.1.07~nozlibcopy/Makefile 2011-12-05 17:53:32.000000000 +0000 @@ -1,7 +1,7 @@ CC = gcc CFLAGS = -Wall DEBUG = -g -LDFLAGS = -lm +LIBS = -lm OPT = -O3 MAXKMERLENGTH=31 CATEGORIES=2 @@ -67,26 +67,26 @@ endif velveth : obj - $(CC) $(CFLAGS) $(OPT) $(LDFLAGS) -o velveth obj/tightString.o obj/run.o obj/recycleBin.o obj/splay.o obj/splayTable.o obj/readSet.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o $(Z_LIB_FILES) + $(CC) $(CFLAGS) $(OPT) $(LDFLAGS) -o velveth obj/tightString.o obj/run.o obj/recycleBin.o obj/splay.o obj/splayTable.o obj/readSet.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o $(Z_LIB_FILES) $(LIBS) velvetg : obj - $(CC) $(CFLAGS) $(OPT) $(LDFLAGS) -o velvetg obj/tightString.o obj/graph.o obj/run2.o obj/fibHeap.o obj/fib.o obj/concatenatedGraph.o obj/passageMarker.o obj/graphStats.o obj/correctedGraph.o obj/dfib.o obj/dfibHeap.o obj/recycleBin.o obj/readSet.o obj/shortReadPairs.o obj/scaffold.o obj/locallyCorrectedGraph.o obj/graphReConstruction.o obj/roadMap.o obj/preGraph.o obj/preGraphConstruction.o obj/concatenatedPreGraph.o obj/readCoherentGraph.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/allocArray.o $(Z_LIB_FILES) + $(CC) $(CFLAGS) $(OPT) $(LDFLAGS) -o velvetg obj/tightString.o obj/graph.o obj/run2.o obj/fibHeap.o obj/fib.o obj/concatenatedGraph.o obj/passageMarker.o obj/graphStats.o obj/correctedGraph.o obj/dfib.o obj/dfibHeap.o obj/recycleBin.o obj/readSet.o obj/shortReadPairs.o obj/scaffold.o obj/locallyCorrectedGraph.o obj/graphReConstruction.o obj/roadMap.o obj/preGraph.o obj/preGraphConstruction.o obj/concatenatedPreGraph.o obj/readCoherentGraph.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/allocArray.o $(Z_LIB_FILES) $(LIBS) debug : override DEF := $(DEF) -D DEBUG debug : cleanobj obj/dbg - $(CC) $(CFLAGS) $(LDFLAGS) $(DEBUG) -o velveth obj/dbg/tightString.o obj/dbg/run.o obj/dbg/recycleBin.o obj/dbg/splay.o obj/dbg/splayTable.o obj/dbg/readSet.o obj/dbg/utility.o obj/dbg/kmer.o obj/dbg/kmerOccurenceTable.o obj/dbg/allocArray.o $(Z_LIB_FILES) - $(CC) $(CFLAGS) $(LDFLAGS) $(DEBUG) -o velvetg obj/dbg/tightString.o obj/dbg/graph.o obj/dbg/run2.o obj/dbg/fibHeap.o obj/dbg/fib.o obj/dbg/concatenatedGraph.o obj/dbg/passageMarker.o obj/dbg/graphStats.o obj/dbg/correctedGraph.o obj/dbg/dfib.o obj/dbg/dfibHeap.o obj/dbg/recycleBin.o obj/dbg/readSet.o obj/dbg/shortReadPairs.o obj/dbg/scaffold.o obj/dbg/locallyCorrectedGraph.o obj/dbg/graphReConstruction.o obj/dbg/roadMap.o obj/dbg/preGraph.o obj/dbg/preGraphConstruction.o obj/dbg/concatenatedPreGraph.o obj/dbg/readCoherentGraph.o obj/dbg/utility.o obj/dbg/kmer.o obj/dbg/kmerOccurenceTable.o obj/dbg/allocArray.o $(Z_LIB_FILES) + $(CC) $(CFLAGS) $(LDFLAGS) $(DEBUG) -o velveth obj/dbg/tightString.o obj/dbg/run.o obj/dbg/recycleBin.o obj/dbg/splay.o obj/dbg/splayTable.o obj/dbg/readSet.o obj/dbg/utility.o obj/dbg/kmer.o obj/dbg/kmerOccurenceTable.o obj/dbg/allocArray.o $(Z_LIB_FILES) $(LIBS) + $(CC) $(CFLAGS) $(LDFLAGS) $(DEBUG) -o velvetg obj/dbg/tightString.o obj/dbg/graph.o obj/dbg/run2.o obj/dbg/fibHeap.o obj/dbg/fib.o obj/dbg/concatenatedGraph.o obj/dbg/passageMarker.o obj/dbg/graphStats.o obj/dbg/correctedGraph.o obj/dbg/dfib.o obj/dbg/dfibHeap.o obj/dbg/recycleBin.o obj/dbg/readSet.o obj/dbg/shortReadPairs.o obj/dbg/scaffold.o obj/dbg/locallyCorrectedGraph.o obj/dbg/graphReConstruction.o obj/dbg/roadMap.o obj/dbg/preGraph.o obj/dbg/preGraphConstruction.o obj/dbg/concatenatedPreGraph.o obj/dbg/readCoherentGraph.o obj/dbg/utility.o obj/dbg/kmer.o obj/dbg/kmerOccurenceTable.o obj/dbg/allocArray.o $(Z_LIB_FILES) $(LIBS) color : override DEF := $(DEF) -D COLOR color : cleanobj obj_de - $(CC) $(CFLAGS) $(OPT) $(LDFLAGS) -o velveth_de obj/tightString.o obj/run.o obj/recycleBin.o obj/splay.o obj/splayTable.o obj/readSet.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/allocArray.o $(Z_LIB_FILES) - $(CC) $(CFLAGS) $(OPT) $(LDFLAGS) -o velvetg_de obj/tightString.o obj/graph.o obj/run2.o obj/fibHeap.o obj/fib.o obj/concatenatedGraph.o obj/passageMarker.o obj/graphStats.o obj/correctedGraph.o obj/dfib.o obj/dfibHeap.o obj/recycleBin.o obj/readSet.o obj/shortReadPairs.o obj/scaffold.o obj/locallyCorrectedGraph.o obj/graphReConstruction.o obj/roadMap.o obj/preGraph.o obj/preGraphConstruction.o obj/concatenatedPreGraph.o obj/readCoherentGraph.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/allocArray.o $(Z_LIB_FILES) + $(CC) $(CFLAGS) $(OPT) $(LDFLAGS) -o velveth_de obj/tightString.o obj/run.o obj/recycleBin.o obj/splay.o obj/splayTable.o obj/readSet.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/allocArray.o $(Z_LIB_FILES) $(LIBS) + $(CC) $(CFLAGS) $(OPT) $(LDFLAGS) -o velvetg_de obj/tightString.o obj/graph.o obj/run2.o obj/fibHeap.o obj/fib.o obj/concatenatedGraph.o obj/passageMarker.o obj/graphStats.o obj/correctedGraph.o obj/dfib.o obj/dfibHeap.o obj/recycleBin.o obj/readSet.o obj/shortReadPairs.o obj/scaffold.o obj/locallyCorrectedGraph.o obj/graphReConstruction.o obj/roadMap.o obj/preGraph.o obj/preGraphConstruction.o obj/concatenatedPreGraph.o obj/readCoherentGraph.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/allocArray.o $(Z_LIB_FILES) $(LIBS) colordebug : override DEF := $(DEF) -D COLOR -D DEBUG colordebug : cleanobj obj/dbg_de - $(CC) $(CFLAGS) $(LDFLAGS) $(DEBUG) -o velveth_de obj/dbg/tightString.o obj/dbg/run.o obj/dbg/recycleBin.o obj/dbg/splay.o obj/dbg/splayTable.o obj/dbg/readSet.o obj/dbg/utility.o obj/dbg/kmer.o obj/dbg/kmerOccurenceTable.o obj/dbg/allocArray.o $(Z_LIB_FILES) - $(CC) $(CFLAGS) $(LDFLAGS) $(DEBUG) -o velvetg_de obj/dbg/tightString.o obj/dbg/graph.o obj/dbg/run2.o obj/dbg/fibHeap.o obj/dbg/fib.o obj/dbg/concatenatedGraph.o obj/dbg/passageMarker.o obj/dbg/graphStats.o obj/dbg/correctedGraph.o obj/dbg/dfib.o obj/dbg/dfibHeap.o obj/dbg/recycleBin.o obj/dbg/readSet.o obj/dbg/shortReadPairs.o obj/dbg/scaffold.o obj/dbg/locallyCorrectedGraph.o obj/dbg/graphReConstruction.o obj/dbg/roadMap.o obj/dbg/preGraph.o obj/dbg/preGraphConstruction.o obj/dbg/concatenatedPreGraph.o obj/dbg/readCoherentGraph.o obj/dbg/utility.o obj/dbg/kmer.o obj/dbg/kmerOccurenceTable.o obj/dbg/allocArray.o $(Z_LIB_FILES) + $(CC) $(CFLAGS) $(LDFLAGS) $(DEBUG) -o velveth_de obj/dbg/tightString.o obj/dbg/run.o obj/dbg/recycleBin.o obj/dbg/splay.o obj/dbg/splayTable.o obj/dbg/readSet.o obj/dbg/utility.o obj/dbg/kmer.o obj/dbg/kmerOccurenceTable.o obj/dbg/allocArray.o $(Z_LIB_FILES) $(LIBS) + $(CC) $(CFLAGS) $(LDFLAGS) $(DEBUG) -o velvetg_de obj/dbg/tightString.o obj/dbg/graph.o obj/dbg/run2.o obj/dbg/fibHeap.o obj/dbg/fib.o obj/dbg/concatenatedGraph.o obj/dbg/passageMarker.o obj/dbg/graphStats.o obj/dbg/correctedGraph.o obj/dbg/dfib.o obj/dbg/dfibHeap.o obj/dbg/recycleBin.o obj/dbg/readSet.o obj/dbg/shortReadPairs.o obj/dbg/scaffold.o obj/dbg/locallyCorrectedGraph.o obj/dbg/graphReConstruction.o obj/dbg/roadMap.o obj/dbg/preGraph.o obj/dbg/preGraphConstruction.o obj/dbg/concatenatedPreGraph.o obj/dbg/readCoherentGraph.o obj/dbg/utility.o obj/dbg/kmer.o obj/dbg/kmerOccurenceTable.o obj/dbg/allocArray.o $(Z_LIB_FILES) $(LIBS) objdir: mkdir -p obj diff -Nru velvet-1.1.06~nozlibcopy/src/correctedGraph.c velvet-1.1.07~nozlibcopy/src/correctedGraph.c --- velvet-1.1.06~nozlibcopy/src/correctedGraph.c 2011-09-22 00:10:44.000000000 +0000 +++ velvet-1.1.07~nozlibcopy/src/correctedGraph.c 2011-12-05 17:53:07.000000000 +0000 @@ -2442,7 +2442,7 @@ return length; } -void clipTipsHard(Graph * graph) +void clipTipsHard(Graph * graph, boolean conserveLong) { IDnum index; Node *current, *twin; @@ -2459,6 +2459,9 @@ if (current == NULL) continue; + + if (conserveLong && getMarker(current)) + continue; twin = getTwinNode(current); @@ -2513,7 +2516,7 @@ } } -void correctGraph(Graph * argGraph, ShortLength * argSequenceLengths, Category * argSequenceCategories) +void correctGraph(Graph * argGraph, ShortLength * argSequenceLengths, Category * argSequenceCategories, boolean conserveLong) { IDnum nodes; IDnum index; @@ -2572,7 +2575,7 @@ deactivateArcLookupTable(graph); concatenateGraph(graph); - clipTipsHard(graph); + clipTipsHard(graph, conserveLong); //Deallocating globals free(times); diff -Nru velvet-1.1.06~nozlibcopy/src/correctedGraph.h velvet-1.1.07~nozlibcopy/src/correctedGraph.h --- velvet-1.1.06~nozlibcopy/src/correctedGraph.h 2011-09-22 00:10:44.000000000 +0000 +++ velvet-1.1.07~nozlibcopy/src/correctedGraph.h 2011-12-05 17:53:07.000000000 +0000 @@ -21,9 +21,9 @@ #ifndef _CORRECTEDGRAPH_H_ #define _CORRECTEDGRAPH_H_ -void clipTipsHard(Graph * graph); +void clipTipsHard(Graph * graph, boolean conserveLong); -void correctGraph(Graph * graph, ShortLength *sequenceLengths, Category * sequenceCategories); +void correctGraph(Graph * graph, ShortLength *sequenceLengths, Category * sequenceCategories, boolean conserveLong); // Black arts: void setMaxReadLength(int value); diff -Nru velvet-1.1.06~nozlibcopy/src/globals.h velvet-1.1.07~nozlibcopy/src/globals.h --- velvet-1.1.06~nozlibcopy/src/globals.h 2011-09-22 00:10:44.000000000 +0000 +++ velvet-1.1.07~nozlibcopy/src/globals.h 2011-12-05 17:53:07.000000000 +0000 @@ -38,7 +38,7 @@ #define VERSION_NUMBER 1 #define RELEASE_NUMBER 1 -#define UPDATE_NUMBER 06 +#define UPDATE_NUMBER 07 #define MAXLINE 5000 diff -Nru velvet-1.1.06~nozlibcopy/src/readSet.c velvet-1.1.07~nozlibcopy/src/readSet.c --- velvet-1.1.06~nozlibcopy/src/readSet.c 2011-09-22 00:10:44.000000000 +0000 +++ velvet-1.1.07~nozlibcopy/src/readSet.c 2011-12-05 17:53:07.000000000 +0000 @@ -1680,11 +1680,19 @@ phase = 0; } } - else + else { phase = 1; + if (index > 0 && previousCat & 1 && !isSecondInPair(reads, index - 1)) + reads->categories[index - 1] = (reads->categories[index - 1] / 2) * 2; + } } previousCat = currentCat; } + + // Safeguard against odd sets of reads + if (!isSecondInPair(reads, reads->readCount - 1)) { + reads->categories[reads->readCount - 1] = (reads->categories[reads->readCount - 1] / 2) * 2; + } } void detachDubiousReads(ReadSet * reads, boolean * dubiousReads) @@ -1913,7 +1921,7 @@ ShortLength *getSequenceLengths(ReadSet * reads, int wordLength) { ShortLength *lengths = callocOrExit(reads->readCount, ShortLength); - ShortLength index; + IDnum index; int lengthOffset = wordLength - 1; for (index = 0; index < reads->readCount; index++) diff -Nru velvet-1.1.06~nozlibcopy/src/run2.c velvet-1.1.07~nozlibcopy/src/run2.c --- velvet-1.1.06~nozlibcopy/src/run2.c 2011-09-22 15:43:04.000000000 +0000 +++ velvet-1.1.07~nozlibcopy/src/run2.c 2011-12-05 17:53:07.000000000 +0000 @@ -63,6 +63,7 @@ puts("\t-very_clean \t\t: remove all the intermediary files (no recalculation possible) (default: no)"); puts("\t-paired_exp_fraction \t: remove all the paired end connections which less than the specified fraction of the expected count (default: 0.1)"); puts("\t-shortMatePaired* \t: for mate-pair libraries, indicate that the library might be contaminated with paired-end reads (default no)"); + puts("\t-conserveLong \t\t: preserve sequences with long reads in them (default no)"); puts(""); puts("Output:"); puts("\tdirectory/contigs.fa\t\t: fasta file of contigs longer than twice hash length"); @@ -109,6 +110,7 @@ short int short_var; boolean exportFilteredNodes = false; int clean = 0; + boolean conserveLong = false; boolean shadows[CATEGORIES]; int coverageMask = 1; @@ -322,6 +324,9 @@ } else if (strcmp(arg, "-very_clean") == 0) { if (strcmp(argv[arg_index], "yes") == 0) clean = 2; + } else if (strcmp(arg, "-conserveLong") == 0) { + if (strcmp(argv[arg_index], "yes") == 0) + conserveLong = 2; } else if (strcmp(arg, "-unused_reads") == 0) { unusedReads = (strcmp(argv[arg_index], "yes") == 0); @@ -389,7 +394,7 @@ roadmapFilename, readTracking, accelerationBits); sequenceLengths = getSequenceLengths(sequences, getWordLength(graph)); - correctGraph(graph, sequenceLengths, sequences->categories); + correctGraph(graph, sequenceLengths, sequences->categories, conserveLong); exportGraph(graphFilename, graph, sequences->tSequences); } else if ((file = fopen(roadmapFilename, "r")) != NULL) { fclose(file); @@ -397,7 +402,8 @@ rdmaps = importRoadMapArray(roadmapFilename); preGraph = newPreGraph_pg(rdmaps, seqFilename); concatenatePreGraph_pg(preGraph); - clipTips_pg(preGraph); + if (!conserveLong) + clipTips_pg(preGraph); exportPreGraph_pg(preGraphFilename, preGraph); destroyPreGraph_pg(preGraph); @@ -408,7 +414,7 @@ roadmapFilename, readTracking, accelerationBits); sequenceLengths = getSequenceLengths(sequences, getWordLength(graph)); - correctGraph(graph, sequenceLengths, sequences->categories); + correctGraph(graph, sequenceLengths, sequences->categories, conserveLong); exportGraph(graphFilename, graph, sequences->tSequences); } else { velvetLog("No Roadmap file to build upon! Please run velveth (see manual)\n"); @@ -479,7 +485,7 @@ lowCovContigsFilename); removeHighCoverageNodes(graph, maxCoverageCutoff, exportFilteredNodes, minContigKmerLength, highCovContigsFilename); - clipTipsHard(graph); + clipTipsHard(graph, conserveLong); if (sequences->readCount > 0 && sequences->categories[0] == REFERENCE) removeLowArcs(graph, coverageCutoff); @@ -564,11 +570,11 @@ remove(graphFilename); strcpy(graphFilename, directory); - strcat(graphFilename, "/Graph2.txt"); + strcat(graphFilename, "/Graph2"); remove(graphFilename); strcpy(graphFilename, directory); - strcat(graphFilename, "/Graph.txt"); + strcat(graphFilename, "/Graph"); remove(graphFilename); } diff -Nru velvet-1.1.06~nozlibcopy/src/run3.c velvet-1.1.07~nozlibcopy/src/run3.c --- velvet-1.1.06~nozlibcopy/src/run3.c 1970-01-01 00:00:00.000000000 +0000 +++ velvet-1.1.07~nozlibcopy/src/run3.c 2011-12-05 17:53:07.000000000 +0000 @@ -0,0 +1,46 @@ +/* +Copyright 2007, 2008 Daniel Zerbino (zerbino@ebi.ac.uk) + + This file is part of Velvet. + + Velvet is free software; you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation; either version 2 of the License, or + (at your option) any later version. + + Velvet is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with Velvet; if not, write to the Free Software + Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA + +*/ +#include +#include +#include + +#include "run.h" + +static void printUsage() +{ + puts("Usage:"); + puts("./columbus_mask directory [options]"); + puts(""); + puts("\tdirectory\t\t\t: working directory name"); + puts(""); +} + +int main(int argc, char ** argv) { + strcpy(seqFilename, directory); + strcat(seqFilename, "/Sequences"); + + strcpy(graphFilename, directory); + strcat(graphFilename, "/LastGraph"); + + graph = importGraph(graphFilename); + + +} diff -Nru velvet-1.1.06~nozlibcopy/src/splayTable.c velvet-1.1.07~nozlibcopy/src/splayTable.c --- velvet-1.1.06~nozlibcopy/src/splayTable.c 2011-09-22 00:10:44.000000000 +0000 +++ velvet-1.1.07~nozlibcopy/src/splayTable.c 2011-12-05 17:53:07.000000000 +0000 @@ -606,69 +606,23 @@ return; } -static void computeClearHSPs(TightString * array, FILE * seqFile, boolean second_in_pair, SplayTable * table, IDnum ** sequenceIDs, Coordinate ** coords, IDnum seqID) { +static void computeClearHSPs(TightString * array, boolean second_in_pair, SplayTable * table, IDnum ** sequenceIDs, Coordinate ** coords, IDnum * mapReferenceIDs, Coordinate * mapCoords, Coordinate mapCount, IDnum seqID) { Coordinate readNucleotideIndex = 0; Kmer word; Kmer antiWord; Kmer polyA; Nucleotide nucleotide; KmerOccurence * hit; - char line[MAXLINE]; - char* start; - char c; - Coordinate mapCount = 0; - Coordinate maxCount = 10; - IDnum * mapReferenceIDs = callocOrExit(maxCount, IDnum); - Coordinate * mapCoords = callocOrExit(maxCount, Coordinate); - long long_var; - long long longlong_var; int penalty; TightString * tString; Coordinate length; clearKmer(&polyA); - -#ifdef _OPENMP - #pragma omp critical - { -#endif - // Get read ID: - if (!fgets(line, MAXLINE, seqFile)) { - puts("Incomplete Sequences file (computeHSPScores)"); -#ifdef DEBUG - abort(); -#endif - exit(1); - } - start = strchr(line, '\t'); - tString = getTightStringInArray(array, seqID - 1); - length = getLength(tString); - *sequenceIDs = callocOrExit(length, IDnum); - *coords = callocOrExit(length, Coordinate); - - // Parse file for mapping info - while (seqFile && (c = getc(seqFile)) != EOF) { - if (c == '>') - break; - - fgets(line, MAXLINE, seqFile); - - if (c == 'M') { - sscanf(line,"\t%li\t%lli\n", &long_var, &longlong_var); - mapReferenceIDs[mapCount] = (IDnum) long_var; - mapCoords[mapCount] = (Coordinate) longlong_var; - - if (++mapCount == maxCount) { - maxCount *= 2; - mapReferenceIDs = reallocOrExit(mapReferenceIDs, maxCount, IDnum); - mapCoords = reallocOrExit(mapCoords, maxCount, Coordinate); - } - } - } -#ifdef _OPENMP - } -#endif + tString = getTightStringInArray(array, seqID - 1); + length = getLength(tString); + *sequenceIDs = callocOrExit(length, IDnum); + *coords = callocOrExit(length, Coordinate); // First pass for unambiguous hits // Fill in the initial word : @@ -774,8 +728,9 @@ void inputSequenceIntoSplayTable(TightString * array, SplayTable * table, - FILE * file, FILE * seqFile, + FILE * file, boolean second_in_pair, + IDnum * mapReferenceIDs, Coordinate * mapCoords, Coordinate mapCount, IDnum seqID) { IDnum * sequenceIDs = NULL; @@ -783,7 +738,7 @@ // If appropriate, get the HSPs on reference sequences if (table->kmerOccurenceTable) - computeClearHSPs(array, seqFile, second_in_pair, table, &sequenceIDs, &coords, seqID); + computeClearHSPs(array, second_in_pair, table, &sequenceIDs, &coords, mapReferenceIDs, mapCoords, mapCount, seqID); // Go through read, eventually with annotations printAnnotations(sequenceIDs, coords, array, table, file, second_in_pair, seqID); @@ -906,7 +861,7 @@ Mask ** referenceMasks = callocOrExit(referenceSequenceCount, Mask*); IDnum index; char line[MAXLINE]; - char c; + char c = '\0'; // Search sequences for masks for (index = 0; index < referenceSequenceCount; index++) { @@ -942,6 +897,8 @@ } } + if (c != '\0') + ungetc(c, file); return referenceMasks; } @@ -957,7 +914,17 @@ IDnum kmerCount; IDnum referenceSequenceCount = 0; struct timeval start, end, diff; + IDnum ** mapReferenceIDs = NULL; + Coordinate ** mapCoords = NULL; + Coordinate * mapCount = NULL; + char line[MAXLINE]; + char c; + IDnum seqID = 0; + long long_var; + long long longlong_var; + Coordinate maxCount = 20; + Coordinate counter = 0; // DEBUG Mask ** referenceMasks; @@ -1036,6 +1003,40 @@ velvetLog("Inputting sequences...