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Merge pull request #581 from ekg/correct-build
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Correct build, update vcflib
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@ekg
ekg committed Dec 19, 2019
2 parents 54bf409 + fae0f09 commit 02bb9d7
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Showing 6 changed files with 23 additions and 26 deletions.
2 changes: 1 addition & 1 deletion intervaltree
Submodule intervaltree updated 4 files
+253 −124 IntervalTree.h
+33 −3 Makefile
+10,203 −0 catch.hpp
+123 −34 interval_tree_test.cpp
16 changes: 6 additions & 10 deletions src/BedReader.cpp
View file
Expand Up @@ -46,32 +46,28 @@ vector<BedTarget> BedReader::entries(void) {
}

bool BedReader::targetsContained(string& seq, long left, long right) {
vector<Interval<BedTarget*> > results;
intervals[seq].findContained(left, right, results);
vector<Interval<int, BedTarget*> > results = intervals[seq].findContained(left, right);
return !results.empty();
}

bool BedReader::targetsOverlap(string& seq, long left, long right) {
vector<Interval<BedTarget*> > results;
intervals[seq].findOverlapping(left, right, results);
vector<Interval<int, BedTarget*> > results = intervals[seq].findOverlapping(left, right);
return !results.empty();
}

vector<BedTarget*> BedReader::targetsContaining(BedTarget& target) {
vector<Interval<BedTarget*> > results;
intervals[target.seq].findContained(target.left, target.right, results);
vector<Interval<int, BedTarget*> > results = intervals[target.seq].findContained(target.left, target.right);
vector<BedTarget*> contained;
for (vector<Interval<BedTarget*> >::iterator r = results.begin(); r != results.end(); ++r) {
for (vector<Interval<int, BedTarget*> >::iterator r = results.begin(); r != results.end(); ++r) {
contained.push_back(r->value);
}
return contained;
}

vector<BedTarget*> BedReader::targetsOverlapping(BedTarget& target) {
vector<Interval<BedTarget*> > results;
intervals[target.seq].findOverlapping(target.left, target.right, results);
vector<Interval<int, BedTarget*> > results = intervals[target.seq].findOverlapping(target.left, target.right);
vector<BedTarget*> overlapping;
for (vector<Interval<BedTarget*> >::iterator r = results.begin(); r != results.end(); ++r) {
for (vector<Interval<int, BedTarget*> >::iterator r = results.begin(); r != results.end(); ++r) {
overlapping.push_back(r->value);
}
return overlapping;
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10 changes: 5 additions & 5 deletions src/BedReader.h
View file
Expand Up @@ -38,7 +38,7 @@ class BedReader : public ifstream {

public:
vector<BedTarget> targets;
map<string, IntervalTree<BedTarget*> > intervals; // intervals by reference sequence
map<string, IntervalTree<int, BedTarget*> > intervals; // intervals by reference sequence

vector<BedTarget> entries(void);

Expand All @@ -60,12 +60,12 @@ class BedReader : public ifstream {
}

void buildIntervals(void) {
map<string, vector<Interval<BedTarget*> > > intervalsBySeq;
map<string, IntervalTree<int, BedTarget*>::interval_vector> intervalsBySeq;
for (vector<BedTarget>::iterator t = targets.begin(); t != targets.end(); ++t) {
intervalsBySeq[t->seq].push_back(Interval<BedTarget*>(t->left, t->right, &*t));
intervalsBySeq[t->seq].push_back(Interval<int, BedTarget*>(t->left, t->right, &*t));
}
for (map<string, vector<Interval<BedTarget*> > >::iterator s = intervalsBySeq.begin(); s != intervalsBySeq.end(); ++s) {
intervals[s->first] = IntervalTree<BedTarget*>(s->second);
for (map<string, IntervalTree<int, BedTarget*>::interval_vector>::const_iterator s = intervalsBySeq.begin(); s != intervalsBySeq.end(); ++s) {
intervals[s->first] = IntervalTree<int, BedTarget*>((IntervalTree<int, BedTarget*>::interval_vector&&)s->second);
}
}