\n"); + if (table->kmerOccurenceTable) { + mapReferenceIDs = callocOrExit(sequenceCount + 1, IDnum*); + mapCoords = callocOrExit(sequenceCount + 1, Coordinate *); + mapCount = callocOrExit(sequenceCount + 1, Coordinate); + + // Parse file for mapping info + while (seqFile && (c = getc(seqFile)) != EOF) { + + if (c == '>') { + mapCount[seqID] = counter; + counter = 0; + maxCount = 20; + fgets(line, MAXLINE, seqFile); + sscanf(line,"%*s\t%li\t", &long_var); + seqID = (IDnum) long_var; + mapReferenceIDs[seqID] = callocOrExit(maxCount, IDnum); + mapCoords[seqID] = callocOrExit(maxCount, Coordinate); + } else if (c == 'M') { + fgets(line, MAXLINE, seqFile); + sscanf(line,"\t%li\t%lli\n", &long_var, &longlong_var); + mapReferenceIDs[seqID][counter] = (IDnum) long_var; + mapCoords[seqID][counter] = (Coordinate) longlong_var; + + if (++counter == maxCount) { + maxCount *= 2; + mapReferenceIDs[seqID] = reallocOrExit(mapReferenceIDs, maxCount, IDnum); + mapCoords[seqID] = reallocOrExit(mapCoords, maxCount, Coordinate); + } + } + } + } + if (seqFile) + fclose(seqFile); + #ifdef _OPENMP producing = 1; #pragma omp parallel sections @@ -1072,9 +1073,14 @@ second_in_pair = reads->categories[index] % 2 && isSecondInPair(reads, index); // Hashing the reads - inputSequenceIntoSplayTable(array, table, - outfile, seqFile, - second_in_pair, index + 1); + if (table->kmerOccurenceTable) + inputSequenceIntoSplayTable(array, table, + outfile, + second_in_pair, mapReferenceIDs[index + 1], mapCoords[index+1], mapCount[index+1], index + 1); + else + inputSequenceIntoSplayTable(array, table, + outfile, + second_in_pair, NULL, NULL, 0, index + 1); } #ifdef _OPENMP for (index = omp_get_max_threads() - 1; index >= 0; index--) @@ -1093,9 +1099,12 @@ velvetLog(" === Sequences loaded in %ld.%06ld s\n", diff.tv_sec, diff.tv_usec); fclose(outfile); - if (seqFile) - fclose(seqFile); + if (mapReferenceIDs) { + free(mapReferenceIDs); + free(mapCoords); + free(mapCount); + } //free(reads->tSequences); //reads->tSequences = NULL; //destroyReadSet(reads); diff -Nru velvet-1.1.06~nozlibcopy/src/tags velvet-1.1.07~nozlibcopy/src/tags --- velvet-1.1.06~nozlibcopy/src/tags 1970-01-01 00:00:00.000000000 +0000 +++ velvet-1.1.07~nozlibcopy/src/tags 2011-12-05 17:53:07.000000000 +0000 @@ -0,0 +1,1456 @@ +!_TAG_FILE_FORMAT 2 /extended format; --format=1 will not append ;" to lines/ +!_TAG_FILE_SORTED 1 /0=unsorted, 1=sorted, 2=foldcase/ +!_TAG_PROGRAM_AUTHOR Darren Hiebert /dhiebert@users.sourceforge.net/ +!_TAG_PROGRAM_NAME Exuberant Ctags // +!_TAG_PROGRAM_URL http://ctags.sourceforge.net /official site/ +!_TAG_PROGRAM_VERSION 5.8 // +ADENINE graph.c 33;" d file: +ADENINE graphReConstruction.c 43;" d file: +ADENINE preGraph.c 38;" d file: +ADENINE preGraphConstruction.c 39;" d file: +ATTRIBUTE utility.h 25;" d +ATTRIBUTE utility.h 27;" d +ATTRIBUTE_PACKED correctedGraph.c /^} ATTRIBUTE_PACKED;$/;" v typeref:struct:tkt_st +ATTRIBUTE_PACKED dfibpriv.h /^} ATTRIBUTE_PACKED;$/;" v typeref:struct:dfibheap +ATTRIBUTE_PACKED dfibpriv.h /^} ATTRIBUTE_PACKED;$/;" v typeref:struct:dfibheap_el +ATTRIBUTE_PACKED globals.h 34;" d +ATTRIBUTE_PACKED globals.h 36;" d +ATTRIBUTE_PACKED graph.c /^} ATTRIBUTE_PACKED; \/\/ 352 Total$/;" v typeref:struct:arc_st +ATTRIBUTE_PACKED graph.c /^} ATTRIBUTE_PACKED; \/\/ 418 Total$/;" v typeref:struct:node_st +ATTRIBUTE_PACKED graph.c /^} ATTRIBUTE_PACKED;$/;" v typeref:struct:gapMarker_st +ATTRIBUTE_PACKED graph.c /^} ATTRIBUTE_PACKED;$/;" v typeref:struct:shortReadMarker_st +ATTRIBUTE_PACKED graphReConstruction.c /^} ATTRIBUTE_PACKED;$/;" v typeref:struct:nodeMask_st +ATTRIBUTE_PACKED graphReConstruction.c /^} ATTRIBUTE_PACKED;$/;" v typeref:struct:referenceMapping_st +ATTRIBUTE_PACKED graphReConstruction.c /^} ATTRIBUTE_PACKED;$/;" v typeref:struct:smallNodeList_st +ATTRIBUTE_PACKED graphStats.c /^} ATTRIBUTE_PACKED;$/;" v typeref:struct:referenceCoord_st +ATTRIBUTE_PACKED kmer.h /^} ATTRIBUTE_PACKED;$/;" v typeref:struct:kmer_st +ATTRIBUTE_PACKED kmerOccurenceTable.c /^} ATTRIBUTE_PACKED;$/;" v typeref:struct:kmerOccurence_st +ATTRIBUTE_PACKED locallyCorrectedGraph.h /^} ATTRIBUTE_PACKED;$/;" v typeref:struct:nodeList_st +ATTRIBUTE_PACKED passageMarker.c /^} ATTRIBUTE_PACKED;$/;" v typeref:struct:passage_st +ATTRIBUTE_PACKED passageMarker.h /^} ATTRIBUTE_PACKED;$/;" v typeref:struct:passageList_st +ATTRIBUTE_PACKED preGraph.c /^} ATTRIBUTE_PACKED;$/;" v typeref:struct:preNode_st +ATTRIBUTE_PACKED preGraph.c /^} ATTRIBUTE_PACKED;$/;" v typeref:struct:preArc_st +ATTRIBUTE_PACKED preGraph.c /^} ATTRIBUTE_PACKED;$/;" v typeref:struct:preMarker_st +ATTRIBUTE_PACKED preGraphConstruction.c /^} ATTRIBUTE_PACKED;$/;" v typeref:struct:insertionMarker_st +ATTRIBUTE_PACKED readCoherentGraph.c /^} ATTRIBUTE_PACKED;$/;" v typeref:struct:rb_connection_st +ATTRIBUTE_PACKED readSet.c /^} ATTRIBUTE_PACKED;$/;" v typeref:struct:referenceCoordinateTable_st +ATTRIBUTE_PACKED readSet.c /^} ATTRIBUTE_PACKED;$/;" v typeref:struct:referenceCoordinate_st +ATTRIBUTE_PACKED roadMap.c /^} ATTRIBUTE_PACKED;$/;" v typeref:struct:annotation_st +ATTRIBUTE_PACKED roadMap.c /^} ATTRIBUTE_PACKED;$/;" v typeref:struct:roadmap_st +ATTRIBUTE_PACKED roadMap.c /^} ATTRIBUTE_PACKED;$/;" v typeref:union:positionPtr +ATTRIBUTE_PACKED scaffold.c /^} ATTRIBUTE_PACKED;$/;" v typeref:struct:connection_st +ATTRIBUTE_PACKED scaffold.c /^} ATTRIBUTE_PACKED;$/;" v typeref:struct:readOccurence_st +ATTRIBUTE_PACKED shortReadPairs.c /^} ATTRIBUTE_PACKED;$/;" v typeref:struct:miniConnection_st +ATTRIBUTE_PACKED splay.c /^} ATTRIBUTE_PACKED;$/;" v typeref:struct:splayNode_st +ATTRIBUTE_PACKED tightString.c /^} ATTRIBUTE_PACKED;$/;" v typeref:struct:tString_st +Adenine tightString.c /^static const Nucleotide Adenine = 0;$/;" v file: +AllocArray allocArray.h /^typedef struct AllocArray_st AllocArray;$/;" t typeref:struct:AllocArray_st +AllocArrayFreeElement allocArray.h /^typedef struct AllocArrayFreeElement_st AllocArrayFreeElement;$/;" t typeref:struct:AllocArrayFreeElement_st +AllocArrayFreeElement_st allocArray.c /^struct AllocArrayFreeElement_st$/;" s file: +AllocArray_st allocArray.h /^struct AllocArray_st$/;" s +Annotation globals.h /^typedef struct annotation_st Annotation;$/;" t typeref:struct:annotation_st +AnnotationList globals.h /^typedef struct annotationList_st AnnotationList;$/;" t typeref:struct:annotationList_st +Arc globals.h /^typedef struct arc_st Arc;$/;" t typeref:struct:arc_st +Arc run.c 26;" d file: +ArrayIdx globals.h /^typedef uint32_t ArrayIdx;$/;" t +ArrayIdx globals.h /^typedef uint64_t ArrayIdx;$/;" t +BACKTRACK_CUTOFF shortReadPairs.c 38;" d file: +BAM readSet.c 1393;" d file: +BLOCKSIZE dfib.c 57;" d file: +BLOCKSIZE fib.c 57;" d file: +BLOCKSIZE graph.c 95;" d file: +BLOCKSIZE graphReConstruction.c 149;" d file: +BLOCKSIZE readCoherentGraph.c 61;" d file: +BLOCKS_ALLOC_SHIFT allocArray.c 186;" d file: +BLOCKS_ALLOC_SIZE allocArray.c 34;" d file: +BLOCKS_ALLOC_SIZE allocArray.c 37;" d file: +BLOCK_SIZE scaffold.c 41;" d file: +BLOCK_SIZE shortReadPairs.c 36;" d file: +BUFFER_SIZE splayTable.c 185;" d file: +BUFFER_SIZE splayTable.c 72;" d file: +CHARS kmer.c 41;" d file: +CHUNKSIZE splay.c 33;" d file: +CYTOSINE graph.c 34;" d file: +CYTOSINE graphReConstruction.c 44;" d file: +CYTOSINE preGraph.c 39;" d file: +CYTOSINE preGraphConstruction.c 40;" d file: +Category globals.h /^typedef int8_t Category;$/;" t +Chunk recycleBin.c /^} Chunk;$/;" t typeref:struct:chunk_st file: +Codon tightString.c /^typedef unsigned char Codon;$/;" t file: +Connection scaffold.h /^typedef struct connection_st Connection;$/;" t typeref:struct:connection_st +ConnectionStack scaffold.c /^typedef struct ConnectionStack_st ConnectionStack;$/;" t typeref:struct:ConnectionStack_st file: +ConnectionStack_st scaffold.c /^struct ConnectionStack_st$/;" s file: +Coordinate globals.h /^typedef int64_t Coordinate;$/;" t +Cytosine tightString.c /^static const Nucleotide Cytosine = 1;$/;" v file: +DECLARE_FAST_ACCESSORS allocArray.h 59;" d +DECLARE_FAST_ACCESSORS preGraph.c /^DECLARE_FAST_ACCESSORS(PREARC, PreArc, preArcMemory)$/;" f +DFibHeap globals.h /^typedef struct dfibheap DFibHeap;$/;" t typeref:struct:dfibheap +DFibHeapNode globals.h /^typedef struct dfibheap_el DFibHeapNode;$/;" t typeref:struct:dfibheap_el +DOTNode graph.c /^void DOTNode(Node * node, FILE * outfile)$/;" f +Descriptor globals.h /^typedef uint8_t Descriptor;$/;" t +ELAND readSet.c 1388;" d file: +FASTA readSet.c 1386;" d file: +FASTA_GZ readSet.c 1389;" d file: +FASTQ readSet.c 1385;" d file: +FASTQ_GZ readSet.c 1390;" d file: +FAST_TO_SLOW correctedGraph.c 2078;" d file: +FILTER0 tightString.c /^static const Codon FILTER0 = ~((Codon) 3);$/;" v file: +FILTER1 tightString.c /^static const Codon FILTER1 = ~(((Codon) 3) << 2);$/;" v file: +FILTER2 tightString.c /^static const Codon FILTER2 = ~(((Codon) 3) << 4);$/;" v file: +FILTER3 tightString.c /^static const Codon FILTER3 = (Codon) ~ ((Codon) 3 << 6);$/;" v file: +FibHeap globals.h /^typedef struct fibheap FibHeap;$/;" t typeref:struct:fibheap +FibHeapNode globals.h /^typedef struct fibheap_el FibHeapNode;$/;" t typeref:struct:fibheap_el +Fmatrix correctedGraph.c /^static double **Fmatrix;$/;" v file: +Fmatrix locallyCorrectedGraph.c /^static double **Fmatrix;$/;" v file: +GAPBLOCKSIZE graph.c 96;" d file: +GERALD readSet.c 1387;" d file: +GUANINE graph.c 35;" d file: +GUANINE graphReConstruction.c 45;" d file: +GUANINE preGraph.c 40;" d file: +GUANINE preGraphConstruction.c 41;" d file: +GapMarker globals.h /^typedef struct gapMarker_st GapMarker;$/;" t typeref:struct:gapMarker_st +Graph globals.h /^typedef struct graph_st Graph;$/;" t typeref:struct:graph_st +Guanine tightString.c /^static const Nucleotide Guanine = 2;$/;" v file: +HASH_BUCKETS_NB splayTable.c 67;" d file: +ID graph.c /^ IDnum ID; \/\/ 32$/;" m struct:node_st file: +IDnum globals.h /^typedef int32_t IDnum;$/;" t +IDnum globals.h /^typedef int64_t IDnum;$/;" t +INCLUDED_RECYCLEBIN_H recycleBin.h 37;" d +INDEL correctedGraph.c /^static const Time INDEL = 0;$/;" v file: +INDEL locallyCorrectedGraph.c /^static const Time INDEL = 0;$/;" v file: +INDEX_LENGTH allocArray.c 41;" d file: +INDEX_LENGTH allocArray.c 43;" d file: +INTS kmer.c 42;" d file: +INT_BITS dfib.c 81;" d file: +INT_BITS fib.c 77;" d file: +InsertionMarker globals.h /^typedef struct insertionMarker_st InsertionMarker;$/;" t typeref:struct:insertionMarker_st +KMER_BYTE_SIZE kmer.h 49;" d +KMER_BYTE_SIZE kmer.h 51;" d +KMER_CHARS kmer.h 56;" d +KMER_INTS kmer.h 55;" d +KMER_LONGLONGS kmer.h 53;" d +KMER_LONGS kmer.h 54;" d +KMER_QUOTIENT kmer.h 46;" d +KMER_REMAINDER kmer.h 47;" d +Kmer globals.h /^typedef struct kmer_st Kmer;$/;" t typeref:struct:kmer_st +KmerKey globals.h /^typedef uint64_t KmerKey;$/;" t +KmerOccurence globals.h /^typedef struct kmerOccurence_st KmerOccurence;$/;" t typeref:struct:kmerOccurence_st +KmerOccurenceTable globals.h /^typedef struct kmerOccurenceTable_st KmerOccurenceTable;$/;" t typeref:struct:kmerOccurenceTable_st +LISTBLOCKSIZE passageMarker.c /^static const int LISTBLOCKSIZE = 10000;$/;" v file: +LN2 readCoherentGraph.c 34;" d file: +LN2 scaffold.c 42;" d file: +LN2 shortReadPairs.c 37;" d file: +LONG globals.h 45;" d +LONGLONGS kmer.c 44;" d file: +LONGS kmer.c 43;" d file: +LONG_NODE_CUTOFF readCoherentGraph.c 33;" d file: +LONG_PAIRED globals.h 46;" d +MAQ_GZ readSet.c 1391;" d file: +MAXDIVERGENCE correctedGraph.c /^static double MAXDIVERGENCE = 0.2;$/;" v file: +MAXDIVERGENCE locallyCorrectedGraph.c /^static double MAXDIVERGENCE = 0.2;$/;" v file: +MAXGAPS correctedGraph.c /^static int MAXGAPS = 3;$/;" v file: +MAXGAPS locallyCorrectedGraph.c /^static int MAXGAPS = 3;$/;" v file: +MAXLINE globals.h 43;" d +MAXNODELENGTH correctedGraph.c /^static int MAXNODELENGTH = 200;$/;" v file: +MAXNODELENGTH locallyCorrectedGraph.c /^static int MAXNODELENGTH = 200;$/;" v file: +MAXREADLENGTH correctedGraph.c /^static int MAXREADLENGTH = 100;$/;" v file: +MAXREADLENGTH locallyCorrectedGraph.c /^static int MAXREADLENGTH = 100;$/;" v file: +MAX_READ_COUNT readCoherentGraph.c 36;" d file: +MAX_READ_LENGTH readCoherentGraph.c 37;" d file: +MULTIPLICITY_CUTOFF readCoherentGraph.c /^static int MULTIPLICITY_CUTOFF = 2;$/;" v file: +Mask graphStats.c /^typedef struct mask_st Mask;$/;" t typeref:struct:mask_st file: +Mask splayTable.c /^typedef struct mask_st Mask;$/;" t typeref:struct:mask_st file: +MiniConnection shortReadPairs.c /^typedef struct miniConnection_st MiniConnection;$/;" t typeref:struct:miniConnection_st file: +NB_PAGES_ALLOC allocArray.c 33;" d file: +NB_PAGES_ALLOC allocArray.c 36;" d file: +NB_PUSH splayTable.c 71;" d file: +NULL globals.h 25;" d +NULL roadMap.c 34;" d file: +NULL_IDX globals.h 50;" d +Node globals.h /^typedef struct node_st Node;$/;" t typeref:struct:node_st +NodeList globals.h /^typedef struct nodeList_st NodeList;$/;" t typeref:struct:nodeList_st +NodeMask graphReConstruction.c /^typedef struct nodeMask_st NodeMask;$/;" t typeref:struct:nodeMask_st file: +Nucleotide globals.h /^typedef int8_t Nucleotide;$/;" t +PEBBLE_ROUND_NUM scaffold.c /^static int PEBBLE_ROUND_NUM = 0;$/;" v file: +PROBABILITY_CUTOFF readCoherentGraph.c 35;" d file: +PassageMarker passageMarker.c /^typedef struct passage_st PassageMarker;$/;" t typeref:struct:passage_st file: +PassageMarkerI globals.h /^typedef ArrayIdx PassageMarkerI;$/;" t +PassageMarkerList globals.h /^typedef struct passageList_st PassageMarkerList;$/;" t typeref:struct:passageList_st +PreArc preGraph.c /^typedef struct preArc_st PreArc;$/;" t typeref:struct:preArc_st file: +PreArcI globals.h /^typedef ArrayIdx PreArcI;$/;" t +PreGraph globals.h /^typedef struct preGraph_st PreGraph;$/;" t typeref:struct:preGraph_st +PreMarker globals.h /^typedef struct preMarker_st PreMarker;$/;" t typeref:struct:preMarker_st +PreNode globals.h /^typedef struct preNode_st PreNode;$/;" t typeref:struct:preNode_st +Probability globals.h /^typedef double Probability;$/;" t +Quality globals.h /^typedef uint8_t Quality;$/;" t +RAW readSet.c 1394;" d file: +RAW_GZ readSet.c 1395;" d file: +RBConnection readCoherentGraph.c /^typedef struct rb_connection_st RBConnection;$/;" t typeref:struct:rb_connection_st file: +READS_PER_LOCK scaffold.c 78;" d file: +REFERENCE globals.h 47;" d +RELEASE_NUMBER globals.h 40;" d +ReadOccurence scaffold.c /^typedef struct readOccurence_st ReadOccurence;$/;" t typeref:struct:readOccurence_st file: +ReadSet globals.h /^typedef struct readSet_st ReadSet;$/;" t typeref:struct:readSet_st +ReadStart globals.h /^typedef struct readStart_st ReadStart;$/;" t typeref:struct:readStart_st +RecycleBin recycleBin.h /^typedef struct recycleBin_st RecycleBin;$/;" t typeref:struct:recycleBin_st +RecycleBin_Node recycleBin.c /^typedef struct RecycleBin_Node {$/;" s file: +RecycleBin_Node recycleBin.c /^} RecycleBin_Node;$/;" t typeref:struct:RecycleBin_Node file: +ReferenceCoord graphStats.c /^typedef struct referenceCoord_st ReferenceCoord;$/;" t typeref:struct:referenceCoord_st file: +ReferenceCoordinate readSet.c /^typedef struct referenceCoordinate_st ReferenceCoordinate;$/;" t typeref:struct:referenceCoordinate_st file: +ReferenceCoordinateTable readSet.c /^typedef struct referenceCoordinateTable_st ReferenceCoordinateTable;$/;" t typeref:struct:referenceCoordinateTable_st file: +ReferenceMapping graphReConstruction.c /^typedef struct referenceMapping_st ReferenceMapping;$/;" t typeref:struct:referenceMapping_st file: +ReferenceMapping graphStats.c /^} ATTRIBUTE_PACKED ReferenceMapping; $/;" t typeref:struct:refMap_st file: +RoadMap globals.h /^typedef struct roadmap_st RoadMap;$/;" t typeref:struct:roadmap_st +RoadMapArray globals.h /^typedef struct roadMapArray_st RoadMapArray;$/;" t typeref:struct:roadMapArray_st +SAM readSet.c 1392;" d file: +SET_BINARY_MODE readSet.c 45;" d file: +SET_BINARY_MODE readSet.c 47;" d file: +SIM correctedGraph.c /^static const Time SIM[4][4] = {$/;" v file: +SIM locallyCorrectedGraph.c /^static const Time SIM[4][4] = {$/;" v file: +SLOW_TO_FAST correctedGraph.c 2077;" d file: +SequenceReader globals.h /^typedef struct sequenceReader_st SequenceReader;$/;" t typeref:struct:sequenceReader_st +ShortLength globals.h /^typedef int16_t ShortLength;$/;" t +ShortLength globals.h /^typedef int32_t ShortLength;$/;" t +ShortReadMarker globals.h /^typedef struct shortReadMarker_st ShortReadMarker;$/;" t typeref:struct:shortReadMarker_st +SingleRotateWithLeft splay.c /^static SplayNode *SingleRotateWithLeft(SplayNode * K2)$/;" f file: +SingleRotateWithRight splay.c /^static SplayNode *SingleRotateWithRight(SplayNode * K1)$/;" f file: +SmallNodeList graphReConstruction.c /^typedef struct smallNodeList_st SmallNodeList;$/;" t typeref:struct:smallNodeList_st file: +Splay splay.c /^static SplayTree *Splay(Kmer * kmer, SplayTree * T)$/;" f file: +SplayNode splay.c /^typedef struct splayNode_st SplayNode;$/;" t typeref:struct:splayNode_st file: +SplayTable globals.h /^typedef struct splayTable_st SplayTable;$/;" t typeref:struct:splayTable_st +SplayTree splay.c /^typedef struct splayNode_st SplayTree;$/;" t typeref:struct:splayNode_st file: +SplayTree splay.h /^typedef struct splayNode_st SplayTree;$/;" t typeref:struct:splayNode_st +StringBuffer utility.h /^StringBuffer;$/;" t typeref:struct:__anon1 +THYMINE graph.c 36;" d file: +THYMINE graphReConstruction.c 46;" d file: +THYMINE preGraph.c 41;" d file: +THYMINE preGraphConstruction.c 42;" d file: +TICKET_BLOCK_SIZE correctedGraph.c 36;" d file: +Thymine tightString.c /^static const Nucleotide Thymine = 3;$/;" v file: +Ticket correctedGraph.c /^typedef struct tkt_st Ticket;$/;" t typeref:struct:tkt_st file: +TightString globals.h /^typedef struct tString_st TightString;$/;" t typeref:struct:tString_st +Time globals.h /^typedef double Time;$/;" t +UNDEFINED kmer.c 40;" d file: +UNRELIABLE_CONNECTION_CUTOFF scaffold.c /^static IDnum UNRELIABLE_CONNECTION_CUTOFF = 5;$/;" v file: +UPDATE_NUMBER globals.h 41;" d +UTILITY_H_ utility.h 22;" d +VERSION_NUMBER globals.h 39;" d +WORDLENGTH correctedGraph.c /^static int WORDLENGTH;$/;" v file: +WORDLENGTH locallyCorrectedGraph.c /^static int WORDLENGTH;$/;" v file: +WORDLENGTH roadMap.h /^ int WORDLENGTH;$/;" m struct:roadMapArray_st +WORDLENGTH splayTable.c /^ int WORDLENGTH;$/;" m struct:splayTable_st file: +_ALLOC_ARRAY_H_ allocArray.h 23;" d +_CONCATENATEDGRAPH_H_ concatenatedGraph.h 22;" d +_CONCATENATEDPREGRAPH_H_ concatenatedPreGraph.h 22;" d +_CORRECTEDGRAPH_H_ correctedGraph.h 22;" d +_DFIBHEAP_H_ dfibHeap.h 22;" d +_DFIBPRIV_H_ dfibpriv.h 51;" d +_DFIB_H_ dfib.h 51;" d +_FIBHEAP_H_ fibHeap.h 22;" d +_FIBPRIV_H_ fibpriv.h 51;" d +_FIB_H_ fib.h 51;" d +_GLOBALS_H_ globals.h 22;" d +_GRAPHRECONSTRUCTION_H_ graphReConstruction.h 22;" d +_GRAPHSTATS_H_ graphStats.h 22;" d +_GRAPH_H_ graph.h 22;" d +_KMEROCCURENCETABLE_H_ kmerOccurenceTable.h 22;" d +_KMER_H_ kmer.h 22;" d +_LOCALLYCORRECTEDGRAPH_H_ locallyCorrectedGraph.h 22;" d +_PASSAGEMARKER_H_ passageMarker.h 22;" d +_PREGRAPHCONSTRUCTION_H_ preGraphConstruction.h 22;" d +_PREGRAPH_H_ preGraph.h 22;" d +_READCOHERENTGRAPH_H_ readCoherentGraph.h 22;" d +_READSET_H_ readSet.h 22;" d +_ROADMAP_H_ roadMap.h 22;" d +_SCAFFOLD_H_ scaffold.h 22;" d +_SHORTREADPAIRS_H_ shortReadPairs.h 22;" d +_SPLAYTABLE_H_ splayTable.h 22;" d +_Splay_H splay.h 22;" d +_TIGHTSTRING_H_ tightString.h 22;" d +abs_ID shortReadPairs.c /^static IDnum abs_ID(IDnum val)$/;" f file: +abs_bool shortReadPairs.c /^static boolean abs_bool(boolean val)$/;" f file: +absorbExtension shortReadPairs.c /^static void absorbExtension(Node * node, Node * extension)$/;" f file: +absorbExtensionInScaffold shortReadPairs.c /^static void absorbExtensionInScaffold(Node * node, Node * source)$/;" f file: +accelerationBits kmerOccurenceTable.c /^ short int accelerationBits;$/;" m struct:kmerOccurenceTable_st file: +accelerationShift kmerOccurenceTable.c /^ short int accelerationShift;$/;" m struct:kmerOccurenceTable_st file: +accelerationTable kmerOccurenceTable.c /^ IDnum *accelerationTable;$/;" m struct:kmerOccurenceTable_st file: +activateArcLookupTable graph.c /^void activateArcLookupTable(Graph * graph)$/;" f +activateGapMarkers graph.c /^void activateGapMarkers(Graph * graph)$/;" f +activateReadStarts graph.c /^void activateReadStarts(Graph * graph)$/;" f +activeNode correctedGraph.c /^static Node *activeNode;$/;" v file: +addBufferToDescriptor graph.c /^static void addBufferToDescriptor(Node * node, Coordinate length)$/;" f file: +addEmptyNodeToGraph graph.c /^Node *addEmptyNodeToGraph(Graph * graph, IDnum ID)$/;" f +addPassageMarker passageMarker.c /^PassageMarkerI addPassageMarker(IDnum sequenceID, Coordinate start,$/;" f +addPreArcToPreNode_pg preGraph.c /^static void addPreArcToPreNode_pg(PreArcI preArc, IDnum preNodeID,$/;" f file: +addPreMarker_pg preGraph.c /^PreMarker * addPreMarker_pg(PreGraph * preGraph, IDnum nodeID, IDnum seqID, Coordinate * start, PreMarker * previous) {$/;" f +addPreNodeToPreGraph_pg preGraph.c /^void addPreNodeToPreGraph_pg(PreGraph * preGraph, Coordinate start,$/;" f +addReadStart graph.c /^void addReadStart(Node * node, IDnum seqID, Coordinate position,$/;" f +addReferenceCoordinate readSet.c /^static void addReferenceCoordinate(ReferenceCoordinateTable * table, char * name, Coordinate start, Coordinate finish, boolean positive_strand) {$/;" f file: +addUncertainPassageMarker passageMarker.c /^PassageMarkerI addUncertainPassageMarker(IDnum sequenceID, Node * node)$/;" f +adjustLongReads shortReadPairs.c /^static void adjustLongReads(Node * target, Coordinate nodeLength)$/;" f file: +adjustShortReads readCoherentGraph.c /^static void adjustShortReads(Node * target, PassageMarkerI pathMarker)$/;" f file: +adjustShortReads shortReadPairs.c /^static void adjustShortReads(Node * target, Node * source)$/;" f file: +adjustShortReadsByLength shortReadPairs.c /^static void adjustShortReadsByLength(Node * target, Coordinate nodeLength)$/;" f file: +admitGroupies readCoherentGraph.c /^static void admitGroupies(Node * source, Node * bypass)$/;" f file: +allocArrayAllocate allocArray.c /^allocArrayAllocate (AllocArray *array)$/;" f +allocArrayArrayAllocate allocArray.c /^ArrayIdx allocArrayArrayAllocate(AllocArray *array)$/;" f +allocArrayArrayFree allocArray.c /^allocArrayArrayFree(AllocArray *array, ArrayIdx idx)$/;" f +allocArrayFree allocArray.c /^allocArrayFree (AllocArray *array, ArrayIdx idx)$/;" f +allocArrayGetElement allocArray.c /^allocArrayGetElement (AllocArray *array, ArrayIdx idx)$/;" f file: +allocExitError utility.c /^static void allocExitError(const char *function, unsigned long long count,$/;" f file: +allocateArc graph.c /^Arc *allocateArc()$/;" f +allocateConnection scaffold.c /^static Connection *allocateConnection()$/;" f file: +allocateConnectionStack scaffold.c /^static ConnectionStack *allocateConnectionStack(void)$/;" f file: +allocateDFibHeapNode dfib.c /^static DFibHeapNode *allocateDFibHeapNode(DFibHeap * heap)$/;" f file: +allocateFibHeapEl fib.c /^static FibHeapNode *allocateFibHeapEl(FibHeap * heap)$/;" f file: +allocateGapMarker graph.c /^static GapMarker *allocateGapMarker()$/;" f file: +allocateKmerOccurences kmerOccurenceTable.c /^void allocateKmerOccurences(IDnum kmerCount, KmerOccurenceTable * table) {$/;" f +allocateMask graphStats.c /^static Mask *allocateMask()$/;" f file: +allocateMask splayTable.c /^static Mask *allocateMask()$/;" f file: +allocateNode graph.c /^Node *allocateNode()$/;" f +allocateNodeList shortReadPairs.c /^static NodeList *allocateNodeList()$/;" f file: +allocateNodeSpace graph.c /^void allocateNodeSpace(Graph * graph, IDnum nodeCount)$/;" f +allocatePassageMarker passageMarker.c /^PassageMarkerI allocatePassageMarker()$/;" f +allocatePassageMarkerList passageMarker.c /^PassageMarkerList *allocatePassageMarkerList()$/;" f +allocatePointer recycleBin.c /^void *allocatePointer(RecycleBin * recycle_bin)$/;" f +allocatePreMarkerCountSpace_pg preGraph.c /^void allocatePreMarkerCountSpace_pg(PreGraph * preGraph)$/;" f +allocatePreMarkerSpace_pg preGraph.c /^void allocatePreMarkerSpace_pg(PreGraph * preGraph) {$/;" f +allocatePreNodeSpace_pg preGraph.c /^void allocatePreNodeSpace_pg(PreGraph * preGraph, IDnum preNodeCount)$/;" f +allocateRBConnection readCoherentGraph.c /^static RBConnection *allocateRBConnection()$/;" f file: +allocateReadToNodeTables scaffold.c /^static ReadOccurence **allocateReadToNodeTables(IDnum * readNodeCounts,$/;" f file: +allocateSmallNodeList graphReConstruction.c /^static SmallNodeList *allocateSmallNodeList()$/;" f file: +allocateSplayNode splay.c /^static SplayNode *allocateSplayNode()$/;" f file: +allocated utility.h /^ size_t allocated;$/;" m struct:__anon1 +annot preGraphConstruction.c /^ Annotation *annot;$/;" m struct:insertionMarker_st file: +annotationBuffer splayTable.c /^StringBuffer *annotationBuffer = NULL;$/;" v +annotationBuffer splayTable.c /^static StringBuffer **annotationBuffer = NULL;$/;" v file: +annotationBufferW splayTable.c /^static StringBuffer **annotationBufferW = NULL;$/;" v file: +annotationCount roadMap.c /^ ShortLength annotationCount;$/;" m struct:roadmap_st file: +annotationOffset preGraphConstruction.c /^Coordinate *annotationOffset = NULL;$/;" v +annotation_st roadMap.c /^struct annotation_st {$/;" s file: +annotations roadMap.h /^ Annotation *annotations;$/;" m struct:roadMapArray_st +appendDescriptors graph.c /^void appendDescriptors(Node * destination, Node * source)$/;" f +appendDescriptors_pg preGraph.c /^void appendDescriptors_pg(Descriptor ** start, int * writeOffset, IDnum preNodeID, PreGraph* preGraph, boolean initial) {$/;" f +appendGap graph.c /^void appendGap(Node * node, Coordinate length, Graph * graph)$/;" f +appendLine splayTable.c /^static void appendLine(char *line, int thread)$/;" f file: +appendNegativeDescriptor_pg preGraph.c /^static void appendNegativeDescriptor_pg(Descriptor ** writePtr, int * writeOffset, IDnum preNodeID, PreGraph * preGraph, boolean initial) {$/;" f file: +appendNodeGaps graph.c /^void appendNodeGaps(Node * destination, Node * source, Graph * graph)$/;" f +appendNodeSequence graph.c /^void appendNodeSequence(Node * node, TightString * sequence,$/;" f +appendPositiveDescriptor_pg preGraph.c /^static void appendPositiveDescriptor_pg(Descriptor ** writePtr, int * writeOffset, IDnum preNodeID, PreGraph * preGraph, boolean initial) {$/;" f file: +appendSequence graph.c /^void appendSequence(Node * node, TightString * reads,$/;" f +appendSequenceToDescriptor graph.c /^static Descriptor *appendSequenceToDescriptor(Descriptor * descr,$/;" f file: +appendStringBuffer utility.c /^void appendStringBuffer(StringBuffer *buffer, char *str)$/;" f +arc graph.c /^ Arc *arc; \/\/ 64$/;" m struct:node_st file: +arcCount graph.c /^ IDnum arcCount; \/\/ 32$/;" m struct:node_st file: +arcCount graph.c /^int arcCount(Node * node)$/;" f +arcLookupTable graph.c /^ Arc **arcLookupTable;$/;" m struct:graph_st file: +arcMemory graph.c /^static RecycleBin *arcMemory = NULL;$/;" v file: +arcMergeSort graph.c /^static void arcMergeSort(Arc ** arcPtr, IDnum count)$/;" f file: +arc_st graph.c /^struct arc_st {$/;" s file: +array readSet.c /^ ReferenceCoordinate * array;$/;" m struct:referenceCoordinateTable_st file: +array roadMap.h /^ RoadMap *array;$/;" m struct:roadMapArray_st +arrayLength readSet.c /^ IDnum arrayLength;$/;" m struct:referenceCoordinateTable_st file: +backReference shortReadPairs.c /^ Connection *backReference;$/;" m struct:miniConnection_st file: +blockSize allocArray.h /^ size_t blockSize;$/;" m struct:AllocArray_st +blocks allocArray.h /^ void **blocks;$/;" m struct:AllocArray_st +blurLastShortReadMarker graph.c /^void blurLastShortReadMarker(Node * node, Graph * graph)$/;" f +boolean globals.h /^typedef int8_t boolean;$/;" t +bufferWritter splayTable.c /^static void bufferWritter(FILE *outFile)$/;" f file: +buildScaffold scaffold.c /^void buildScaffold(Graph * argGraph,$/;" f +bypass readCoherentGraph.c /^static Node *bypass()$/;" f file: +callocOrExit utility.h 39;" d +callocOrExit3 utility.c /^void *callocOrExit3(size_t count, size_t size, const char *name)$/;" f +callocOrExitWithoutCast utility.h 49;" d +catDescriptors graph.c /^static void catDescriptors(Descriptor * descr, Coordinate destinationLength, Descriptor * copy, Coordinate sourceLength) $/;" f file: +categories readSet.h /^ Category *categories;$/;" m struct:readSet_st +ceillog2 dfib.c /^static inline IDnum ceillog2(IDnum a)$/;" f file: +ceillog2 fib.c /^static inline IDnum ceillog2(IDnum a)$/;" f file: +charLeftFilter kmer.c /^static const uint8_t charLeftFilter = (uint8_t) 3 << 6; $/;" v file: +charWordFilter kmer.c /^static uint8_t charWordFilter = (uint8_t) ((int8_t) -1); $/;" v file: +chars kmer.h /^ uint8_t chars;$/;" m struct:kmer_st +checkNode shortReadPairs.c /^void checkNode(Node* node) {$/;" f +chooseDestination graphStats.c /^static Node *chooseDestination(PassageMarkerList * list)$/;" f file: +chooseNextInternalPreNode preGraphConstruction.c /^static IDnum chooseNextInternalPreNode(IDnum currentPreNodeID,$/;" f file: +chunk_list recycleBin.c /^ Chunk *chunk_list;$/;" m struct:recycleBin_st file: +chunk_pos recycleBin.c /^ int chunk_pos;$/;" m struct:recycleBin_st file: +chunk_st recycleBin.c /^typedef struct chunk_st {$/;" s file: +clean scaffold.c /^ unsigned char clean;$/;" m struct:connection_st file: +cleanMemory shortReadPairs.c /^static void cleanMemory()$/;" f file: +cleanScaffoldMemory scaffold.c /^void cleanScaffoldMemory() {$/;" f +cleanUpMemory preGraphConstruction.c /^cleanUpMemory(PreGraph * preGraph, RoadMapArray * rdmaps, IDnum * chains)$/;" f file: +cleanUpRedundancy correctedGraph.c /^static void cleanUpRedundancy()$/;" f file: +cleanUpRedundancy_local locallyCorrectedGraph.c /^static void cleanUpRedundancy_local()$/;" f file: +clearKmer kmer.c /^void clearKmer(Kmer * kmer) {$/;" f +clipTipsHard correctedGraph.c /^void clipTipsHard(Graph * graph)$/;" f +clipTipsVeryHardLocally locallyCorrectedGraph.c /^static void clipTipsVeryHardLocally()$/;" f file: +clipTips_pg concatenatedPreGraph.c /^void clipTips_pg(PreGraph * preGraph)$/;" f +collectReferenceCoords graphStats.c /^static ReferenceCoord * collectReferenceCoords(char * sequencesFilename, IDnum referenceCount) {$/;" f file: +comesFromNode shortReadPairs.c /^static boolean comesFromNode(PassageMarkerI marker, Node * node)$/;" f file: +commonLength graphStats.c /^Coordinate commonLength(Node * node, IDnum firstStrain)$/;" f +commonNodeReads graph.c /^ShortReadMarker *commonNodeReads(Node * nodeA, Node * nodeB, Graph * graph,$/;" f +compareCoords graphStats.c /^static int compareCoords(const void * A, const void * B) {$/;" f file: +compareIDnums graph.c /^static inline int compareIDnums(const void *A, const void *B)$/;" f file: +compareInsertionMarkers preGraphConstruction.c /^int compareInsertionMarkers(const void *A, const void *B)$/;" f +compareKmerOccurences kmerOccurenceTable.c /^int compareKmerOccurences(void const *A, void const *B)$/;" f +compareKmers kmer.c /^int compareKmers(Kmer* k1, Kmer* k2) {$/;" f +compareNodeCovs graphStats.c /^int compareNodeCovs(const void * A, const void * B) {$/;" f +compareNodeMasks graphReConstruction.c /^static int compareNodeMasks(const void * ptrA, const void * ptrB) {$/;" f file: +comparePaths correctedGraph.c /^static void comparePaths(Node * destination, Node * origin)$/;" f file: +comparePaths_local locallyCorrectedGraph.c /^static void comparePaths_local(Node * destination, Node * origin)$/;" f file: +compareReadOccurences scaffold.c /^int compareReadOccurences(const void *A, const void * B) {$/;" f +compareRefCoords readSet.c /^static int compareRefCoords(const void * ptrA, const void * ptrB) {$/;" f file: +compareRefMaps graphReConstruction.c /^static int compareRefMaps(const void * ptrA, const void * ptrB) {$/;" f file: +compareReferenceMappings graphStats.c /^static int compareReferenceMappings(const void * A, const void * B) {$/;" f file: +compareSequences correctedGraph.c /^compareSequences(TightString * sequence1, TightString * sequence2)$/;" f file: +compareSequences locallyCorrectedGraph.c /^compareSequences(TightString * sequence1, TightString * sequence2)$/;" f file: +compareShortReadMarkers graph.c /^static inline int compareShortReadMarkers(const void *A, const void *B)$/;" f file: +computeClearHSPs splayTable.c /^static void computeClearHSPs(TightString * array, boolean second_in_pair, SplayTable * table, IDnum ** sequenceIDs, Coordinate ** coords, IDnum * mapReferenceIDs, Coordinate * mapCoords, Coordinate mapCount, IDnum seqID) {$/;" f file: +computeNodeMasks graphReConstruction.c /^static NodeMask * computeNodeMasks(ReferenceMapping * referenceMappings, Coordinate arrayLength, Graph * graph) {$/;" f file: +computeNodeToNodeMappings scaffold.c /^static Connection **computeNodeToNodeMappings(ReadOccurence ** readNodes,$/;" f file: +computePartialReadToNodeMappingLong scaffold.c /^static void computePartialReadToNodeMappingLong(IDnum nodeID,$/;" f file: +computePartialReadToNodeMappingShort scaffold.c /^static void computePartialReadToNodeMappingShort(IDnum nodeID,$/;" f file: +computeReadToNodeCounts scaffold.c /^static IDnum *computeReadToNodeCounts(Coordinate *totalCount)$/;" f file: +computeReadToNodeMappings scaffold.c /^static ReadOccurence **computeReadToNodeMappings(IDnum * readNodeCounts,$/;" f file: +computeReferenceMappings graphReConstruction.c /^static ReferenceMapping * computeReferenceMappings(char * preGraphFilename, ReadSet * reads, Coordinate * referenceMappingLength, IDnum * referenceCount) {$/;" f file: +computeSecondInPair readSet.c /^static void computeSecondInPair(ReadSet * reads)$/;" f file: +computeSubsequentNodesLength graphStats.c /^Coordinate computeSubsequentNodesLength(Node * node)$/;" f +computeVirtualNodeLength graphStats.c /^Coordinate computeVirtualNodeLength(Node * node)$/;" f +concatenateCommonTodoLists correctedGraph.c /^static void concatenateCommonTodoLists(Node * nodeA, Node * nodeB)$/;" f file: +concatenateGraph concatenatedGraph.c /^void concatenateGraph(Graph * graph)$/;" f +concatenateLongReads shortReadPairs.c /^static void concatenateLongReads(Node * node, Node * candidate,$/;" f file: +concatenateNodesAndVaccinate correctedGraph.c /^static void concatenateNodesAndVaccinate(Node * nodeA, Node * nodeB,$/;" f file: +concatenatePassageMarkers passageMarker.c /^void concatenatePassageMarkers(PassageMarkerI marker,$/;" f +concatenatePathNodes correctedGraph.c /^static void concatenatePathNodes(PassageMarkerI pathStart)$/;" f file: +concatenatePreGraph_pg concatenatedPreGraph.c /^void concatenatePreGraph_pg(PreGraph * preGraph)$/;" f +concatenatePreNodes concatenatedPreGraph.c /^static void concatenatePreNodes(IDnum preNodeAID, PreArcI oldPreArc,$/;" f file: +concatenateReadStarts concatenatedGraph.c /^void concatenateReadStarts(Node * target, Node * source, Graph * graph)$/;" f +concatenateReferenceMarkers_H2H_pg preGraph.c /^static void concatenateReferenceMarkers_H2H_pg(IDnum preNodeAID, IDnum preNodeBID, PreGraph * preGraph, Coordinate totalOffset) {$/;" f file: +concatenateReferenceMarkers_H2T_pg preGraph.c /^static void concatenateReferenceMarkers_H2T_pg(IDnum preNodeAID, IDnum preNodeBID, PreGraph * preGraph, Coordinate totalOffset) {$/;" f file: +concatenateReferenceMarkers_T2H_pg preGraph.c /^static void concatenateReferenceMarkers_T2H_pg(IDnum preNodeAID, IDnum preNodeBID, PreGraph * preGraph, Coordinate totalOffset) {$/;" f file: +concatenateReferenceMarkers_T2T_pg preGraph.c /^static void concatenateReferenceMarkers_T2T_pg(IDnum preNodeAID, IDnum preNodeBID, PreGraph * preGraph, Coordinate totalOffset) {$/;" f file: +concatenateReferenceMarkers_pg preGraph.c /^void concatenateReferenceMarkers_pg(IDnum preNodeAID, IDnum preNodeBID, PreGraph * preGraph, Coordinate totalOffset) {$/;" f +concatenateStringOfNodes concatenatedGraph.c /^void concatenateStringOfNodes(Node * nodeA, Graph * graph)$/;" f +concatenateTodoListIntoActive correctedGraph.c /^static void concatenateTodoListIntoActive(Node * nodeB)$/;" f file: +concatenateTodoLists correctedGraph.c /^static void concatenateTodoLists(Node * nodeA, Node * nodeB)$/;" f file: +confidenceScores readSet.h /^ Quality **confidenceScores;$/;" m struct:readSet_st +connectAnnotation preGraphConstruction.c /^static void connectAnnotation(IDnum * currentPreNodeID, Annotation * annot,$/;" f file: +connectPassageMarkers passageMarker.c /^connectPassageMarkers(PassageMarkerI previous, PassageMarkerI next,$/;" f +connectPreNodeToTheNext preGraphConstruction.c /^static void connectPreNodeToTheNext(IDnum * currentPreNodeID,$/;" f file: +connectPreNodes preGraphConstruction.c /^static void connectPreNodes(RoadMapArray * rdmaps, PreGraph * preGraph,$/;" f file: +connection scaffold.c /^ Connection *connection;$/;" m struct:ConnectionStack_st file: +connectionMemory scaffold.c /^static RecycleBin *connectionMemory = NULL;$/;" v file: +connectionSingleRotateWithLeft scaffold.c /^static Connection *connectionSingleRotateWithLeft(Connection * K2)$/;" f file: +connectionSingleRotateWithRight scaffold.c /^static Connection *connectionSingleRotateWithRight(Connection * K1)$/;" f file: +connectionStackMemory scaffold.c /^RecycleBin *connectionStackMemory = NULL;$/;" v +connection_st scaffold.c /^struct connection_st {$/;" s file: +convertInsertionMarkers preGraphConstruction.c /^static void convertInsertionMarkers(InsertionMarker * insertionMarkers,$/;" f file: +convertMarker preGraphConstruction.c /^static void convertMarker(InsertionMarker * marker, IDnum nodeID)$/;" f file: +convertSequences readSet.c /^void convertSequences(ReadSet * rs)$/;" f +coord roadMap.c /^ ShortLength coord;$/;" m union:positionPtr file: +copyDownDescriptor graph.c /^static void copyDownDescriptor(Descriptor ** writePtr, int *writeOffset,$/;" f file: +copyDownSequence graph.c /^static void copyDownSequence(Descriptor ** writePtr, int *writeOffset,$/;" f file: +copyKmers kmer.c /^void copyKmers(Kmer* k1, Kmer* k2) {$/;" f +copyMarkers graphStats.c /^static PassageMarkerList *copyMarkers(Node * node)$/;" f file: +copyPassageMarkerList passageMarker.c /^PassageMarkerList *copyPassageMarkerList(PassageMarkerList * list)$/;" f +copyPreMarker preGraph.c /^static void copyPreMarker(PreMarker * dest, PreMarker * source, IDnum preNodeAID, PreGraph * preGraph) {$/;" f file: +correctGraph correctedGraph.c /^void correctGraph(Graph * argGraph, ShortLength * argSequenceLengths, Category * argSequenceCategories)$/;" f +correctGraphLocally locallyCorrectedGraph.c /^void correctGraphLocally(Node * argStart)$/;" f +countCoOccurences scaffold.c /^static unsigned char * countCoOccurences(IDnum * coOccurencesCount,$/;" f file: +countLocalBreakpoints graphStats.c /^int countLocalBreakpoints(PassageMarkerI marker, IDnum firstStrain)$/;" f +countMappings graphReConstruction.c /^static IDnum countMappings(char * preGraphFilename) {$/;" f file: +countPreNodes preGraphConstruction.c /^countPreNodes(RoadMapArray * rdmaps, PreGraph * preGraph,$/;" f file: +countReferenceKmers splayTable.c /^static Coordinate countReferenceKmers(ReadSet * reads, int wordLength) {$/;" f file: +countShortReads scaffold.c /^static IDnum **countShortReads(Graph * graph, ReadSet * reads)$/;" f file: +createAnalogousArc graph.c /^void createAnalogousArc(Node * originNode, Node * destinationNode,$/;" f +createAnalogousPreArc_pg preGraph.c /^void createAnalogousPreArc_pg(IDnum originPreNodeID,$/;" f +createArc graph.c /^Arc *createArc(Node * originNode, Node * destinationNode, Graph * graph)$/;" f +createConnection scaffold.c /^static void createConnection(IDnum nodeID,$/;" f file: +createNewConnection scaffold.c /^Connection *createNewConnection(IDnum nodeID, IDnum node2ID,$/;" f +createNodeLocks graphReConstruction.c /^createNodeLocks(Graph *graph)$/;" f file: +createNodeLocks preGraphConstruction.c /^static void createNodeLocks(PreGraph *preGraph)$/;" f file: +createNodeLocks scaffold.c /^createNodeLocks(Graph *graph)$/;" f file: +createNodeReadStartArrays graph.c /^void createNodeReadStartArrays(Graph * graph)$/;" f +createPreArc_pg preGraph.c /^PreArcI createPreArc_pg(IDnum originPreNodeID, IDnum destinationPreNodeID,$/;" f +createPreMarkers preGraphConstruction.c /^static void createPreMarkers(RoadMapArray * rdmaps, PreGraph * preGraph,$/;" f file: +createPreNodes preGraphConstruction.c /^createPreNodes(RoadMapArray * rdmaps, PreGraph * preGraph,$/;" f file: +createReadPairingArray readSet.c /^void createReadPairingArray(ReadSet* reads)$/;" f +createReadsLocks scaffold.c /^createReadsLocks()$/;" f file: +createTwinConnection scaffold.c /^static void createTwinConnection(IDnum nodeID, IDnum node2ID,$/;" f file: +createTwinConnectionInTree scaffold.c /^static void createTwinConnectionInTree(IDnum nodeID,$/;" f file: +currentBlocks allocArray.h /^ size_t currentBlocks;$/;" m struct:AllocArray_st +currentElements allocArray.h /^ size_t currentElements;$/;" m struct:AllocArray_st +dbgCounter correctedGraph.c /^static IDnum dbgCounter;$/;" v file: +dbgCounter readCoherentGraph.c /^static IDnum dbgCounter = 0;$/;" v file: +deactivateArcLookupTable graph.c /^void deactivateArcLookupTable(Graph * graph)$/;" f +deactivateGapMarkers graph.c /^void deactivateGapMarkers(Graph * graph)$/;" f +deactivateLocalCorrectionSettings locallyCorrectedGraph.c /^void deactivateLocalCorrectionSettings()$/;" f +deactivateReadStarts graph.c /^void deactivateReadStarts(Graph * graph)$/;" f +deallocateArc graph.c /^void deallocateArc(Arc * arc)$/;" f +deallocateConnection scaffold.c /^static void deallocateConnection(Connection * connect)$/;" f file: +deallocateConnectionStack scaffold.c /^static void deallocateConnectionStack(ConnectionStack *stack)$/;" f file: +deallocateDFibHeapNode dfib.c /^static void deallocateDFibHeapNode(DFibHeapNode * a, DFibHeap * heap)$/;" f file: +deallocateFibHeapEl fib.c /^static void deallocateFibHeapEl(FibHeapNode * a, FibHeap * heap)$/;" f file: +deallocateMask graphStats.c /^static void deallocateMask(Mask * mask)$/;" f file: +deallocateNode graph.c /^void deallocateNode(Node * node)$/;" f +deallocateNodeList shortReadPairs.c /^static void deallocateNodeList(NodeList * nodeList)$/;" f file: +deallocatePassageMarker passageMarker.c /^static void deallocatePassageMarker(PassageMarkerI marker)$/;" f file: +deallocatePassageMarkerList passageMarker.c /^void deallocatePassageMarkerList(PassageMarkerList * marker)$/;" f +deallocatePointer recycleBin.c /^void deallocatePointer(RecycleBin * recycle_bin, void *data)$/;" f +deallocatePreArc_pg preGraph.c /^void deallocatePreArc_pg(PreArcI preArc)$/;" f +deallocateRBConnection readCoherentGraph.c /^static void deallocateRBConnection(RBConnection * nodeList)$/;" f file: +deallocateSmallNodeList graphReConstruction.c /^static void deallocateSmallNodeList(SmallNodeList * smallNodeList)$/;" f file: +deleteNextPassageMarker passageMarker.c /^void deleteNextPassageMarker(PassageMarkerI marker, Graph * graph)$/;" f +descriptor graph.c /^ Descriptor *descriptor; \/\/ 64$/;" m struct:node_st file: +descriptor preGraph.c /^ Descriptor *descriptor;$/;" m struct:preNode_st file: +destination graph.c /^ Node *destination; \/\/ 64$/;" m struct:arc_st file: +destination scaffold.c /^ Node *destination;$/;" m struct:connection_st file: +destroyAllPassageMarkers passageMarker.c /^void destroyAllPassageMarkers()$/;" f +destroyAllSplayTrees splay.c /^void destroyAllSplayTrees()$/;" f +destroyAllocArray allocArray.c /^destroyAllocArray (AllocArray *array)$/;" f +destroyAllocArrayArray allocArray.c /^void destroyAllocArrayArray(AllocArray *allocArray)$/;" f +destroyAllocArrayChunks allocArray.c /^destroyAllocArrayChunks (AllocArray *array)$/;" f +destroyAnnotationBuffers splayTable.c /^static void destroyAnnotationBuffers(void)$/;" f file: +destroyArc graph.c /^void destroyArc(Arc * arc, Graph * graph)$/;" f +destroyConnection scaffold.c /^void destroyConnection(Connection * connect, IDnum nodeID)$/;" f +destroyConnectionStackMemory scaffold.c /^static void destroyConnectionStackMemory(void)$/;" f file: +destroyDHeap dfibHeap.c /^void destroyDHeap(DFibHeap * heap)$/;" f +destroyGraph graph.c /^void destroyGraph(Graph * graph)$/;" f +destroyHeap fibHeap.c /^void destroyHeap(FibHeap * heap)$/;" f +destroyKmerOccurenceTable kmerOccurenceTable.c /^void destroyKmerOccurenceTable(KmerOccurenceTable * kmerTable) {$/;" f +destroyNode graph.c /^void destroyNode(Node * node, Graph * graph)$/;" f +destroyNodeInDHeap dfibHeap.c /^void destroyNodeInDHeap(DFibHeapNode * node, DFibHeap * heap)$/;" f +destroyNodeInHeap fibHeap.c /^void destroyNodeInHeap(FibHeapNode * node, FibHeap * heap)$/;" f +destroyNodeList shortReadPairs.c /^static void destroyNodeList(NodeList * nodeList)$/;" f file: +destroyNodePassageMarkers graphStats.c /^destroyNodePassageMarkers(Graph *graph,$/;" f file: +destroyPassageMarker passageMarker.c /^void destroyPassageMarker(PassageMarkerI marker)$/;" f +destroyPassageMarkerList correctedGraph.c /^static void destroyPassageMarkerList(PassageMarkerList ** list)$/;" f file: +destroyPassageMarkerList graphStats.c /^static void destroyPassageMarkerList(PassageMarkerList ** list)$/;" f file: +destroyPaths correctedGraph.c /^static void destroyPaths()$/;" f file: +destroyPaths locallyCorrectedGraph.c /^static void destroyPaths()$/;" f file: +destroyPreArc_pg preGraph.c /^void destroyPreArc_pg(PreArcI preArc, PreGraph * preGraph)$/;" f +destroyPreGraph_pg preGraph.c /^void destroyPreGraph_pg(PreGraph * preGraph)$/;" f +destroyPreNode_pg preGraph.c /^void destroyPreNode_pg(IDnum preNodeID, PreGraph * preGraph)$/;" f +destroyReadSet readSet.c /^void destroyReadSet(ReadSet * reads)$/;" f +destroyRecycleBin recycleBin.c /^void destroyRecycleBin(RecycleBin * recycleBin)$/;" f +destroyRecycleBinArray recycleBin.c /^void destroyRecycleBinArray(RecycleBin * recycleBin)$/;" f +destroyRecycleBinChunks recycleBin.c /^static void destroyRecycleBinChunks(RecycleBin * recycleBin)$/;" f file: +destroyReferenceCoordinateTable readSet.c /^static void destroyReferenceCoordinateTable(ReferenceCoordinateTable * table) {$/;" f file: +destroyRoadMapArray roadMap.c /^void destroyRoadMapArray(RoadMapArray * rdmaps) {$/;" f +destroySmallNodeListMemmory graphReConstruction.c /^static void destroySmallNodeListMemmory(void)$/;" f file: +destroySplayTable splayTable.c /^void destroySplayTable(SplayTable * splayTable)$/;" f +destroyStringBuffer utility.c /^void destroyStringBuffer(StringBuffer *buffer, boolean freeString)$/;" f +destroyTightString tightString.c /^void destroyTightString(TightString * tString)$/;" f +detachDubiousReads readSet.c /^void detachDubiousReads(ReadSet * reads, boolean * dubiousReads)$/;" f +determineEligibleStartingPoints correctedGraph.c /^static void determineEligibleStartingPoints()$/;" f file: +dfh_Dl dfibpriv.h /^ IDnum dfh_Dl;$/;" m struct:dfibheap +dfh_cascading_cut dfib.c /^static void dfh_cascading_cut(DFibHeap * h, DFibHeapNode * y)$/;" f file: +dfh_checkcons dfib.c /^static void dfh_checkcons(DFibHeap * h)$/;" f file: +dfh_compare dfib.c /^static int dfh_compare(DFibHeap * h, DFibHeapNode * a, DFibHeapNode * b)$/;" f file: +dfh_comparedata dfib.c /^dfh_comparedata(DFibHeap * h, Time key, void *data, DFibHeapNode * b)$/;" f file: +dfh_cons dfibpriv.h /^ DFibHeapNode **dfh_cons;$/;" m struct:dfibheap +dfh_consolidate dfib.c /^static void dfh_consolidate(DFibHeap * h)$/;" f file: +dfh_cut dfib.c /^static void dfh_cut(DFibHeap * h, DFibHeapNode * x, DFibHeapNode * y)$/;" f file: +dfh_delete dfib.c /^void *dfh_delete(DFibHeap * h, DFibHeapNode * x)$/;" f +dfh_deleteheap dfib.c /^void dfh_deleteheap(DFibHeap * h)$/;" f +dfh_extractmin dfib.c /^void *dfh_extractmin(DFibHeap * h)$/;" f +dfh_extractminel dfib.c /^static DFibHeapNode *dfh_extractminel(DFibHeap * h)$/;" f file: +dfh_heaplink dfib.c /^static void dfh_heaplink(DFibHeap * h, DFibHeapNode * y, DFibHeapNode * x)$/;" f file: +dfh_insertel dfib.c /^static void dfh_insertel(DFibHeap * h, DFibHeapNode * x)$/;" f file: +dfh_insertkey dfib.c /^DFibHeapNode *dfh_insertkey(DFibHeap * h, Time key, void *data)$/;" f +dfh_insertrootlist dfib.c /^static void dfh_insertrootlist(DFibHeap * h, DFibHeapNode * x)$/;" f file: +dfh_makekeyheap dfib.c /^DFibHeap *dfh_makekeyheap()$/;" f +dfh_min dfibpriv.h /^ DFibHeapNode *dfh_min;$/;" m struct:dfibheap +dfh_n dfibpriv.h /^ IDnum dfh_n;$/;" m struct:dfibheap +dfh_removerootlist dfib.c /^static void dfh_removerootlist(DFibHeap * h, DFibHeapNode * x)$/;" f file: +dfh_replacedata dfib.c /^void *dfh_replacedata(DFibHeapNode * x, void *data)$/;" f +dfh_replacekey dfib.c /^Time dfh_replacekey(DFibHeap * h, DFibHeapNode * x, Time key)$/;" f +dfh_replacekeydata dfib.c /^void *dfh_replacekeydata(DFibHeap * h, DFibHeapNode * x,$/;" f +dfh_root dfibpriv.h /^ DFibHeapNode *dfh_root;$/;" m struct:dfibheap +dfhe_child dfibpriv.h /^ DFibHeapNode *dfhe_child;$/;" m struct:dfibheap_el +dfhe_data dfibpriv.h /^ void *dfhe_data;$/;" m struct:dfibheap_el +dfhe_degree dfibpriv.h /^ int dfhe_degree;$/;" m struct:dfibheap_el +dfhe_insertafter dfib.c /^static void dfhe_insertafter(DFibHeapNode * a, DFibHeapNode * b)$/;" f file: +dfhe_insertbefore dfib.c /^static inline void dfhe_insertbefore(DFibHeapNode * a, DFibHeapNode * b)$/;" f file: +dfhe_key dfibpriv.h /^ Time dfhe_key;$/;" m struct:dfibheap_el +dfhe_left dfibpriv.h /^ DFibHeapNode *dfhe_left;$/;" m struct:dfibheap_el +dfhe_mark dfibpriv.h /^ boolean dfhe_mark;$/;" m struct:dfibheap_el +dfhe_newelem dfib.c /^static DFibHeapNode *dfhe_newelem(DFibHeap * h)$/;" f file: +dfhe_p dfibpriv.h /^ DFibHeapNode *dfhe_p;$/;" m struct:dfibheap_el +dfhe_remove dfib.c /^static DFibHeapNode *dfhe_remove(DFibHeapNode * x)$/;" f file: +dfhe_right dfibpriv.h /^ DFibHeapNode *dfhe_right;$/;" m struct:dfibheap_el +dfibheap dfibpriv.h /^struct dfibheap {$/;" s +dfibheap_el dfibpriv.h /^struct dfibheap_el {$/;" s +dfibheap_el_getKey dfib.c /^Time dfibheap_el_getKey(DFibHeapNode * node)$/;" f +dfibheap_getSize dfib.c /^IDnum dfibheap_getSize(DFibHeap * heap)$/;" f +dheap correctedGraph.c /^static DFibHeap *dheap;$/;" v file: +dheap locallyCorrectedGraph.c /^static DFibHeap *dheap;$/;" v file: +dheapNodes correctedGraph.c /^static DFibHeapNode **dheapNodes;$/;" v file: +dheapNodes locallyCorrectedGraph.c /^static DFibHeapNode **dheapNodes;$/;" v file: +direct_count scaffold.c /^ IDnum direct_count;$/;" m struct:connection_st file: +directlyAppendDescriptors graph.c /^void directlyAppendDescriptors(Node * destination, Node * source, Coordinate totalLength)$/;" f +disconnectNextPassageMarker passageMarker.c /^void disconnectNextPassageMarker(PassageMarkerI marker, Graph * graph)$/;" f +displayGeneralStatistics graphStats.c /^void displayGeneralStatistics(Graph * graph, char *filename, ReadSet * reads)$/;" f +displayLocalBreakpoint graphStats.c /^void displayLocalBreakpoint(PassageMarkerI strainMarker,$/;" f +distance scaffold.c /^ float distance;$/;" m struct:connection_st file: +distance shortReadPairs.c /^ IDnum distance;$/;" m struct:miniConnection_st file: +doFindOrInsertOccurenceInSplayTree splayTable.c /^doFindOrInsertOccurenceInSplayTree(Kmer * kmer, IDnum * seqID,$/;" f file: +done correctedGraph.c /^static Ticket *done;$/;" v file: +doubleStrandedGraph graph.c /^boolean doubleStrandedGraph(Graph * graph) {$/;" f +double_strand preGraph.c /^ boolean double_strand;$/;" m struct:preGraph_st file: +double_strand roadMap.h /^ boolean double_strand;$/;" m struct:roadMapArray_st +double_strand splayTable.c /^ boolean double_strand;$/;" m struct:splayTable_st file: +double_stranded graph.c /^ boolean double_stranded;$/;" m struct:graph_st file: +elementSize allocArray.h /^ size_t elementSize;$/;" m struct:AllocArray_st +elementsAllocated allocArray.h /^ size_t elementsAllocated;$/;" m struct:AllocArray_st +elementsRecycled allocArray.h /^ size_t elementsRecycled;$/;" m struct:AllocArray_st +eligibleStartingPoints correctedGraph.c /^static IDnum *eligibleStartingPoints;$/;" v file: +emptyGraph graph.c /^Graph *emptyGraph(IDnum sequenceCount, int wordLength)$/;" f +emptyNode graph.c /^Node *emptyNode()$/;" f +emptyPreGraph_pg preGraph.c /^PreGraph *emptyPreGraph_pg(IDnum sequenceCount, IDnum referenceCount, int wordLength, boolean double_strand)$/;" f +estimateLibraryInsertLength scaffold.c /^static void estimateLibraryInsertLength(IDnum * coOccurences, IDnum coOccurencesCount, Category libID) {$/;" f file: +estimateLibraryInsertLengths scaffold.c /^static void estimateLibraryInsertLengths(IDnum ** coOccurences, IDnum * coOccurencesCounts) {$/;" f file: +estimateMissingInsertLengths scaffold.c /^static void estimateMissingInsertLengths(ReadOccurence ** readNodes, IDnum * readNodeCounts, IDnum * readPairs, Category * cats) {$/;" f file: +estimated scaffold.c /^static boolean estimated[CATEGORIES + 1];$/;" v file: +estimated_cov graphStats.c /^double estimated_cov(Graph * graph, char * directory)$/;" f +exitErrorf utility.c /^void exitErrorf(int exitStatus, boolean showErrno, const char *format, ...)$/;" f +expandLongNode shortReadPairs.c /^static boolean expandLongNode(Node * node, boolean force_jumps)$/;" f file: +expandLongNodes shortReadPairs.c /^static boolean expandLongNodes(boolean force_jumps)$/;" f file: +expandNode graph.c /^TightString *expandNode(Node * node, int WORDLENGTH)$/;" f +expandNodeFragment graph.c /^char *expandNodeFragment(Node * node, Coordinate contigStart,$/;" f +expectedNumberOfConnections scaffold.c /^static IDnum expectedNumberOfConnections(IDnum IDA, Connection * connect,$/;" f file: +expected_coverage readCoherentGraph.c /^static double expected_coverage = 1;$/;" v file: +exploitShortReadPairs shortReadPairs.c /^void exploitShortReadPairs(Graph * argGraph,$/;" f +exportAMOSContig graphStats.c /^static void exportAMOSContig(FILE * outfile, ReadSet * reads, Node * node,$/;" f file: +exportAMOSContigs graphStats.c /^void exportAMOSContigs(char *filename, Graph * graph,$/;" f +exportAMOSLib graphStats.c /^static void exportAMOSLib(FILE * outfile, Graph * graph, Category cat)$/;" f file: +exportAMOSMarker graphStats.c /^static void exportAMOSMarker(FILE * outfile, PassageMarkerI marker,$/;" f file: +exportAMOSNode graphStats.c /^static void exportAMOSNode(FILE * outfile, ReadSet * reads, Node * node,$/;" f file: +exportAMOSRead graphStats.c /^static void exportAMOSRead(FILE * outfile, TightString * tString,$/;" f file: +exportAMOSReverseShortMarker graphStats.c /^static void exportAMOSReverseShortMarker(FILE * outfile,$/;" f file: +exportAMOSShortMarker graphStats.c /^static void exportAMOSShortMarker(FILE * outfile, ShortReadMarker * marker,$/;" f file: +exportArc graph.c /^static void exportArc(FILE * outfile, Arc * arc)$/;" f file: +exportArcSequence graphStats.c /^void exportArcSequence(Arc * arc, FILE * outfile, int WORDLENGTH,$/;" f +exportGraph graph.c /^void exportGraph(char *filename, Graph * graph, TightString * sequences)$/;" f +exportLongNodeMapping graphStats.c /^static void exportLongNodeMapping(FILE * outfile, Node * node, ReadSet * reads, ReferenceCoord * refCoords, int wordLength) {$/;" f file: +exportLongNodeMappings graphStats.c /^void exportLongNodeMappings(char *filename, Graph * graph, ReadSet * reads,$/;" f +exportLongNodeSequence graphStats.c /^static void exportLongNodeSequence(FILE * outfile, Node * node, Graph * graph, ReadSet * reads, ShortLength * readLengths, IDnum cutoff) {$/;" f file: +exportLongNodeSequences graphStats.c /^void exportLongNodeSequences(char *filename, Graph * graph,$/;" f +exportMarker passageMarker.c /^void exportMarker(FILE * outfile, PassageMarkerI marker,$/;" f +exportNode graph.c /^static void exportNode(FILE * outfile, Node * node, void *withSequence)$/;" f file: +exportPreGraph_pg preGraph.c /^void exportPreGraph_pg(char *filename, PreGraph * preGraph)$/;" f +exportPreMarker preGraph.c /^static void exportPreMarker(FILE * outfile, PreMarker* preMarker) {$/;" f file: +exportPreNode_pg preGraph.c /^static void exportPreNode_pg(FILE * outfile, PreNode * preNode, IDnum ID,$/;" f file: +exportPreReference_pg preGraph.c /^static void exportPreReference_pg(FILE * outfile, IDnum index, PreGraph * preGraph) {$/;" f file: +exportTightString tightString.c /^void exportTightString(FILE * outfile, TightString * sequence, IDnum index)$/;" f +exportUnusedReads graphStats.c /^void exportUnusedReads(Graph* graph, ReadSet * reads, Coordinate minContigKmerLength, char* directory) {$/;" f +extractBackOfNodeReads graph.c /^ShortReadMarker *extractBackOfNodeReads(Node * node, Coordinate breakpoint,$/;" f +extractFrontOfNodeReads graph.c /^ShortReadMarker *extractFrontOfNodeReads(Node * node,$/;" f +extractPassageMarker passageMarker.c /^void extractPassageMarker(PassageMarkerI marker)$/;" f +extractSequence correctedGraph.c /^extractSequence(PassageMarkerI path, TightString * sequence)$/;" f file: +extractSequence locallyCorrectedGraph.c /^extractSequence(PassageMarkerI path, TightString * sequence)$/;" f file: +false globals.h 30;" d +fastPath correctedGraph.c /^static PassageMarkerI fastPath;$/;" v file: +fastPath locallyCorrectedGraph.c /^static PassageMarkerI fastPath;$/;" v file: +fastSequence correctedGraph.c /^static TightString *fastSequence;$/;" v file: +fastSequence locallyCorrectedGraph.c /^static TightString *fastSequence;$/;" v file: +fastToSlowMapping correctedGraph.c /^static Coordinate *fastToSlowMapping;$/;" v file: +fh_Dl fibpriv.h /^ IDnum fh_Dl;$/;" m struct:fibheap +fh_cascading_cut fib.c /^static void fh_cascading_cut(FibHeap * h, FibHeapNode * y)$/;" f file: +fh_checkcons fib.c /^static void fh_checkcons(FibHeap * h)$/;" f file: +fh_cmp_fnct fibpriv.h /^ Coordinate(*fh_cmp_fnct) (void *, void *);$/;" m struct:fibheap +fh_compare fib.c /^static int fh_compare(FibHeap * h, FibHeapNode * a, FibHeapNode * b)$/;" f file: +fh_comparedata fib.c /^fh_comparedata(FibHeap * h, Coordinate key, void *data, FibHeapNode * b)$/;" f file: +fh_cons fibpriv.h /^ FibHeapNode **fh_cons;$/;" m struct:fibheap +fh_consolidate fib.c /^static void fh_consolidate(FibHeap * h)$/;" f file: +fh_cut fib.c /^static void fh_cut(FibHeap * h, FibHeapNode * x, FibHeapNode * y)$/;" f file: +fh_delete fib.c /^void *fh_delete(FibHeap * h, FibHeapNode * x)$/;" f +fh_deleteheap fib.c /^void fh_deleteheap(FibHeap * h)$/;" f +fh_destroyheap fib.c /^static void fh_destroyheap(FibHeap * h)$/;" f file: +fh_extractmin fib.c /^void *fh_extractmin(FibHeap * h)$/;" f +fh_extractminel fib.c /^static FibHeapNode *fh_extractminel(FibHeap * h)$/;" f file: +fh_heaplink fib.c /^static void fh_heaplink(FibHeap * h, FibHeapNode * y, FibHeapNode * x)$/;" f file: +fh_initheap fib.c /^static void fh_initheap(FibHeap * new)$/;" f file: +fh_insert fib.c /^FibHeapNode *fh_insert(FibHeap * h, void *data)$/;" f +fh_insertel fib.c /^static void fh_insertel(FibHeap * h, FibHeapNode * x)$/;" f file: +fh_insertkey fib.c /^FibHeapNode *fh_insertkey(FibHeap * h, Coordinate key, void *data)$/;" f +fh_insertrootlist fib.c /^static void fh_insertrootlist(FibHeap * h, FibHeapNode * x)$/;" f file: +fh_keys fibpriv.h /^ boolean fh_keys;$/;" m struct:fibheap +fh_makeheap fib.c /^FibHeap *fh_makeheap()$/;" f +fh_makekeyheap fib.c /^FibHeap *fh_makekeyheap()$/;" f +fh_min fib.c /^void *fh_min(FibHeap * h)$/;" f +fh_min fibpriv.h /^ FibHeapNode *fh_min;$/;" m struct:fibheap +fh_minkey fib.c /^Coordinate fh_minkey(FibHeap * h)$/;" f +fh_n fibpriv.h /^ IDnum fh_n;$/;" m struct:fibheap +fh_neginf fibpriv.h /^ void *fh_neginf;$/;" m struct:fibheap +fh_removerootlist fib.c /^static void fh_removerootlist(FibHeap * h, FibHeapNode * x)$/;" f file: +fh_replacedata fib.c /^void *fh_replacedata(FibHeapNode * x, void *data)$/;" f +fh_replacekey fib.c /^Coordinate fh_replacekey(FibHeap * h, FibHeapNode * x, Coordinate key)$/;" f +fh_replacekeydata fib.c /^void *fh_replacekeydata(FibHeap * h, FibHeapNode * x,$/;" f +fh_root fibpriv.h /^ FibHeapNode *fh_root;$/;" m struct:fibheap +fh_setcmp fib.c /^voidcmp fh_setcmp(FibHeap * h, voidcmp fnct)$/;" f +fh_setneginf fib.c /^void *fh_setneginf(FibHeap * h, void *data)$/;" f +fh_union fib.c /^FibHeap *fh_union(FibHeap * ha, FibHeap * hb)$/;" f +fhe_child fibpriv.h /^ FibHeapNode *fhe_child;$/;" m struct:fibheap_el +fhe_data fibpriv.h /^ void *fhe_data;$/;" m struct:fibheap_el +fhe_degree fibpriv.h /^ int fhe_degree;$/;" m struct:fibheap_el +fhe_initelem fib.c /^static void fhe_initelem(FibHeapNode * e)$/;" f file: +fhe_insertafter fib.c /^static void fhe_insertafter(FibHeapNode * a, FibHeapNode * b)$/;" f file: +fhe_insertbefore fib.c /^static inline void fhe_insertbefore(FibHeapNode * a, FibHeapNode * b)$/;" f file: +fhe_key fibpriv.h /^ Coordinate fhe_key;$/;" m struct:fibheap_el +fhe_left fibpriv.h /^ FibHeapNode *fhe_left;$/;" m struct:fibheap_el +fhe_mark fibpriv.h /^ boolean fhe_mark;$/;" m struct:fibheap_el +fhe_newelem fib.c /^static FibHeapNode *fhe_newelem(FibHeap * h)$/;" f file: +fhe_p fibpriv.h /^ FibHeapNode *fhe_p;$/;" m struct:fibheap_el +fhe_remove fib.c /^static FibHeapNode *fhe_remove(FibHeapNode * x)$/;" f file: +fhe_right fibpriv.h /^ FibHeapNode *fhe_right;$/;" m struct:fibheap_el +fibheap fibpriv.h /^struct fibheap {$/;" s +fibheap_el fibpriv.h /^struct fibheap_el {$/;" s +fillNewConnectionInTree scaffold.c /^static void fillNewConnectionInTree(Connection *connect,$/;" f file: +fillReferenceCoordinateTable readSet.c /^static void fillReferenceCoordinateTable(char *filename, ReferenceCoordinateTable * refCoords, IDnum counter)$/;" f file: +fillTightStringWithString tightString.c /^static void fillTightStringWithString(TightString * tString,$/;" f file: +fillUpGraph graphReConstruction.c /^static void fillUpGraph(ReadSet * reads,$/;" f file: +findConnection scaffold.c /^static Connection* findConnection(IDnum nodeID,$/;" f file: +findIDnumInArray graph.c /^boolean findIDnumInArray(IDnum query, IDnum * array, IDnum arrayLength)$/;" f +findInTree splay.c /^Kmer * findInTree(Kmer * X, SplayTree ** T)$/;" f +findKmerInKmerOccurenceTable kmerOccurenceTable.c /^KmerOccurence *findKmerInKmerOccurenceTable(Kmer * kmer,$/;" f +findLowCoverageRegions graphStats.c /^static Mask * findLowCoverageRegions(Node * node, Graph * graph, IDnum cutoff, ReadSet * reads, ShortLength * readLengths) {$/;" f file: +findOppositeNode shortReadPairs.c /^static void findOppositeNode(Node * node, Node ** oppositeNode,$/;" f file: +findOrCreateConnection scaffold.c /^static Connection* findOrCreateConnection(IDnum nodeID,$/;" f file: +findOrInsertOccurenceInSplayTable splayTable.c /^static boolean findOrInsertOccurenceInSplayTable(Kmer * kmer, IDnum * seqID,$/;" f file: +findOrInsertOccurenceInSplayTree splay.c /^findOrInsertOccurenceInSplayTree(Kmer * kmer, IDnum * seqID,$/;" f +findReferenceCoordinate readSet.c /^static ReferenceCoordinate * findReferenceCoordinate(ReferenceCoordinateTable * table, char * name, Coordinate start, Coordinate finish, boolean positive_strand) {$/;" f file: +findReferenceMapping graphReConstruction.c /^static ReferenceMapping * findReferenceMapping(IDnum seqID, Coordinate refCoord, ReferenceMapping * referenceMappings, Coordinate referenceMappingCount) {$/;" f file: +finish graphReConstruction.c /^ IDnum finish;$/;" m struct:nodeMask_st file: +finish graphStats.c /^ Coordinate finish;$/;" m struct:mask_st file: +finish graphStats.c /^ IDnum finish;$/;" m struct:refMap_st file: +finish graphStats.c /^ IDnum finish;$/;" m struct:referenceCoord_st file: +finish readSet.c /^ Coordinate finish;$/;" m struct:referenceCoordinate_st file: +finish roadMap.c /^ union positionPtr finish; \/\/ 32$/;" m struct:annotation_st typeref:union:annotation_st::positionPtr file: +finish splayTable.c /^ Coordinate finish;$/;" m struct:mask_st file: +finishOffset passageMarker.c /^ IDnum finishOffset;$/;" m struct:passage_st file: +foldSymmetricalNode correctedGraph.c /^static void foldSymmetricalNode(Node * node)$/;" f file: +foldSymmetricalNodeReads graph.c /^void foldSymmetricalNodeReads(Node * node, Graph * graph)$/;" f +freeDoneTickets correctedGraph.c /^static void freeDoneTickets()$/;" f file: +freeElements allocArray.h /^ AllocArrayFreeElement *freeElements;$/;" m struct:AllocArray_st +frontReference shortReadPairs.c /^ Connection *frontReference;$/;" m struct:miniConnection_st file: +gapMarkerMemory graph.c /^static RecycleBin *gapMarkerMemory = NULL;$/;" v file: +gapMarker_st graph.c /^struct gapMarker_st {$/;" s file: +gapMarkers graph.c /^ GapMarker **gapMarkers;$/;" m struct:graph_st file: +gapMergeSort graph.c /^static void gapMergeSort(GapMarker ** gapPtr, IDnum count)$/;" f file: +genomeMarker graphStats.c /^PassageMarkerI genomeMarker(Node * node, IDnum firstStrain)$/;" f +genomeMarkerCount graphStats.c /^IDnum genomeMarkerCount(Node * node, IDnum firstStrain)$/;" f +getAbsolutePassMarkerSeqID passageMarker.c /^IDnum getAbsolutePassMarkerSeqID(PassageMarkerI marker)$/;" f +getAnchors correctedGraph.c /^static PassageMarkerList *getAnchors(PassageMarkerI marker, Node * nodeA,$/;" f file: +getAnnotSequenceID roadMap.c /^IDnum getAnnotSequenceID(Annotation * annot)$/;" f +getAnnotationCount roadMap.c /^IDnum getAnnotationCount(RoadMap * rdmap)$/;" f +getAnnotationInArray roadMap.c /^Annotation *getAnnotationInArray(Annotation * annot, Coordinate index)$/;" f +getAnnotationLength roadMap.c /^Coordinate getAnnotationLength(Annotation * annot)$/;" f +getArc graph.c /^Arc *getArc(Node * node)$/;" f +getArcBetweenNodes graph.c /^Arc *getArcBetweenNodes(Node * originNode, Node * destinationNode,$/;" f +getConnection scaffold.c /^Connection * getConnection(Node * node) {$/;" f +getConnectionDestination scaffold.c /^Node * getConnectionDestination(Connection * connect) {$/;" f +getConnectionDirectCount scaffold.c /^IDnum getConnectionDirectCount(Connection * connect) {$/;" f +getConnectionDistance scaffold.c /^Coordinate getConnectionDistance(Connection * connect) {$/;" f +getConnectionPairedCount scaffold.c /^IDnum getConnectionPairedCount(Connection * connect) {$/;" f +getConnectionVariance scaffold.c /^double getConnectionVariance(Connection * connect) {$/;" f +getDestination graph.c /^Node *getDestination(Arc * arc)$/;" f +getDestination_pg preGraph.c /^IDnum getDestination_pg(PreArcI preArc, IDnum preNodeID)$/;" f +getFinish roadMap.c /^Coordinate getFinish(Annotation * annot)$/;" f +getFinishID roadMap.c /^IDnum getFinishID(Annotation * annot)$/;" f +getFinishOffset passageMarker.c /^Coordinate getFinishOffset(PassageMarkerI marker)$/;" f +getGap graph.c /^GapMarker *getGap(Node * node, Graph * graph)$/;" f +getGapFinish graph.c /^Coordinate getGapFinish(GapMarker * marker)$/;" f +getGapStart graph.c /^Coordinate getGapStart(GapMarker * marker)$/;" f +getInsertLength graph.c /^Coordinate getInsertLength(Graph * graph, Category cat)$/;" f +getInsertLength_var graph.c /^double getInsertLength_var(Graph * graph, Category cat)$/;" f +getInsertionMarkerPosition preGraphConstruction.c /^Coordinate getInsertionMarkerPosition(InsertionMarker * marker)$/;" f +getKey dfibHeap.c /^Time getKey(DFibHeapNode * node)$/;" f +getKmerKey kmer.c /^KmerKey getKmerKey(Kmer * kmer) {$/;" f +getKmerOccurenceNodeID kmerOccurenceTable.c /^IDnum getKmerOccurenceNodeID(KmerOccurence * occurence) {$/;" f +getKmerOccurencePosition kmerOccurenceTable.c /^Coordinate getKmerOccurencePosition(KmerOccurence * occurence) {$/;" f +getLength tightString.c /^IDnum getLength(TightString * tString)$/;" f +getLongCoverage graphStats.c /^static Coordinate getLongCoverage(Node * node) {$/;" f file: +getLongReadCoords graphStats.c /^static void getLongReadCoords(Coordinate * starts, Coordinate * stops, Node * node, Graph * graph, ReadSet * reads, IDnum offset) {$/;" f file: +getMarkedNodeList shortReadPairs.c /^NodeList *getMarkedNodeList()$/;" f +getMarker graph.c /^PassageMarkerI getMarker(Node * node)$/;" f +getMostAppropriateHit splayTable.c /^static KmerOccurence * getMostAppropriateHit(Coordinate readCoord, Coordinate readLength, boolean direct, KmerOccurence * kmerOccurence, IDnum mapCount, IDnum * mapSequenceID, Coordinate * mapCoord, int wordLength) {$/;" f file: +getMultiplicity graph.c /^IDnum getMultiplicity(Arc * arc)$/;" f +getMultiplicity_pg preGraph.c /^IDnum getMultiplicity_pg(PreArcI preArc)$/;" f +getNearestHSPIndex splayTable.c /^static Coordinate getNearestHSPIndex(Coordinate position, IDnum * sequenceIDs, Coordinate sequenceLength) {$/;" f file: +getNextAnnotation roadMap.c /^Annotation *getNextAnnotation(Annotation * annot)$/;" f +getNextArc graph.c /^Arc *getNextArc(Arc * arc)$/;" f +getNextConnection scaffold.c /^Connection * getNextConnection(Connection * connect) {$/;" f +getNextGap graph.c /^GapMarker *getNextGap(GapMarker * marker)$/;" f +getNextInNode passageMarker.c /^PassageMarkerI getNextInNode(PassageMarkerI marker)$/;" f +getNextInSequence passageMarker.c /^PassageMarkerI getNextInSequence(PassageMarkerI marker)$/;" f +getNextKmerOccurence kmerOccurenceTable.c /^KmerOccurence * getNextKmerOccurence(KmerOccurence * current) {$/;" f +getNextPreArc_pg preGraph.c /^PreArcI getNextPreArc_pg(PreArcI preArc, IDnum preNodeID)$/;" f +getNode passageMarker.c /^Node *getNode(PassageMarkerI marker)$/;" f +getNodeDHeapNode correctedGraph.c /^static DFibHeapNode *getNodeDHeapNode(Node * node)$/;" f file: +getNodeID graph.c /^IDnum getNodeID(Node * node)$/;" f +getNodeInGraph graph.c /^Node *getNodeInGraph(Graph * graph, IDnum nodeID)$/;" f +getNodeLength graph.c /^Coordinate getNodeLength(Node * node)$/;" f +getNodePrevious correctedGraph.c /^static Node *getNodePrevious(Node * node)$/;" f file: +getNodePrevious locallyCorrectedGraph.c /^static Node *getNodePrevious(Node * node)$/;" f file: +getNodeReadCount graph.c /^IDnum getNodeReadCount(Node * node, Graph * graph)$/;" f +getNodeReadCounts graph.c /^IDnum *getNodeReadCounts(Graph * graph)$/;" f +getNodeReads graph.c /^ShortReadMarker *getNodeReads(Node * node, Graph * graph)$/;" f +getNodeStatus graph.c /^boolean getNodeStatus(Node * node)$/;" f +getNodeTime correctedGraph.c /^static Time getNodeTime(Node * node)$/;" f file: +getNodeTime locallyCorrectedGraph.c /^static Time getNodeTime(Node * node)$/;" f file: +getNodeToReadMappings graph.c /^ShortReadMarker **getNodeToReadMappings(Graph * graph)$/;" f +getNucleotide tightString.c /^Nucleotide getNucleotide(Coordinate nucleotideIndex, TightString * tString)$/;" f +getNucleotideChar tightString.c /^char getNucleotideChar(Coordinate nucleotideIndex, TightString * tString)$/;" f +getNucleotideInDescriptor graph.c /^static Nucleotide getNucleotideInDescriptor(Descriptor * descriptor,$/;" f file: +getNucleotideInDescriptor_pg preGraph.c /^static Nucleotide getNucleotideInDescriptor_pg(Descriptor * descriptor,$/;" f file: +getNucleotideInNode graph.c /^Nucleotide getNucleotideInNode(Node * node, Coordinate index) {$/;" f +getOrigin graph.c /^Node *getOrigin(Arc * arc)$/;" f +getOriginalVirtualCoverage graph.c /^Coordinate getOriginalVirtualCoverage(Node * node, Category category)$/;" f +getOtherEnd_pg preGraph.c /^IDnum getOtherEnd_pg(PreArcI preArc, IDnum preNodeID)$/;" f +getPassageMarkerFinish passageMarker.c /^Coordinate getPassageMarkerFinish(PassageMarkerI marker)$/;" f +getPassageMarkerLength passageMarker.c /^Coordinate getPassageMarkerLength(PassageMarkerI marker)$/;" f +getPassageMarkerSequenceID passageMarker.c /^IDnum getPassageMarkerSequenceID(PassageMarkerI marker)$/;" f +getPassageMarkerStart passageMarker.c /^Coordinate getPassageMarkerStart(PassageMarkerI marker)$/;" f +getPassageMarkerStatus passageMarker.c /^boolean getPassageMarkerStatus(PassageMarkerI marker)$/;" f +getPosition roadMap.c /^Coordinate getPosition(Annotation * annot)$/;" f +getPreArcBetweenPreNodes_pg preGraph.c /^PreArcI getPreArcBetweenPreNodes_pg(IDnum originPreNodeID,$/;" f +getPreArc_pg preGraph.c /^PreArcI getPreArc_pg(IDnum preNodeID, PreGraph * preGraph)$/;" f +getPreNodeInPreGraph_pg preGraph.c /^PreNode *getPreNodeInPreGraph_pg(PreGraph * preGraph, IDnum preNodeID)$/;" f +getPreNodeLength_pg preGraph.c /^Coordinate getPreNodeLength_pg(IDnum preNodeID, PreGraph * preGraph)$/;" f +getPreviousInSequence passageMarker.c /^PassageMarkerI getPreviousInSequence(PassageMarkerI marker)$/;" f +getRecycleBinInArray recycleBin.c /^RecycleBin *getRecycleBinInArray(RecycleBin *recycleBin,$/;" f +getReferenceCount graphStats.c /^static IDnum getReferenceCount(ReadSet * reads) {$/;" f file: +getRoadMapInArray roadMap.c /^RoadMap *getRoadMapInArray(RoadMapArray * array, IDnum index)$/;" f +getSequenceLengths readSet.c /^ShortLength *getSequenceLengths(ReadSet * reads, int wordLength)$/;" f +getShortReadCoords graphStats.c /^static void getShortReadCoords(Coordinate * starts, Coordinate * stops, Node * node, Graph * graph, ShortLength * readLengths) {$/;" f file: +getShortReadMarkerAtIndex graph.c /^ShortReadMarker *getShortReadMarkerAtIndex(ShortReadMarker * array,$/;" f +getShortReadMarkerID graph.c /^IDnum getShortReadMarkerID(ShortReadMarker * marker)$/;" f +getShortReadMarkerOffset graph.c /^inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker)$/;" f +getShortReadMarkerPosition graph.c /^inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker)$/;" f +getShortReadTwinCoords graphStats.c /^static void getShortReadTwinCoords(Coordinate * starts, Coordinate * stops, Node * node, Graph * graph, ShortLength * readLengths, IDnum offset) {$/;" f file: +getStart roadMap.c /^Coordinate getStart(Annotation * annot)$/;" f +getStartID roadMap.c /^IDnum getStartID(Annotation * annot)$/;" f +getStartOffset passageMarker.c /^Coordinate getStartOffset(PassageMarkerI marker)$/;" f +getTightStringInArray tightString.c /^TightString *getTightStringInArray(TightString * tString,$/;" f +getTipLength correctedGraph.c /^static Coordinate getTipLength(Node * node)$/;" f file: +getTotalCoverage graph.c /^Coordinate getTotalCoverage(Node * node)$/;" f +getTwinConnection scaffold.c /^Connection * getTwinConnection(Connection * connect) {$/;" f +getTwinMarker passageMarker.c /^PassageMarkerI getTwinMarker(PassageMarkerI marker)$/;" f +getTwinNode graph.c /^Node *getTwinNode(Node * node)$/;" f +getUniqueness graph.c /^boolean getUniqueness(Node * node)$/;" f +getVirtualCoverage graph.c /^Coordinate getVirtualCoverage(Node * node)$/;" f +getVirtualCoverage graph.c /^Coordinate getVirtualCoverage(Node * node, Category category)$/;" f +getWordLength graph.c /^int getWordLength(Graph * graph)$/;" f +getWordLength_pg preGraph.c /^int getWordLength_pg(PreGraph * preGraph)$/;" f +ghostThreadSequenceThroughGraph graphReConstruction.c /^static void ghostThreadSequenceThroughGraph(TightString * tString,$/;" f file: +goToEndOfLine readSet.c /^void goToEndOfLine(char *line, FILE * file)$/;" f +goesToNode readCoherentGraph.c /^static boolean goesToNode(PassageMarkerI marker, Node * node)$/;" f file: +goesToNode shortReadPairs.c /^static boolean goesToNode(PassageMarkerI marker, Node * node)$/;" f file: +graph correctedGraph.c /^static Graph *graph;$/;" v file: +graph locallyCorrectedGraph.c /^static Graph *graph;$/;" v file: +graph readCoherentGraph.c /^static Graph *graph = NULL;$/;" v file: +graph scaffold.c /^static Graph *graph;$/;" v file: +graph shortReadPairs.c /^static Graph *graph;$/;" v file: +graph_st graph.c /^struct graph_st {$/;" s file: +handicapNode shortReadPairs.c /^void handicapNode(Node * node)$/;" f +hasReferenceMarker graphStats.c /^static boolean hasReferenceMarker(Node * node, ReadSet * reads) {$/;" f file: +hasSingleArc graph.c /^boolean hasSingleArc(Node * node)$/;" f +hasSinglePreArc_pg preGraph.c /^boolean hasSinglePreArc_pg(IDnum preNodeID, PreGraph * preGraph)$/;" f +hash_kmer splayTable.c /^static KmerKey hash_kmer(Kmer * kmer)$/;" f file: +id_a correctedGraph.c /^ IDnum id_a;$/;" m struct:tkt_st file: +identifyUniqueNodes readCoherentGraph.c /^static void identifyUniqueNodes(boolean(*isUniqueFunction) (Node *))$/;" f file: +idx allocArray.c /^ ArrayIdx idx;$/;" m struct:AllocArrayFreeElement_st file: +importGraph graph.c /^Graph *importGraph(char *filename)$/;" f +importPreGraph graphReConstruction.c /^Graph *importPreGraph(char *preGraphFilename, ReadSet * reads, char * roadmapFilename, $/;" f +importReadSet readSet.c /^ReadSet *importReadSet(char *filename)$/;" f +importReferenceRoadMapArray roadMap.c /^RoadMapArray *importReferenceRoadMapArray(char *filename)$/;" f +importRoadMapArray roadMap.c /^RoadMapArray *importRoadMapArray(char *filename)$/;" f +incrementAnnotationCoordinates roadMap.c /^void incrementAnnotationCoordinates(Annotation * annot)$/;" f +incrementConnectionDistance scaffold.c /^void incrementConnectionDistance(Connection * connect, Coordinate increment) {$/;" f +incrementFinishOffset passageMarker.c /^void incrementFinishOffset(PassageMarkerI marker, Coordinate offset)$/;" f +incrementNodeReferenceMarkerCount_pg preGraph.c /^void incrementNodeReferenceMarkerCount_pg(PreGraph * preGraph, IDnum preNodeID) {$/;" f +incrementOriginalVirtualCoverage graph.c /^void incrementOriginalVirtualCoverage(Node * node, Category category,$/;" f +incrementReadStartCount graph.c /^void incrementReadStartCount(Node * node, Graph * graph)$/;" f +incrementStartOffset passageMarker.c /^void incrementStartOffset(PassageMarkerI marker, Coordinate offset)$/;" f +incrementVirtualCoverage graph.c /^void incrementVirtualCoverage(Node * node, Category category,$/;" f +incrementVirtualCoverage graph.c /^void incrementVirtualCoverage(Node * node,$/;" f +initAllocArray allocArray.c /^static void initAllocArray(AllocArray * array, size_t elementSize, char * name) $/;" f file: +initAllocArrayArray allocArray.c /^static void initAllocArrayArray(AllocArray *array,$/;" f file: +initAnnotationBuffers splayTable.c /^static void initAnnotationBuffers(void)$/;" f file: +initConnectionStackMemory scaffold.c /^static void initConnectionStackMemory(void)$/;" f file: +initRecycleBin recycleBin.c /^static void initRecycleBin(RecycleBin *recycleBin,$/;" f file: +initSmallNodeListMemory graphReConstruction.c /^static void initSmallNodeListMemory(void)$/;" f file: +initSplayTreeMemory splay.c /^void initSplayTreeMemory(void)$/;" f +initializeReferenceMapping graphStats.c /^static void initializeReferenceMapping(ReferenceMapping * refMap, PassageMarkerI marker, Node * node) {$/;" f file: +initializeTodoLists correctedGraph.c /^static void initializeTodoLists()$/;" f file: +injectShortReads graph.c /^void injectShortReads(ShortReadMarker * sourceArray, IDnum sourceLength,$/;" f +inline globals.h 53;" d +inputReferenceIntoSplayTable splayTable.c /^void inputReferenceIntoSplayTable(TightString * tString,$/;" f +inputSequenceArrayIntoSplayTableAndArchive splayTable.c /^void inputSequenceArrayIntoSplayTableAndArchive(ReadSet * reads,$/;" f +inputSequenceIntoSplayTable splayTable.c /^void inputSequenceIntoSplayTable(TightString * array,$/;" f +insertIntoTree splay.c /^void insertIntoTree(Kmer * kmer, SplayTree ** T)$/;" f +insertLengths graph.c /^ Coordinate insertLengths[CATEGORIES + 1];$/;" m struct:graph_st file: +insertLengths_var graph.c /^ double insertLengths_var[CATEGORIES + 1];$/;" m struct:graph_st file: +insertNodeIntoDHeap dfibHeap.c /^DFibHeapNode *insertNodeIntoDHeap(DFibHeap * heap, Time key,$/;" f +insertNodeIntoHeap fibHeap.c /^FibHeapNode *insertNodeIntoHeap(FibHeap * heap, Coordinate key,$/;" f +insertPassageMarker graph.c /^void insertPassageMarker(PassageMarkerI marker, Node * destination)$/;" f +insertionMarker_st preGraphConstruction.c /^struct insertionMarker_st {$/;" s file: +int32 readSet.c /^static int int32(const unsigned char * ptr)$/;" f file: +intLeftFilter kmer.c /^static const uint16_t intLeftFilter = (uint16_t) 3 << 14; $/;" v file: +intWordFilter kmer.c /^static uint16_t intWordFilter = (uint16_t) ((int16_t) -1); $/;" v file: +integrateDerivativeDistances shortReadPairs.c /^static void integrateDerivativeDistances(Connection * connect,$/;" f file: +ints kmer.h /^ uint16_t ints;$/;" m struct:kmer_st +isDestinationToMarker passageMarker.c /^boolean isDestinationToMarker(PassageMarkerI marker, Node * node)$/;" f +isEligibleTip concatenatedPreGraph.c /^static boolean isEligibleTip(IDnum index, PreGraph * preGraph, Coordinate$/;" f file: +isInitial passageMarker.c /^boolean isInitial(PassageMarkerI marker)$/;" f +isLocalDeadEnd locallyCorrectedGraph.c /^static boolean isLocalDeadEnd(Node * node)$/;" f file: +isLocalTwinDeadEnd locallyCorrectedGraph.c /^static boolean isLocalTwinDeadEnd(Node * node)$/;" f file: +isLocallyInitial concatenatedGraph.c /^static boolean isLocallyInitial(PassageMarkerI marker) {$/;" f file: +isLoop_pg preGraph.c /^boolean isLoop_pg(PreArcI preArc)$/;" f +isMixed graphStats.c /^boolean isMixed(Node * node, IDnum firstStrain)$/;" f +isNodeMemorized graphReConstruction.c /^static inline boolean isNodeMemorized(Node * node, SmallNodeList * nodePile)$/;" f file: +isOnlyGenome graphStats.c /^boolean isOnlyGenome(Node * node, IDnum firstStrain)$/;" f +isOnlyStrain graphStats.c /^boolean isOnlyStrain(Node * node, IDnum firstStrain)$/;" f +isPreviousToNode correctedGraph.c /^static boolean isPreviousToNode(Node * previous, Node * target)$/;" f file: +isPreviousToNode locallyCorrectedGraph.c /^static boolean isPreviousToNode(Node * previous, Node * target)$/;" f file: +isSNP graphStats.c /^boolean isSNP(Node * node, IDnum firstStrain, int WORDLENGTH)$/;" f +isSecondInPair readSet.c /^boolean isSecondInPair(ReadSet * reads, IDnum index)$/;" f +isStart preGraphConstruction.c /^ boolean isStart;$/;" m struct:insertionMarker_st file: +isTerminal passageMarker.c /^boolean isTerminal(PassageMarkerI marker)$/;" f +isUniqueSolexa readCoherentGraph.c /^boolean isUniqueSolexa(Node * node)$/;" f +keyFilter kmer.c /^static uint64_t keyFilter = 0;$/;" v file: +keyFilterIndex kmer.c /^static int keyFilterIndex = UNDEFINED;$/;" v file: +keyFilterLength kmer.c /^static int keyFilterLength = 0;$/;" v file: +keyFilterOffset kmer.c /^static int keyFilterOffset = 0;$/;" v file: +keyInAccelerationTable kmerOccurenceTable.c /^static inline KmerKey keyInAccelerationTable(Kmer * kmer,$/;" f file: +kmer kmerOccurenceTable.c /^ Kmer kmer;$/;" m struct:kmerOccurence_st file: +kmer splay.c /^ Kmer kmer;$/;" m struct:splayNode_st file: +kmerFilterIndex kmer.c /^static int kmerFilterIndex = UNDEFINED;$/;" v file: +kmerFilterLength kmer.c /^static int kmerFilterLength = 0;$/;" v file: +kmerFilterOffset kmer.c /^static int kmerFilterOffset = 0;$/;" v file: +kmerOccurenceIndex kmerOccurenceTable.c /^ IDnum kmerOccurenceIndex;$/;" m struct:kmerOccurenceTable_st file: +kmerOccurencePtr kmerOccurenceTable.c /^ KmerOccurence * kmerOccurencePtr;$/;" m struct:kmerOccurenceTable_st file: +kmerOccurenceTable splayTable.c /^ KmerOccurenceTable *kmerOccurenceTable;$/;" m struct:splayTable_st file: +kmerOccurenceTable_st kmerOccurenceTable.c /^struct kmerOccurenceTable_st {$/;" s file: +kmerOccurence_st kmerOccurenceTable.c /^struct kmerOccurence_st {$/;" s file: +kmerProbabilities readSet.h /^ Probability **kmerProbabilities;$/;" m struct:readSet_st +kmerTable kmerOccurenceTable.c /^ KmerOccurence *kmerTable;$/;" m struct:kmerOccurenceTable_st file: +kmerTableSize kmerOccurenceTable.c /^ IDnum kmerTableSize;$/;" m struct:kmerOccurenceTable_st file: +kmer_st kmer.h /^struct kmer_st {$/;" s +labels readSet.h /^ char **labels;$/;" m struct:readSet_st +left scaffold.c /^ Connection *left;$/;" m struct:connection_st file: +left splay.c /^ struct splayNode_st *left;$/;" m struct:splayNode_st typeref:struct:splayNode_st::splayNode_st file: +length graph.c /^ IDnum length; \/\/ 32$/;" m struct:node_st file: +length graph.c /^ IDnum length;$/;" m struct:gapMarker_st file: +length graphReConstruction.c /^ IDnum length;$/;" m struct:referenceMapping_st file: +length preGraph.c /^ IDnum length;$/;" m struct:preMarker_st file: +length preGraph.c /^ IDnum length;$/;" m struct:preNode_st file: +length roadMap.c /^ ShortLength length; \/\/ 32$/;" m struct:annotation_st file: +length roadMap.h /^ IDnum length;$/;" m struct:roadMapArray_st +length tightString.c /^ IDnum length;$/;" m struct:tString_st file: +length utility.h /^ size_t length;$/;" m struct:__anon1 +listMemory passageMarker.c /^static RecycleBin *listMemory = NULL;$/;" v file: +listMemory readCoherentGraph.c /^static RecycleBin *listMemory = NULL;$/;" v file: +localScaffold shortReadPairs.c /^static MiniConnection *localScaffold = NULL;$/;" v file: +lockNode graphReConstruction.c /^static inline void lockNode(Node *node)$/;" f file: +lockNode preGraphConstruction.c /^static void lockNode(IDnum preNodeID)$/;" f file: +lockRead scaffold.c /^static inline void lockRead(IDnum readID)$/;" f file: +lockTwoNodes graphReConstruction.c /^static inline void lockTwoNodes(Node *node, Node *node2)$/;" f file: +lockTwoNodes preGraphConstruction.c /^static void lockTwoNodes(IDnum preNodeID, IDnum preNode2ID)$/;" f file: +lockTwoNodes scaffold.c /^static inline void lockTwoNodes(IDnum nodeID, IDnum node2ID)$/;" f file: +logFinalStats graphStats.c /^void logFinalStats(Graph * graph, Coordinate minContigKmerLength, char *directory)$/;" f +logInstructions readSet.c /^void logInstructions(int argc, char **argv, char *directory)$/;" f +longLeftFilter kmer.c /^static const uint32_t longLeftFilter = (uint32_t) 3 << 30; $/;" v file: +longLongKeyFilterIndex kmer.c /^static int longLongKeyFilterIndex = KMER_LONGLONGS - 1;$/;" v file: +longLongKmerFilter kmer.c /^static uint64_t longLongKmerFilter = (uint64_t) ((int64_t) -1); $/;" v file: +longLongKmerFilterIndex kmer.c /^static int longLongKmerFilterIndex = KMER_LONGLONGS - 1;$/;" v file: +longLongLeftFilter kmer.c /^static const uint64_t longLongLeftFilter = (uint64_t) 3 << 62; $/;" v file: +longLongWordFilter kmer.c /^static uint64_t longLongWordFilter = (uint64_t) ((int64_t) -1); $/;" v file: +longWordFilter kmer.c /^static uint32_t longWordFilter = (uint32_t) ((int32_t) -1); $/;" v file: +longlongs kmer.h /^ uint64_t longlongs[KMER_LONGLONGS];$/;" m struct:kmer_st +longs kmer.h /^ uint32_t longs;$/;" m struct:kmer_st +lowCoverageRegions graphStats.c /^static Mask * lowCoverageRegions(Coordinate * starts, Coordinate * stops, size_t length, IDnum cutoff, Coordinate nodeLength) {$/;" f file: +main run.c /^int main(int argc, char **argv)$/;" f +main run2.c /^int main(int argc, char **argv)$/;" f +main run3.c /^int main(int argc, char ** argv) {$/;" f +mallocOrExit utility.h 37;" d +mallocOrExit3 utility.c /^void *mallocOrExit3(size_t count, size_t size, const char *name)$/;" f +mallocOrExitWithoutCast utility.h 47;" d +mapDistancesOntoPaths correctedGraph.c /^static Coordinate mapDistancesOntoPaths()$/;" f file: +mapSlowOntoFast correctedGraph.c /^static void mapSlowOntoFast()$/;" f file: +markInterestingNodes shortReadPairs.c /^static void markInterestingNodes(Node * node)$/;" f file: +markedNodes shortReadPairs.c /^static NodeList *markedNodes;$/;" v file: +marker graph.c /^ PassageMarkerI marker; \/\/ 32$/;" m struct:node_st file: +marker passageMarker.h /^ PassageMarkerI marker;$/;" m struct:passageList_st +marker readCoherentGraph.c /^ PassageMarkerI marker;$/;" m struct:rb_connection_st file: +markerCount graph.c /^IDnum markerCount(Node * node)$/;" f +markerFollowsPath correctedGraph.c /^static boolean markerFollowsPath(PassageMarkerI marker,$/;" f file: +markerLeadsToArc correctedGraph.c /^static boolean markerLeadsToArc(PassageMarkerI marker, Node * nodeA,$/;" f file: +markerLeadsToNode correctedGraph.c /^static boolean markerLeadsToNode(PassageMarkerI marker, Node * node)$/;" f file: +markerMemory passageMarker.c /^static AllocArray *markerMemory = NULL;$/;" v file: +maskMemory graphStats.c /^static RecycleBin * maskMemory = NULL;$/;" v file: +maskMemory splayTable.c /^static RecycleBin * maskMemory = NULL;$/;" v file: +mask_st graphStats.c /^struct mask_st {$/;" s file: +mask_st splayTable.c /^struct mask_st {$/;" s file: +mateReads readSet.h /^ IDnum *mateReads;$/;" m struct:readSet_st +max correctedGraph.c /^static Time max(Time A, Time B, Time C)$/;" f file: +max locallyCorrectedGraph.c /^static Time max(Time A, Time B, Time C)$/;" f file: +maxBlocks allocArray.h /^ size_t maxBlocks;$/;" m struct:AllocArray_st +maxElements allocArray.h /^ size_t maxElements;$/;" m struct:AllocArray_st +maxLength graphStats.c /^Coordinate maxLength(Graph * graph)$/;" f +measureCoOccurences scaffold.c /^static void measureCoOccurences(IDnum ** coOccurences,$/;" f file: +memorizeNode graphReConstruction.c /^static inline void memorizeNode(Node * node, SmallNodeList ** nodePile)$/;" f file: +mergeArcLists graph.c /^static Arc *mergeArcLists(Arc * left, Arc * right)$/;" f file: +mergeDescriptors graph.c /^static inline Descriptor *mergeDescriptors(Descriptor * descr,$/;" f file: +mergeDescriptorsF2F_pg preGraph.c /^static inline Descriptor *mergeDescriptorsF2F_pg(Descriptor * descr,$/;" f file: +mergeDescriptorsH2H_pg preGraph.c /^static inline Descriptor *mergeDescriptorsH2H_pg(Descriptor * descr,$/;" f file: +mergeDescriptors_pg preGraph.c /^static inline Descriptor *mergeDescriptors_pg(Descriptor * descr,$/;" f file: +mergeGapMarkerLists graph.c /^static GapMarker *mergeGapMarkerLists(GapMarker * left, GapMarker * right)$/;" f file: +mergeNodeReads graph.c /^void mergeNodeReads(Node * target, Node * source, Graph * graph)$/;" f +min graph.c /^static inline Coordinate min(Coordinate A, Coordinate B)$/;" f file: +minKeyOfHeap fibHeap.c /^Coordinate minKeyOfHeap(FibHeap * heap)$/;" f +min_short graph.c /^static inline ShortLength min_short(ShortLength A, ShortLength B)$/;" f file: +miniConnection_st shortReadPairs.c /^struct miniConnection_st {$/;" s file: +multCounter readCoherentGraph.c /^static IDnum multCounter = 0;$/;" v file: +multiplicity graph.c /^ IDnum multiplicity; \/\/ 32$/;" m struct:arc_st file: +multiplicity preGraph.c /^ IDnum multiplicity;$/;" m struct:preArc_st file: +multiplicity readCoherentGraph.c /^ IDnum multiplicity;$/;" m struct:rb_connection_st file: +n50 graphStats.c /^Coordinate n50(Graph * graph)$/;" f +name allocArray.h /^ char *name;$/;" m struct:AllocArray_st +name graphStats.c /^ char * name;$/;" m struct:referenceCoord_st file: +name readSet.c /^ char * name;$/;" m struct:referenceCoordinate_st file: +nbPush splayTable.c /^static int *nbPush = NULL;$/;" v file: +nbThreads allocArray.h /^ int nbThreads;$/;" m struct:AllocArray_st +newAllocArray allocArray.c /^newAllocArray (size_t elementSize, char *name)$/;" f +newAllocArrayArray allocArray.c /^AllocArray *newAllocArrayArray(unsigned int n,$/;" f +newDFibHeap dfibHeap.c /^DFibHeap *newDFibHeap()$/;" f +newDescriptor graph.c /^static Descriptor *newDescriptor(IDnum sequenceID, Coordinate start,$/;" f file: +newDescriptor_pg preGraph.c /^static Descriptor *newDescriptor_pg(Coordinate length, FILE * file,$/;" f file: +newFibHeap fibHeap.c /^FibHeap *newFibHeap()$/;" f +newKmerOccurenceTable kmerOccurenceTable.c /^KmerOccurenceTable * newKmerOccurenceTable(short int accelerationBits, int wordLength) {$/;" f +newMask graphStats.c /^static Mask * newMask(Coordinate position)$/;" f file: +newMask splayTable.c /^static Mask * newMask(Coordinate position)$/;" f file: +newNegativeDescriptor graph.c /^static Descriptor *newNegativeDescriptor(IDnum sequenceID,$/;" f file: +newNode graph.c /^Node *newNode(IDnum sequenceID, Coordinate start, Coordinate finish,$/;" f +newPassageMarker passageMarker.c /^PassageMarkerI newPassageMarker(IDnum seqID, Coordinate start,$/;" f +newPassageMarkerList passageMarker.c /^PassageMarkerList *newPassageMarkerList(PassageMarkerI marker,$/;" f +newPositiveDescriptor graph.c /^static Descriptor *newPositiveDescriptor(IDnum sequenceID,$/;" f file: +newPreGraph_pg preGraphConstruction.c /^PreGraph *newPreGraph_pg(RoadMapArray * rdmapArray, char *sequenceFilename)$/;" f +newReadCoverage graphStats.c /^Coordinate newReadCoverage(Node * node, IDnum firstStrain)$/;" f +newReadSet readSet.c /^ReadSet *newReadSet()$/;" f +newRecycleBin recycleBin.c /^RecycleBin *newRecycleBin(size_t node_size, int nodes_per_chunk)$/;" f +newRecycleBinArray recycleBin.c /^RecycleBin *newRecycleBinArray(unsigned int n,$/;" f +newReferenceCoordinateTable readSet.c /^static ReferenceCoordinateTable * newReferenceCoordinateTable() {$/;" f file: +newSplayTable splayTable.c /^SplayTable *newSplayTable(int WORDLENGTH, boolean double_strand)$/;" f +newStringBuffer utility.c /^StringBuffer *newStringBuffer(size_t size)$/;" f +newTicket correctedGraph.c /^static Ticket *newTicket()$/;" f file: +newTightString tightString.c /^TightString *newTightString(Coordinate length)$/;" f +newTightStringArrayFromStringArray tightString.c /^TightString *newTightStringArrayFromStringArray(char **sequences,$/;" f +next allocArray.c /^ AllocArrayFreeElement *next;$/;" m struct:AllocArrayFreeElement_st file: +next correctedGraph.c /^ Ticket *next;$/;" m struct:tkt_st file: +next graph.c /^ Arc *next; \/\/ 64$/;" m struct:arc_st file: +next graph.c /^ GapMarker *next;$/;" m struct:gapMarker_st file: +next graphReConstruction.c /^ SmallNodeList *next;$/;" m struct:smallNodeList_st