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4 changes: 2 additions & 2 deletions src/Fasta.cpp
View file
Expand Up @@ -262,7 +262,7 @@ string FastaReference::getRawSequence(string seqname) {
int seqlen = newlines_in_sequence + entry.length;
char* seq = (char*) calloc (seqlen + 1, sizeof(char));
fseek64(file, entry.offset, SEEK_SET);
fread(seq, sizeof(char), seqlen, file);
size_t x = fread(seq, sizeof(char), seqlen, file);
seq[seqlen] = '\0';
char* pbegin = seq;
char* pend = seq + (seqlen/sizeof(char));
Expand Down Expand Up @@ -305,7 +305,7 @@ string FastaReference::getRawSubSequence(string seqname, int start, int length)
int seqlen = length + newlines_inside;
char* seq = (char*) calloc (seqlen + 1, sizeof(char));
fseek64(file, (off_t) (entry.offset + newlines_before + start), SEEK_SET);
fread(seq, sizeof(char), (off_t) seqlen, file);
size_t x = fread(seq, sizeof(char), (off_t) seqlen, file);
seq[seqlen] = '\0';
char* pbegin = seq;
char* pend = seq + (seqlen/sizeof(char));
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15 changes: 8 additions & 7 deletions src/Makefile
View file
Expand Up @@ -6,7 +6,7 @@

# Compiler

CXXFLAGS=-O3 -D_FILE_OFFSET_BITS=64 -g -ggdb
CXXFLAGS=-O3 -D_FILE_OFFSET_BITS=64 -g -ggdb -std=c++11
CXX=g++ ${CXXFLAGS}
C=gcc

Expand All @@ -27,7 +27,7 @@ TABIX_ROOT=$(VCFLIB_ROOT)/tabixpp
HTSLIB_ROOT=$(SEQLIB_ROOT)/htslib

LIBS = -lz -llzma -lbz2 -lm -lpthread
INCLUDE = -I../src -I../ttmath -I$(VCFLIB_ROOT)/src/ -I$(VCFLIB_ROOT)/smithwaterman/ -I$(VCFLIB_ROOT)/multichoose/ -I$(VCFLIB_ROOT)/filevercmp/ -I$(VCFLIB_ROOT)/fastahack/ -I$(HTSLIB_ROOT) -I$(SEQLIB_ROOT)
INCLUDE = -I../src -I../ttmath -I$(VCFLIB_ROOT)/src/ -I$(VCFLIB_ROOT)/smithwaterman/ -I$(VCFLIB_ROOT)/multichoose/ -I$(VCFLIB_ROOT)/filevercmp/ -I$(VCFLIB_ROOT)/fastahack/ -I$(HTSLIB_ROOT) -I$(SEQLIB_ROOT) -I$(TABIX_ROOT)
#INCLUDE = -I../ttmath -I$(BAMTOOLS_ROOT)/src/ -I$(VCFLIB_ROOT)/src/ -I$(TABIX_ROOT)/ -I$(VCFLIB_ROOT)/smithwaterman/ -I$(VCFLIB_ROOT)/multichoose/ -I$(VCFLIB_ROOT)/filevercmp/ -I$(VCFLIB_ROOT)/fastahack/ -I$(HTSLIB_ROOT) -I$(SEQLIB_ROOT) -I$(SEQLIB_ROOT)/htslib

all: autoversion ../bin/freebayes ../bin/bamleftalign
Expand Down Expand Up @@ -82,7 +82,7 @@ OBJECTS=BedReader.o \
../vcflib/smithwaterman/LeftAlign.o \
../vcflib/smithwaterman/Repeats.o \
../vcflib/smithwaterman/IndelAllele.o \
Variant.o \
$(VCFLIB_ROOT)/lib/libvcflib.a \
$(SEQLIB_ROOT)/src/libseqlib.a \
$(SEQLIB_ROOT)/bwa/libbwa.a \
$(SEQLIB_ROOT)/fermi-lite/libfml.a \
Expand All @@ -92,7 +92,7 @@ HEADERS=multichoose.h version_git.h