file: +next graphStats.c /^ Mask* next;$/;" m struct:mask_st file: +next locallyCorrectedGraph.h /^ NodeList *next;$/;" m struct:nodeList_st +next passageMarker.h /^ PassageMarkerList *next;$/;" m struct:passageList_st +next preGraph.c /^ PreMarker * next;$/;" m struct:preMarker_st file: +next readCoherentGraph.c /^ RBConnection *next;$/;" m struct:rb_connection_st file: +next recycleBin.c /^ struct RecycleBin_Node *next;$/;" m struct:RecycleBin_Node typeref:struct:RecycleBin_Node::RecycleBin_Node file: +next recycleBin.c /^ struct chunk_st *next;$/;" m struct:chunk_st typeref:struct:chunk_st::chunk_st file: +next scaffold.c /^ ConnectionStack *next;$/;" m struct:ConnectionStack_st file: +next splayTable.c /^ Mask* next;$/;" m struct:mask_st file: +nextInLookupTable graph.c /^ Arc *nextInLookupTable; \/\/ 64$/;" m struct:arc_st file: +nextInNode passageMarker.c /^ PassageMarkerI nextInNode;$/;" m struct:passage_st file: +nextInSequence passageMarker.c /^ PassageMarkerI nextInSequence;$/;" m struct:passage_st file: +nextLeft preGraph.c /^ PreArcI nextLeft; \/* Index of the previous PreArc *\/$/;" m struct:preArc_st file: +nextRight preGraph.c /^ PreArcI nextRight; \/* Index of the next PreArc *\/$/;" m struct:preArc_st file: +nextStartingPoint correctedGraph.c /^static Node *nextStartingPoint()$/;" f file: +nextTodoTicket correctedGraph.c /^static IDnum nextTodoTicket()$/;" f file: +node graphReConstruction.c /^ Node *node;$/;" m struct:smallNodeList_st file: +node locallyCorrectedGraph.h /^ Node *node;$/;" m struct:nodeList_st +node passageMarker.c /^ struct node_st *node;$/;" m struct:passage_st typeref:struct:passage_st::node_st file: +node readCoherentGraph.c /^ Node *node;$/;" m struct:rb_connection_st file: +nodeCount graph.c /^ IDnum nodeCount;$/;" m struct:graph_st file: +nodeCount graph.c /^IDnum nodeCount(Graph * graph)$/;" f +nodeGenomicMultiplicity graphStats.c /^int nodeGenomicMultiplicity(Node * node, IDnum firstStrain)$/;" f +nodeID graphReConstruction.c /^ IDnum nodeID;$/;" m struct:nodeMask_st file: +nodeID graphReConstruction.c /^ IDnum nodeID;$/;" m struct:referenceMapping_st file: +nodeID kmerOccurenceTable.c /^ IDnum nodeID;$/;" m struct:kmerOccurence_st file: +nodeID roadMap.c /^ IDnum nodeID;$/;" m union:positionPtr file: +nodeID scaffold.c /^ IDnum nodeID;$/;" m struct:readOccurence_st file: +nodeList shortReadPairs.c /^ NodeList *nodeList;$/;" m struct:miniConnection_st file: +nodeListMemory readCoherentGraph.c /^static RecycleBin *nodeListMemory = NULL;$/;" v file: +nodeListMemory shortReadPairs.c /^static RecycleBin *nodeListMemory = NULL;$/;" v file: +nodeList_st locallyCorrectedGraph.h /^struct nodeList_st {$/;" s +nodeLocks graphReConstruction.c /^static omp_lock_t *nodeLocks = NULL;$/;" v file: +nodeLocks preGraphConstruction.c /^static omp_lock_t *nodeLocks = NULL;$/;" v file: +nodeLocks scaffold.c /^static omp_lock_t *nodeLocks = NULL;$/;" v file: +nodeMask_st graphReConstruction.c /^struct nodeMask_st {$/;" s file: +nodeMemory dfibpriv.h /^ RecycleBin *nodeMemory;$/;" m struct:dfibheap +nodeMemory fibpriv.h /^ RecycleBin *nodeMemory;$/;" m struct:fibheap +nodeMemory graph.c /^static RecycleBin *nodeMemory = NULL;$/;" v file: +nodeReadCounts graph.c /^ IDnum *nodeReadCounts;$/;" m struct:graph_st file: +nodeReads graph.c /^ ShortReadMarker **nodeReads;$/;" m struct:graph_st file: +nodeReferenceMarkerCounts preGraph.c /^ IDnum * nodeReferenceMarkerCounts;$/;" m struct:preGraph_st file: +nodeReferenceMarkers preGraph.c /^ PreMarker ** nodeReferenceMarkers;$/;" m struct:preGraph_st file: +nodeStart graphReConstruction.c /^ IDnum nodeStart;$/;" m struct:referenceMapping_st file: +node_size recycleBin.c /^ size_t node_size;$/;" m struct:recycleBin_st file: +node_st graph.c /^struct node_st {$/;" s file: +nodes graph.c /^ Node **nodes;$/;" m struct:graph_st file: +nodes_per_chunk recycleBin.c /^ int nodes_per_chunk;$/;" m struct:recycleBin_st file: +norm scaffold.c /^static double norm(double X)$/;" f file: +normInt scaffold.c /^static double normInt(double X, double Y)$/;" f file: +nullCounter readCoherentGraph.c /^static IDnum nullCounter = 0;$/;" v file: +offset graph.c /^ ShortLength offset;$/;" m struct:shortReadMarker_st file: +offset kmerOccurenceTable.c /^ IDnum offset;$/;" m struct:kmerOccurence_st file: +offset scaffold.c /^ IDnum offset;$/;" m struct:readOccurence_st file: +orderInsertionMarkers preGraphConstruction.c /^orderInsertionMarkers(InsertionMarker ** insMarkers,$/;" f file: +orderNodeReadStartArrays graph.c /^void orderNodeReadStartArrays(Graph * graph)$/;" f +originalVirtualCoverage graph.c /^ IDnum originalVirtualCoverage[CATEGORIES]; \/\/ 32 * 2$/;" m struct:node_st file: +outDegree graph.c /^int outDegree(Node * node)$/;" f +pairedCategories readSet.c /^int pairedCategories(ReadSet * reads)$/;" f +paired_count scaffold.c /^ IDnum paired_count;$/;" m struct:connection_st file: +paired_exp_fraction scaffold.c /^static double paired_exp_fraction = 0.1;$/;" v file: +parseDataAndReadFiles readSet.c /^void parseDataAndReadFiles(char * filename, int argc, char **argv, boolean * double_strand, boolean * noHash)$/;" f +passageList_st passageMarker.h /^struct passageList_st {$/;" s +passageMarkerDirection passageMarker.c /^int passageMarkerDirection(PassageMarkerI marker)$/;" f +passage_st passageMarker.c /^struct passage_st {$/;" s file: +path readCoherentGraph.c /^static PassageMarkerI path = NULL_IDX;$/;" v file: +pathContainsReference correctedGraph.c /^static boolean pathContainsReference(PassageMarkerI path) {$/;" f file: +pathIsClear shortReadPairs.c /^static NodeList *pathIsClear(Node * node, Node * oppositeNode,$/;" f file: +popConnectionStack scaffold.c /^static Connection *popConnectionStack(ConnectionStack **stack)$/;" f file: +popNodeRecord shortReadPairs.c /^static Node *popNodeRecord()$/;" f file: +popNucleotide kmer.c /^Nucleotide popNucleotide(Kmer * kmer) {$/;" f +position graph.c /^ IDnum position;$/;" m struct:gapMarker_st file: +position graph.c /^ IDnum position;$/;" m struct:shortReadMarker_st file: +position kmerOccurenceTable.c /^ IDnum position;$/;" m struct:kmerOccurence_st file: +position roadMap.c /^ ShortLength position; \/\/ 32$/;" m struct:annotation_st file: +position scaffold.c /^ IDnum position;$/;" m struct:readOccurence_st file: +position splay.c /^ Coordinate position;$/;" m struct:splayNode_st file: +positionPtr roadMap.c /^union positionPtr {$/;" u file: +positive_strand graphStats.c /^ boolean positive_strand;$/;" m struct:referenceCoord_st file: +positive_strand readSet.c /^ boolean positive_strand;$/;" m struct:referenceCoordinate_st file: +preArcLeft preGraph.c /^ PreArcI preArcLeft;$/;" m struct:preNode_st file: +preArcMemory preGraph.c /^static AllocArray *preArcMemory = NULL;$/;" v file: +preArcRight preGraph.c /^ PreArcI preArcRight;$/;" m struct:preNode_st file: +preArc_st preGraph.c /^struct preArc_st {$/;" s file: +preGraph_st preGraph.c /^struct preGraph_st {$/;" s file: +preMarker_st preGraph.c /^struct preMarker_st {$/;" s file: +preNodeCount preGraph.c /^ IDnum preNodeCount;$/;" m struct:preGraph_st file: +preNodeCount_pg preGraph.c /^IDnum preNodeCount_pg(PreGraph * preGraph)$/;" f +preNodeID preGraph.c /^ IDnum preNodeID; \/* SF TODO only the sign seems to matter. Could replace with char or bit field *\/$/;" m struct:preMarker_st file: +preNodeIDLeft preGraph.c /^ IDnum preNodeIDLeft;$/;" m struct:preArc_st file: +preNodeIDRight preGraph.c /^ IDnum preNodeIDRight;$/;" m struct:preArc_st file: +preNodeStart preGraph.c /^ IDnum preNodeStart;$/;" m struct:preMarker_st file: +preNode_st preGraph.c /^struct preNode_st {$/;" s file: +preNodes preGraph.c /^ PreNode *preNodes;$/;" m struct:preGraph_st file: +prepareGraphForLocalCorrections locallyCorrectedGraph.c /^void prepareGraphForLocalCorrections(Graph * argGraph)$/;" f +previous correctedGraph.c /^static Node **previous;$/;" v file: +previous graph.c /^ Arc *previous; \/\/ 64$/;" m struct:arc_st file: +previous locallyCorrectedGraph.c /^static Node **previous;$/;" v file: +previous locallyCorrectedGraph.h /^ NodeList *previous;$/;" m struct:nodeList_st +previous preGraph.c /^ PreMarker * previous;$/;" m struct:preMarker_st file: +previousInNode passageMarker.c /^ PassageMarkerI previousInNode;$/;" m struct:passage_st file: +printAnnotations splayTable.c /^static void printAnnotations(IDnum *sequenceIDs, Coordinate * coords,$/;" f file: +printConnections scaffold.c /^void printConnections(ReadSet * reads, boolean * shadows)$/;" f +printKmer kmer.c /^void printKmer(Kmer * kmer) {$/;" f +printScaffold scaffold.c /^void printScaffold(Graph * argGraph,$/;" f +printShortCounts graphStats.c /^static void printShortCounts(FILE * outfile, Node * node, Graph * graph, ReadSet * reads)$/;" f file: +printUsage readSet.c /^static void printUsage()$/;" f file: +printUsage run.c /^static void printUsage()$/;" f file: +printUsage run2.c /^static void printUsage()$/;" f file: +printUsage run3.c /^static void printUsage()$/;" f file: +producing splayTable.c /^static boolean producing = 1;$/;" v file: +programName utility.c /^static const char *programName = NULL;$/;" v file: +progressStatus correctedGraph.c /^static boolean *progressStatus;$/;" v file: +projectFromLongRead scaffold.c /^static void projectFromLongRead(Node * node, PassageMarkerI marker,$/;" f file: +projectFromNode scaffold.c /^static void projectFromNode(IDnum nodeID,$/;" f file: +projectFromReadPair scaffold.c /^static void projectFromReadPair(Node * node, ReadOccurence * readOccurence,$/;" f file: +projectFromShortRead scaffold.c /^static void projectFromShortRead(Node * node,$/;" f file: +projectFromSingleRead scaffold.c /^static void projectFromSingleRead(Node * node,$/;" f file: +projectGraphToFile graphStats.c /^void projectGraphToFile(Graph * graph, char *filename, int WORDLENGTH,$/;" f +pushBuffer splayTable.c /^static void pushBuffer(int thread)$/;" f file: +pushBufferCommit splayTable.c /^static void pushBufferCommit(int thread)$/;" f file: +pushConnectionStack scaffold.c /^static void pushConnectionStack(ConnectionStack **stack, Connection *connection)$/;" f file: +pushNeighbours shortReadPairs.c /^static boolean pushNeighbours(Node * node, Node * oppositeNode,$/;" f file: +pushNucleotide kmer.c /^void pushNucleotide(Kmer * kmer, Nucleotide nucleotide) {$/;" f +rb_connection_st readCoherentGraph.c /^struct rb_connection_st {$/;" s file: +reConnectAnnotation preGraphConstruction.c /^static void reConnectAnnotation(IDnum * currentPreNodeID, Annotation * annot,$/;" f file: +readBAMFile readSet.c /^static void readBAMFile(FILE *outfile, char *filename, Category cat, IDnum *sequenceIndex, ReferenceCoordinateTable * refCoords)$/;" f file: +readBAMint32 readSet.c /^static int readBAMint32(gzFile file)$/;" f file: +readCoherentGraph readCoherentGraph.c /^void readCoherentGraph(Graph * inGraph, boolean(*isUnique) (Node * node),$/;" f +readCount readSet.h /^ IDnum readCount;$/;" m struct:readSet_st +readCoverage graphStats.c /^Coordinate readCoverage(Node * node)$/;" f +readElandFile readSet.c /^static void readElandFile(FILE* outfile, char *filename, Category cat, IDnum * sequenceIndex)$/;" f file: +readFastAFile readSet.c /^static void readFastAFile(FILE* outfile, char *filename, Category cat, IDnum * sequenceIndex, ReferenceCoordinateTable * refCoords)$/;" f file: +readFastAGZFile readSet.c /^static void readFastAGZFile(FILE* outfile, char *filename, Category cat, IDnum * sequenceIndex)$/;" f file: +readFastQFile readSet.c /^static void readFastQFile(FILE* outfile, char *filename, Category cat, IDnum * sequenceIndex)$/;" f file: +readFastQGZFile readSet.c /^static void readFastQGZFile(FILE * outfile, char *filename, Category cat, IDnum *sequenceIndex)$/;" f file: +readID graph.c /^ IDnum readID;$/;" m struct:shortReadMarker_st file: +readMAQGZFile readSet.c /^static void readMAQGZFile(FILE* outfile, char *filename, Category cat, IDnum * sequenceIndex)$/;" f file: +readNucleotide tightString.c /^char readNucleotide(Nucleotide nucleotide)$/;" f +readOccurence_st scaffold.c /^struct readOccurence_st {$/;" s file: +readPassageMarker passageMarker.c /^char *readPassageMarker(PassageMarkerI marker)$/;" f +readPreGraphFile graph.c /^Graph *readPreGraphFile(char *preGraphFilename, boolean * double_strand)$/;" f +readRawFile readSet.c /^static void readRawFile(FILE* outfile, char *filename, Category cat, IDnum * sequenceIndex)$/;" f file: +readRawGZFile readSet.c /^static void readRawGZFile(FILE * outfile, char *filename, Category cat, IDnum *sequenceIndex)$/;" f file: +readSAMFile readSet.c /^static void readSAMFile(FILE *outfile, char *filename, Category cat, IDnum *sequenceIndex, ReferenceCoordinateTable * refCoords)$/;" f file: +readSet_st readSet.h /^struct readSet_st {$/;" s +readSolexaFile readSet.c /^static void readSolexaFile(FILE* outfile, char *filename, Category cat, IDnum * sequenceIndex)$/;" f file: +readStartsAreActivated graph.c /^boolean readStartsAreActivated(Graph * graph)$/;" f +readTightString tightString.c /^char *readTightString(TightString * tString)$/;" f +readTightStringFragment tightString.c /^void readTightStringFragment(TightString * tString, Coordinate start,$/;" f +readjustConnection scaffold.c /^void readjustConnection(Connection * connect, Coordinate distance,$/;" f +readjustConnectionInTree scaffold.c /^static void readjustConnectionInTree(Connection *connect,$/;" f file: +readjustMiniConnection shortReadPairs.c /^static void readjustMiniConnection(Node * node,$/;" f file: +readsLocks scaffold.c /^static omp_lock_t *readsLocks = NULL;$/;" v file: +reallocOrExit utility.h 41;" d +reallocOrExit4 utility.c /^void *reallocOrExit4(void *ptr, size_t count, size_t size, const char *name)$/;" f +reallocOrExitReferenceMarkers preGraph.c /^static PreMarker * reallocOrExitReferenceMarkers(PreGraph * preGraph, IDnum preNodeID, IDnum length) {$/;" f file: +reallocOrExitWithoutCast utility.h 51;" d +reallocateNodeDescriptor graph.c /^void reallocateNodeDescriptor(Node * node, Coordinate length) {$/;" f +recenterLocalScaffold shortReadPairs.c /^static void recenterLocalScaffold(Node * node, Coordinate oldLength)$/;" f file: +recenterNode shortReadPairs.c /^static void recenterNode(Node * node, Coordinate oldLength)$/;" f file: +reconnectPassageMarker shortReadPairs.c /^static void reconnectPassageMarker(PassageMarkerI marker, Node * node,$/;" f file: +recordKmerOccurence kmerOccurenceTable.c /^void recordKmerOccurence(Kmer * kmer, IDnum nodeID, Coordinate position, KmerOccurenceTable * table) {$/;" f +recordNode shortReadPairs.c /^static NodeList *recordNode(Node * node)$/;" f file: +recordReferenceMappings graphReConstruction.c /^static ReferenceMapping * recordReferenceMappings(char * preGraphFilename, IDnum arrayLength) {$/;" f file: +recycle recycleBin.c /^ RecycleBin_Node *recycle;$/;" m struct:recycleBin_st file: +recycleBin_st recycleBin.c /^struct recycleBin_st {$/;" s file: +reduceNode graph.c /^void reduceNode(Node * node)$/;" f +reduceSlowNodes correctedGraph.c /^static void reduceSlowNodes(PassageMarkerI slowMarker, Node * finish)$/;" f file: +refFinish graphStats.c /^ IDnum refFinish;$/;" m struct:refMap_st file: +refID graphStats.c /^ IDnum refID;$/;" m struct:refMap_st file: +refMap_st graphStats.c /^typedef struct refMap_st {$/;" s file: +refReadCoverage graphStats.c /^Coordinate refReadCoverage(Node * node, IDnum firstStrain)$/;" f +refStart graphStats.c /^ IDnum refStart;$/;" m struct:refMap_st file: +referenceCoord_st graphStats.c /^struct referenceCoord_st {$/;" s file: +referenceCoordinateTable_st readSet.c /^struct referenceCoordinateTable_st {$/;" s file: +referenceCoordinate_st readSet.c /^struct referenceCoordinate_st {$/;" s file: +referenceCount preGraph.c /^ IDnum referenceCount;$/;" m struct:preGraph_st file: +referenceCount roadMap.h /^ IDnum referenceCount;$/;" m struct:roadMapArray_st +referenceGraphKmers graphReConstruction.c /^static KmerOccurenceTable *referenceGraphKmers(char *preGraphFilename,$/;" f file: +referenceID graphReConstruction.c /^ IDnum referenceID;$/;" m struct:referenceMapping_st file: +referenceID preGraph.c /^ IDnum referenceID;$/;" m struct:preMarker_st file: +referenceID readSet.c /^ IDnum referenceID;$/;" m struct:referenceCoordinate_st file: +referenceMapping_st graphReConstruction.c /^struct referenceMapping_st {$/;" s file: +referenceMarkersAreActivated_pg preGraph.c /^boolean referenceMarkersAreActivated_pg(PreGraph * preGraph) {$/;" f +referenceStart graphReConstruction.c /^ IDnum referenceStart;$/;" m struct:referenceMapping_st file: +referenceStart preGraph.c /^ IDnum referenceStart;$/;" m struct:preMarker_st file: +referenceStarts preGraph.c /^ PreMarker ** referenceStarts;$/;" m struct:preGraph_st file: +reference_coordinate_double_strand readSet.c /^static Coordinate reference_coordinate_double_strand = true;$/;" v file: +remapBackOfNodeArcsOntoNeighbour correctedGraph.c /^static void remapBackOfNodeArcsOntoNeighbour(Node * source, Node * target)$/;" f file: +remapBackOfNodeDescriptorOntoNeighbour correctedGraph.c /^static void remapBackOfNodeDescriptorOntoNeighbour(Node * source,$/;" f file: +remapBackOfNodeMarkersOntoNeighbour correctedGraph.c /^remapBackOfNodeMarkersOntoNeighbour(Node * source,$/;" f file: +remapBackOfNodeOntoNeighbour correctedGraph.c /^remapBackOfNodeOntoNeighbour(Node * source, PassageMarkerI sourceMarker,$/;" f file: +remapBackOfNodeTimesOntoNeighbour correctedGraph.c /^static void remapBackOfNodeTimesOntoNeighbour(Node * source, Node * target)$/;" f file: +remapEmptyPathArcsOntoMiddlePathSimple correctedGraph.c /^static void remapEmptyPathArcsOntoMiddlePathSimple(PassageMarkerI emptyPath,$/;" f file: +remapEmptyPathMarkersOntoMiddlePathDevious correctedGraph.c /^static void remapEmptyPathMarkersOntoMiddlePathDevious(PassageMarkerI emptyPath,$/;" f file: +remapEmptyPathMarkersOntoMiddlePathSimple correctedGraph.c /^static void remapEmptyPathMarkersOntoMiddlePathSimple(PassageMarkerI emptyPath,$/;" f file: +remapEmptyPathOntoMiddlePath correctedGraph.c /^remapEmptyPathOntoMiddlePath(PassageMarkerI emptyPath,$/;" f file: +remapNodeArcsOntoNeighbour correctedGraph.c /^static void remapNodeArcsOntoNeighbour(Node * source, Node * target)$/;" f file: +remapNodeArcsOntoTarget correctedGraph.c /^static void remapNodeArcsOntoTarget(Node * source, Node * target)$/;" f file: +remapNodeFibHeapReferencesOntoNode correctedGraph.c /^remapNodeFibHeapReferencesOntoNode(Node * source, Node * target)$/;" f file: +remapNodeInwardReferencesOntoNode