# executables

freebayes ../bin/freebayes: freebayes.o $(OBJECTS) $(HEADERS) $(seqlib)
freebayes ../bin/freebayes: freebayes.o $(OBJECTS) $(HEADERS) $(SEQLIB_ROOT)/src/libseqlib.a $(HTSLIB_ROOT)/libhts.a
$(CXX) $(CXXFLAGS) $(INCLUDE) freebayes.o $(OBJECTS) -o ../bin/freebayes $(LIBS)

alleles ../bin/alleles: alleles.o $(OBJECTS) $(HEADERS) $(seqlib)
Expand Down Expand Up @@ -194,12 +194,13 @@ LeftAlign.o: LeftAlign.h LeftAlign.cpp $(HTSLIB_ROOT)/libhts.a
IndelAllele.o: IndelAllele.cpp IndelAllele.h
$(CXX) $(CXXFLAGS) $(INCLUDE) -c IndelAllele.cpp

Variant.o: $(VCFLIB_ROOT)/src/Variant.h $(VCFLIB_ROOT)/src/Variant.cpp
$(CXX) $(CXXFLAGS) $(INCLUDE) -c $(VCFLIB_ROOT)/src/Variant.cpp
$(VCFLIB_ROOT)/lib/libvcflib.a: $(VCFLIB_ROOT)/src/*.h $(VCFLIB_ROOT)/src/*.cpp
cd $(VCFLIB_ROOT) && $(MAKE) libvcflib.a
# $(CXX) $(CXXFLAGS) $(INCLUDE) -c $(VCFLIB_ROOT)/src/Variant.cpp
# $(CXX) -std=c++11 $(CFLAGS) $(INCLUDE) -c $(VCFLIB_ROOT)/src/Variant.cpp

../vcflib/tabixpp/tabix.o:
cd $(TABIX_ROOT)/ && $(MAKE) && cp tabix.hpp ../../src/
cd $(TABIX_ROOT)/ && $(MAKE)

../vcflib/smithwaterman/SmithWatermanGotoh.o: ../vcflib/smithwaterman/SmithWatermanGotoh.h ../vcflib/smithwaterman/SmithWatermanGotoh.cpp
cd ../vcflib/smithwaterman && $(MAKE)
Expand Down
2 changes: 1 addition & 1 deletion vcflib
Submodule vcflib updated 53 files
+3 −0 .gitmodules
+11 −6 .travis.yml
+50 −31 Makefile
+136 −127 README.md
+1 −1 filevercmp
+1 −1 intervaltree
+1 −0 libVCFH
+1 −1 multichoose
+6 −0 samples/empty.vcf
+2 −2 scripts/vcf2bed.py
+12 −12 scripts/vcf2sqlite.py
+3 −4 scripts/vcfclearid
+3 −4 scripts/vcfclearinfo
+4 −4 scripts/vcffirstheader
+4 −4 scripts/vcfnulldotslashdot
+13 −15 src/BedReader.h
+597 −17 src/Variant.cpp
+91 −19 src/Variant.h
+1 −1 src/abba-baba.cpp
+1 −1 src/cdflib.cpp
+1 −1 src/genotypeSummary.cpp
+2 −2 src/gl-XPEHH.cpp
+3 −3 src/hapLrt.cpp
+10 −6 src/join.h
+2 −2 src/permuteGPAT++.cpp
+2 −2 src/permuteGPATsmoother.cpp
+1 −1 src/permuteRegions.cpp
+1 −1 src/permuteSmooth.cpp
+1 −1 src/plotHaps.cpp
+64 −62 src/segmentFst.cpp
+7 −1 src/smoother.cpp
+1 −1 src/split.h
+203 −158 src/ssw.cpp
+111 −48 src/ssw.hpp
+182 −107 src/ssw_cpp.cpp
+38 −31 src/ssw_cpp.hpp
+26 −7 src/vcf2fasta.cpp
+97 −128 src/vcf2tsv.cpp
+23 −6 src/vcfannotategenotypes.cpp
+13 −6 src/vcfdistance.cpp
+37 −37 src/vcffilter.cpp
+4 −2 src/vcffixup.cpp
+10 −1 src/vcfgeno2haplo.cpp
+10 −9 src/vcfgenotypes.cpp
+13 −17 src/vcfintersect.cpp
+2 −2 src/vcfld.cpp
+105 −0 src/vcfnormalizesvs.cpp
+11 −12 src/vcfroc.cpp
+1,682 −0 src/vec128int.h
+380 −0 src/veclib_types.h
+1 −1 tabixpp
+1 −1 test/Makefile
+ − test/tests/main

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