correctedGraph.c /^static void remapNodeInwardReferencesOntoNode(Node * source, Node * target)$/;" f file: +remapNodeMarkersOntoNeighbour correctedGraph.c /^static void remapNodeMarkersOntoNeighbour(Node * source,$/;" f file: +remapNodeOntoNeighbour correctedGraph.c /^static void remapNodeOntoNeighbour(Node * source,$/;" f file: +remapNodeTimesOntoForwardMiddlePath correctedGraph.c /^static void remapNodeTimesOntoForwardMiddlePath(Node * source,$/;" f file: +remapNodeTimesOntoNeighbour correctedGraph.c /^static void remapNodeTimesOntoNeighbour(Node * source, Node * target)$/;" f file: +remapNodeTimesOntoTargetNode correctedGraph.c /^static void remapNodeTimesOntoTargetNode(Node * source, Node * target)$/;" f file: +remapNodeTimesOntoTwinMiddlePath correctedGraph.c /^static void remapNodeTimesOntoTwinMiddlePath(Node * source,$/;" f file: +removeDead graphStats.c /^static boolean removeDead(PassageMarkerList ** list)$/;" f file: +removeHighCoverageNodes graphStats.c /^void removeHighCoverageNodes(Graph * graph, double maxCov, boolean export, Coordinate minLength, char *filename)$/;" f +removeLowArcs graphStats.c /^void removeLowArcs(Graph * graph, double cutoff) {$/;" f +removeLowArcsFromNode graphStats.c /^static void removeLowArcsFromNode(Node* node, Graph * graph, double cutoff) {$/;" f file: +removeLowCoverageNodesAndDenounceDubiousReads graphStats.c /^boolean *removeLowCoverageNodesAndDenounceDubiousReads(Graph * graph,$/;" f +removeLowCoverageReferenceNodes graphStats.c /^void removeLowCoverageReferenceNodes(Graph * graph, double minCov, double minLongCov, ReadSet * reads)$/;" f +removeLowLongCoverageNodesAndDenounceDubiousReads graphStats.c /^void removeLowLongCoverageNodesAndDenounceDubiousReads(Graph * graph,$/;" f +removeNextNodeFromDHeap dfibHeap.c /^Node *removeNextNodeFromDHeap(DFibHeap * heap)$/;" f +removeNextNodeFromHeap fibHeap.c /^struct node_st *removeNextNodeFromHeap(FibHeap * heap)$/;" f +removeNodeAndDenounceDubiousReads graphStats.c /^removeNodeAndDenounceDubiousReads(Graph *graph,$/;" f file: +removePreArcFromList_pg preGraph.c /^void removePreArcFromList_pg(PreArcI preArc, IDnum preNodeID,$/;" f +removeStrainMarkers graphStats.c /^void removeStrainMarkers(Node * node, IDnum firstStrain)$/;" f +removeUnreliableConnections scaffold.c /^static void removeUnreliableConnections(ReadSet * reads, boolean *shadows)$/;" f file: +renumberNodes graph.c /^void renumberNodes(Graph * graph)$/;" f +renumberPreNodes_pg preGraph.c /^void renumberPreNodes_pg(PreGraph * preGraph)$/;" f +replaceKeyInDHeap dfibHeap.c /^Time replaceKeyInDHeap(DFibHeap * heap, DFibHeapNode * node, Time newKey)$/;" f +replaceKeyInHeap fibHeap.c /^Coordinate replaceKeyInHeap(FibHeap * heap, FibHeapNode * node,$/;" f +replaceValueInDHeap dfibHeap.c /^void replaceValueInDHeap(DFibHeapNode * node, Node * newValue)$/;" f +replaceValueInHeap fibHeap.c /^void replaceValueInHeap(FibHeapNode * node, Node * newValue)$/;" f +resetKeyFilter kmer.c /^void resetKeyFilter(int keyLength) {$/;" f +resetMiniConnection shortReadPairs.c /^static void resetMiniConnection(Node * node, MiniConnection * localConnect,$/;" f file: +resetNodeStatus graph.c /^void resetNodeStatus(Graph * graph)$/;" f +resetStringBuffer utility.c /^void resetStringBuffer(StringBuffer *buffer)$/;" f +resetWordFilter kmer.c /^void resetWordFilter(int wordLength) {$/;" f +resizeReferenceCoordinateTable readSet.c /^static void resizeReferenceCoordinateTable(ReferenceCoordinateTable * table, IDnum extraLength) {$/;" f file: +reverseCatDescriptors graph.c /^static void reverseCatDescriptors(Descriptor * descr, Coordinate destinationLength, Descriptor * copy, Coordinate sourceLength, Coordinate totalLength) $/;" f file: +reverseComplementSequence readSet.c /^static void reverseComplementSequence(char * str)$/;" f file: +reversePushNucleotide kmer.c /^void reversePushNucleotide(Kmer * kmer, Nucleotide nucleotide) {$/;" f +right scaffold.c /^ Connection *right;$/;" m struct:connection_st file: +right splay.c /^ struct splayNode_st *right;$/;" m struct:splayNode_st typeref:struct:splayNode_st::splayNode_st file: +roadMapArray_st roadMap.h /^struct roadMapArray_st {$/;" s +roadmap_st roadMap.c /^struct roadmap_st {$/;" s file: +scaffold scaffold.c /^static Connection **scaffold = NULL;$/;" v file: +scanReferenceSequences splayTable.c /^Mask ** scanReferenceSequences(FILE * file, IDnum referenceSequenceCount) {$/;" f +secondInPair readSet.h /^ unsigned char *secondInPair;$/;" m struct:readSet_st +seqID splay.c /^ IDnum seqID;$/;" m struct:splayNode_st file: +sequence tightString.c /^ Codon *sequence;$/;" m struct:tString_st file: +sequenceCategories correctedGraph.c /^static Category *sequenceCategories;$/;" v file: +sequenceCount graph.c /^ IDnum sequenceCount;$/;" m struct:graph_st file: +sequenceCount graph.c /^IDnum sequenceCount(Graph * graph)$/;" f +sequenceCount preGraph.c /^ IDnum sequenceCount;$/;" m struct:preGraph_st file: +sequenceCount_pg preGraph.c /^IDnum sequenceCount_pg(PreGraph * preGraph)$/;" f +sequenceID passageMarker.c /^ IDnum sequenceID;$/;" m struct:passage_st file: +sequenceID roadMap.c /^ IDnum sequenceID; \/\/ 32$/;" m struct:annotation_st file: +sequenceLengths correctedGraph.c /^static ShortLength *sequenceLengths;$/;" v file: +sequences readCoherentGraph.c /^static TightString *sequences = NULL;$/;" v file: +sequences readSet.h /^ char **sequences;$/;" m struct:readSet_st +setAllConnectionsClean scaffold.c /^static void setAllConnectionsClean(void)$/;" f file: +setEmptyMiniConnection shortReadPairs.c /^static void setEmptyMiniConnection(Node * node)$/;" f file: +setFinishID roadMap.c /^void setFinishID(Annotation * annot, IDnum nodeID)$/;" f +setFinishOffset passageMarker.c /^void setFinishOffset(PassageMarkerI marker, Coordinate offset)$/;" f +setInsertLengths graph.c /^void setInsertLengths(Graph * graph, Category cat, Coordinate insertLength,$/;" f +setInsertionMarkers preGraphConstruction.c /^setInsertionMarkers(RoadMapArray * rdmaps,$/;" f file: +setLocalMaxDivergence locallyCorrectedGraph.c /^void setLocalMaxDivergence(double value)$/;" f +setLocalMaxGaps locallyCorrectedGraph.c /^void setLocalMaxGaps(int value)$/;" f +setLocalMaxReadLength locallyCorrectedGraph.c /^void setLocalMaxReadLength(int value)$/;" f +setMarker graph.c /^void setMarker(Node * node, PassageMarkerI marker)$/;" f +setMaxDivergence correctedGraph.c /^void setMaxDivergence(double value)$/;" f +setMaxGaps correctedGraph.c /^void setMaxGaps(int value)$/;" f +setMaxReadLength correctedGraph.c /^void setMaxReadLength(int value)$/;" f +setMultiplicity graph.c /^void setMultiplicity(Arc * arc, IDnum mult)$/;" f +setMultiplicityCutoff readCoherentGraph.c /^void setMultiplicityCutoff(int value)$/;" f +setMultiplicity_pg preGraph.c /^void setMultiplicity_pg(PreArcI preArc, IDnum mult)$/;" f +setNextInNode passageMarker.c /^void setNextInNode(PassageMarkerI marker, PassageMarkerI next)$/;" f +setNextInSequence passageMarker.c /^void setNextInSequence(PassageMarkerI previous, PassageMarkerI next)$/;" f +setNextPreArc_pg preGraph.c /^static void setNextPreArc_pg(PreArcI preArc, IDnum preNodeID,$/;" f file: +setNodeDHeapNode correctedGraph.c /^static void setNodeDHeapNode(Node * node, DFibHeapNode * dheapNode)$/;" f file: +setNodePrevious correctedGraph.c /^static void setNodePrevious(Node * previousNode, Node * node)$/;" f file: +setNodeStatus graph.c /^void setNodeStatus(Node * node, boolean status)$/;" f +setNodeTime correctedGraph.c /^static void setNodeTime(Node * node, Time time)$/;" f file: +setNodeTime locallyCorrectedGraph.c /^static void setNodeTime(Node * node, Time time)$/;" f file: +setOriginalVirtualCoverage graph.c /^void setOriginalVirtualCoverage(Node * node, Category category,$/;" f +setPairedExpFraction scaffold.c /^void setPairedExpFraction(double x) {$/;" f +setPassageMarkerFinish passageMarker.c /^void setPassageMarkerFinish(PassageMarkerI marker, Coordinate finish)$/;" f +setPassageMarkerStart passageMarker.c /^void setPassageMarkerStart(PassageMarkerI marker, Coordinate start)$/;" f +setPassageMarkerStatus passageMarker.c /^void setPassageMarkerStatus(PassageMarkerI marker, boolean status)$/;" f +setPreNodeDescriptor_pg preGraph.c /^void setPreNodeDescriptor_pg(Descriptor * descr, Coordinate length, IDnum preNodeID, PreGraph * preGraph) {$/;" f +setPreviousInSequence passageMarker.c /^void setPreviousInSequence(PassageMarkerI previous, PassageMarkerI next)$/;" f +setProgramName utility.c /^void setProgramName(const char *name)$/;" f +setShortReadMarkerOffset graph.c /^inline void setShortReadMarkerOffset(ShortReadMarker * marker,$/;" f +setShortReadMarkerPosition graph.c /^inline void setShortReadMarkerPosition(ShortReadMarker * marker,$/;" f +setSingleNodeStatus graph.c /^void setSingleNodeStatus(Node * node, boolean status)$/;" f +setStartID roadMap.c /^void setStartID(Annotation * annot, IDnum nodeID)$/;" f +setStartOffset passageMarker.c /^void setStartOffset(PassageMarkerI marker, Coordinate offset)$/;" f +setTightStringLength tightString.c /^void setTightStringLength(TightString * tString, Coordinate length)$/;" f +setTopOfTheNode passageMarker.c /^void setTopOfTheNode(PassageMarkerI marker)$/;" f +setUniqueness graph.c /^void setUniqueness(Node * node, boolean value)$/;" f +setUnreliableConnectionCutoff scaffold.c /^void setUnreliableConnectionCutoff(int val)$/;" f +setVirtualCoverage graph.c /^void setVirtualCoverage(Node * node, Category category,$/;" f +setVirtualCoverage graph.c /^void setVirtualCoverage(Node * node,$/;" f +shareReadStarts graph.c /^void shareReadStarts(Node * target, Node * source, Graph * graph)$/;" f +shiftRight kmer.c /^static void shiftRight(Kmer * kmer) {$/;" f file: +shortReadMarker_st graph.c /^struct shortReadMarker_st {$/;" s file: +simpleArcCount graph.c /^int simpleArcCount(Node * node)$/;" f +simplePreArcCount_pg preGraph.c /^char simplePreArcCount_pg(IDnum preNodeID, PreGraph * preGraph)$/;" f +simplifyNode correctedGraph.c /^static void simplifyNode(Node * node)$/;" f file: +slowPath correctedGraph.c /^static PassageMarkerI slowPath;$/;" v file: +slowPath locallyCorrectedGraph.c /^static PassageMarkerI slowPath;$/;" v file: +slowSequence correctedGraph.c /^static TightString *slowSequence;$/;" v file: +slowSequence locallyCorrectedGraph.c /^static TightString *slowSequence;$/;" v file: +slowToFastMapping correctedGraph.c /^static Coordinate *slowToFastMapping;$/;" v file: +smallNodeListMemory graphReConstruction.c /^static RecycleBin *smallNodeListMemory = NULL;$/;" v file: +smallNodeList_st graphReConstruction.c /^struct smallNodeList_st {$/;" s file: +sortCoords graphStats.c /^static void sortCoords(Coordinate * array, IDnum length) {$/;" f file: +sortGapMarkers graph.c /^void sortGapMarkers(Graph * graph)$/;" f +sortKmerOccurenceTable kmerOccurenceTable.c /^void sortKmerOccurenceTable(KmerOccurenceTable * table) {$/;" f +sortNodeArcs graph.c /^static void sortNodeArcs(Node * node)$/;" f file: +sortNodeGapMarkers graph.c /^static void sortNodeGapMarkers(Node * node, Graph * graph)$/;" f file: +sortReferenceCoordinateTable readSet.c /^static void sortReferenceCoordinateTable(ReferenceCoordinateTable * table) {$/;" f file: +splayConnection scaffold.c /^static Connection *splayConnection(Connection * T, IDnum nodeID)$/;" f file: +splayNode_st splay.c /^struct splayNode_st {$/;" s file: +splayTable_st splayTable.c /^struct splayTable_st {$/;" s file: +splayToList scaffold.c /^static void splayToList(Connection **connection)$/;" f file: +splitNodeDescriptor graph.c /^void splitNodeDescriptor(Node * source, Node * target, Coordinate offset)$/;" f +spreadReadIDs graph.c /^void spreadReadIDs(ShortReadMarker * reads, IDnum readCount, Node * node,$/;" f +start graphReConstruction.c /^ IDnum start;$/;" m struct:nodeMask_st file: +start graphStats.c /^ Coordinate start;$/;" m struct:mask_st file: +start graphStats.c /^ IDnum start;$/;" m struct:refMap_st file: +start graphStats.c /^ IDnum start;$/;" m struct:referenceCoord_st file: +start locallyCorrectedGraph.c /^static Node *start;$/;" v file: +start passageMarker.c /^ IDnum start;$/;" m struct:passage_st file: +start readSet.c /^ Coordinate start;$/;" m struct:referenceCoordinate_st file: +start roadMap.c /^ union positionPtr start; \/\/ 32$/;" m struct:annotation_st typeref:union:annotation_st::positionPtr file: +start splayTable.c /^ Coordinate start;$/;" m struct:mask_st file: +startingNode correctedGraph.c /^static Node *startingNode;$/;" v file: +status graph.c /^ boolean status; \/\/ 1$/;" m struct:node_st file: +status passageMarker.c /^ boolean status;$/;" m struct:passage_st file: +str utility.h /^ char *str;$/;" m struct:__anon1 +swap dfib.c 73;" d file: +swap fib.c 69;" d file: +tSeqMem readSet.h /^ char *tSeqMem;$/;" m struct:readSet_st +tSequences readSet.h /^ TightString *tSequences;$/;" m struct:readSet_st +tString_st tightString.c /^struct tString_st {$/;" s file: +table splayTable.c /^ SplayTree **table;$/;" m struct:splayTable_st file: +tableLocks splayTable.c /^ omp_lock_t *tableLocks;$/;" m struct:splayTable_st file: +terminalReferenceMarker graphStats.c /^static boolean terminalReferenceMarker(Node * node, ReadSet * reads) {$/;" f file: +testConnection scaffold.c /^static boolean testConnection(IDnum IDA,$/;" f file: +threadSequenceThroughGraph graphReConstruction.c /^static void threadSequenceThroughGraph(TightString * tString,$/;" f file: +ticketMemory correctedGraph.c /^static RecycleBin *ticketMemory;$/;" v file: +timersub utility.h 93;" d +times correctedGraph.c /^static Time *times;$/;" v file: +times locallyCorrectedGraph.c /^static Time *times;$/;" v file: +tkt_st correctedGraph.c /^struct tkt_st {$/;" s file: +todo correctedGraph.c /^static Ticket **todo;$/;" v file: +todoLists correctedGraph.c /^static Ticket **todoLists;$/;" v file: +totalAssemblyLength graphStats.c /^Coordinate totalAssemblyLength(Graph * graph)$/;" f +tourBus correctedGraph.c /^static void tourBus(Node * startingPoint)$/;" f file: +tourBusArc correctedGraph.c /^static void tourBusArc(Node * origin, Arc * arc, Time originTime)$/;" f file: +tourBusArc_local locallyCorrectedGraph.c /^static void tourBusArc_local(Node * origin, Arc * arc, Time originTime)$/;" f file: +tourBusNode correctedGraph.c /^static void tourBusNode(Node * node)$/;" f file: +tourBusNode_local locallyCorrectedGraph.c /^static void tourBusNode_local(Node * node)$/;" f file: +tourBus_local locallyCorrectedGraph.c /^static void tourBus_local(Node * startingPoint)$/;" f file: +transferNodeData correctedGraph.c /^static void transferNodeData(Node * source, Node * target)$/;" f file: +transposePassageMarker passageMarker.c /^void transposePassageMarker(PassageMarkerI marker, Node * node)$/;" f +treeMemory splay.c /^static RecycleBin *treeMemory = NULL;$/;" v file: +trimLongReadTips readCoherentGraph.c /^static void trimLongReadTips()$/;" f file: +true globals.h 29;" d +twin scaffold.c /^ Connection *twin;$/;" m struct:connection_st file: +twinArc graph.c /^ Arc *twinArc; \/\/ 64$/;" m struct:arc_st file: +twinMarker passageMarker.c /^ PassageMarkerI twinMarker;$/;" m struct:passage_st file: +twinNode graph.c /^ Node *twinNode; \/\/ 64$/;" m struct:node_st file: +unLockNode graphReConstruction.c /^static inline void unLockNode(Node *node)$/;" f file: +unLockNode preGraphConstruction.c /^static void unLockNode(IDnum preNodeID)$/;" f file: +unLockRead scaffold.c /^static inline void unLockRead(IDnum readID)$/;" f file: +unLockTwoNodes graphReConstruction.c /^static inline void unLockTwoNodes(Node *node, Node *node2)$/;" f file: +unLockTwoNodes preGraphConstruction.c /^static void unLockTwoNodes(IDnum preNodeID, IDnum preNode2ID)$/;" f file: +unLockTwoNodes scaffold.c /^static inline void unLockTwoNodes(IDnum nodeID, IDnum node2ID)$/;" f file: +unMemorizeNodes graphReConstruction.c /^static void unMemorizeNodes(SmallNodeList ** nodePile)$/;" f file: +uniqueNodesConnect readCoherentGraph.c /^static boolean uniqueNodesConnect(Node * startingNode)$/;" f file: +uniqueness graph.c /^ boolean uniqueness; \/\/ 1$/;" m struct:node_st file: +unmarkInterestingNodes shortReadPairs.c /^static void unmarkInterestingNodes()$/;" f file: +unmarkNode shortReadPairs.c /^void unmarkNode(Node * node, MiniConnection * localConnect)$/;" f +updateMarkers graphStats.c /^static void updateMarkers(PassageMarkerList * list)$/;" f file: +updateMembers readCoherentGraph.c /^static void updateMembers(Node * bypass, Node * nextNode)$/;" f file: +updateNodeStatus correctedGraph.c /^static void updateNodeStatus(Node * node)$/;" f file: +updatePreArcData_pg preGraph.c /^static void updatePreArcData_pg(PreArcI preArc, IDnum oldPreNodeID,$/;" f file: +usedReads graphStats.c /^IDnum usedReads(Graph * graph, Coordinate minContigLength) $/;" f +variance scaffold.c /^ float variance;$/;" m struct:connection_st file: +variance shortReadPairs.c /^ float variance;$/;" m struct:miniConnection_st file: +velvetFprintf utility.c /^void velvetFprintf(FILE * file, const char * format, ...) $/;" f +velvetFprintfReferenceMapping graphStats.c /^static void velvetFprintfReferenceMapping(FILE * file, ReferenceMapping * mapping, ReferenceCoord * refCoords, int wordLength) {$/;" f file: +velvetLog utility.c /^void velvetLog(const char *format, ...)$/;" f +velvetifySequence readSet.c /^static void velvetifySequence(char * str) {$/;" f file: +virtualCoverage graph.c /^ IDnum virtualCoverage; \/\/ 32 * 2$/;" m struct:node_st file: +virtualCoverage graph.c /^ IDnum virtualCoverage[CATEGORIES]; \/\/ 32 * 2$/;" m struct:node_st file: +voidcmp fib.h /^typedef Coordinate(*voidcmp) (void *, void *);$/;" t +wordLength graph.c /^ int wordLength;$/;" m struct:graph_st file: +wordLength preGraph.c /^ int wordLength;$/;" m struct:preGraph_st file: +writeBuffers splayTable.c /^static void writeBuffers(FILE *outFile, int nbThreads)$/;" f file: +writeFastaSequence readSet.c /^static void writeFastaSequence(FILE * outfile, const char * str)$/;" f file: +writeNucleotide tightString.c /^void writeNucleotide(Nucleotide nucleotide, Codon * codonPtr, int position)$/;" f +writeNucleotideAtPosition tightString.c /^writeNucleotideAtPosition(Nucleotide nucleotide, Coordinate position,$/;" f +writeNucleotideInDescriptor graph.c /^static void writeNucleotideInDescriptor(Nucleotide nucleotide,$/;" f file: +writeNucleotideInDescriptor_pg preGraph.c /^static void writeNucleotideInDescriptor_pg(Nucleotide nucleotide,$/;" f file: +writeNucleotideNumber tightString.c /^writeNucleotideNumber(Nucleotide nucleotide, Codon * codonPtr,$/;" f