diff --git a/Makefile b/Makefile
index 211eff54775984fc7f6eaa90765b163b83f081c6..4b1f5242e9b4cb6ac7769973c926bce3eca72513 100644
--- a/Makefile
+++ b/Makefile
@@ -16,11 +16,11 @@ export BIN_DIR = bin
export SRC_DIR = src
export UTIL_DIR = src/utils
export CXX = g++
-ifeq ($(DEBUG),1)
-export CXXFLAGS = -Wall -O0 -g -fno-inline -fkeep-inline-functions -D_FILE_OFFSET_BITS=64 -fPIC -DDEBUG -D_DEBUG
-else
+#ifeq ($(DEBUG),1)
+#export CXXFLAGS = -Wall -O0 -g -fno-inline -fkeep-inline-functions -D_FILE_OFFSET_BITS=64 -fPIC -DDEBUG -D_DEBUG
+#else
export CXXFLAGS = -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC
-endif
+#endif
export LIBS = -lz
export BT_ROOT = src/utils/BamTools/
@@ -42,7 +42,7 @@ SUBDIRS = $(SRC_DIR)/annotateBed \
$(SRC_DIR)/genomeCoverageBed \
$(SRC_DIR)/getOverlap \
$(SRC_DIR)/groupBy \
- $(SRC_DIR)/intersectBed \
+ $(SRC_DIR)/intersectFile \
$(SRC_DIR)/jaccard \
$(SRC_DIR)/linksBed \
$(SRC_DIR)/maskFastaFromBed \
@@ -50,10 +50,12 @@ SUBDIRS = $(SRC_DIR)/annotateBed \
$(SRC_DIR)/mergeBed \
$(SRC_DIR)/multiBamCov \
$(SRC_DIR)/multiIntersectBed \
+ $(SRC_DIR)/nekSandbox1 \
$(SRC_DIR)/nucBed \
$(SRC_DIR)/pairToBed \
$(SRC_DIR)/pairToPair \
$(SRC_DIR)/randomBed \
+ $(SRC_DIR)/regressTest \
$(SRC_DIR)/reldist \
$(SRC_DIR)/shuffleBed \
$(SRC_DIR)/slopBed \
@@ -65,12 +67,17 @@ SUBDIRS = $(SRC_DIR)/annotateBed \
$(SRC_DIR)/windowMaker
UTIL_SUBDIRS = $(SRC_DIR)/utils/bedFile \
+ $(SRC_DIR)/utils/BinTree \
$(SRC_DIR)/utils/version \
$(SRC_DIR)/utils/bedGraphFile \
$(SRC_DIR)/utils/chromsweep \
+ $(SRC_DIR)/utils/Contexts \
+ $(SRC_DIR)/utils/FileRecordTools \
+ $(SRC_DIR)/utils/general \
$(SRC_DIR)/utils/gzstream \
$(SRC_DIR)/utils/fileType \
$(SRC_DIR)/utils/bedFilePE \
+ $(SRC_DIR)/utils/NewChromsweep \
$(SRC_DIR)/utils/sequenceUtilities \
$(SRC_DIR)/utils/tabFile \
$(SRC_DIR)/utils/BamTools \
@@ -78,7 +85,7 @@ UTIL_SUBDIRS = $(SRC_DIR)/utils/bedFile \
$(SRC_DIR)/utils/BlockedIntervals \
$(SRC_DIR)/utils/Fasta \
$(SRC_DIR)/utils/VectorOps \
- $(SRC_DIR)/utils/genomeFile
+ $(SRC_DIR)/utils/GenomeFile
BUILT_OBJECTS = $(OBJ_DIR)/*.o
diff --git a/src/bedToBam/Makefile b/src/bedToBam/Makefile
index e527b3199e65d65b127244b18a8a843d9cee8ada..01a548a66679eac647868c3c4030498ddc529a87 100644
--- a/src/bedToBam/Makefile
+++ b/src/bedToBam/Makefile
@@ -8,7 +8,7 @@ BIN_DIR = ../../bin/
INCLUDES = -I$(UTILITIES_DIR)/bedFile/ \
-I$(UTILITIES_DIR)/version/ \
-I$(UTILITIES_DIR)/gzstream/ \
- -I$(UTILITIES_DIR)/genomeFile/ \
+ -I$(UTILITIES_DIR)/GenomeFile/ \
-I$(UTILITIES_DIR)/lineFileUtilities/ \
-I$(UTILITIES_DIR)/fileType/ \
-I$(UTILITIES_DIR)/BamTools/include \
diff --git a/src/bedToBam/bedToBam.cpp b/src/bedToBam/bedToBam.cpp
index 6de2708f7e58d7dde8f0efddcd0025a494d74b69..f7261286ffe8fa58a5e4bcb82dcd14d1b7baae05 100644
--- a/src/bedToBam/bedToBam.cpp
+++ b/src/bedToBam/bedToBam.cpp
@@ -11,7 +11,7 @@
******************************************************************************/
#include "lineFileUtilities.h"
#include "bedFile.h"
-#include "genomeFile.h"
+#include "GenomeFile.h"
#include "version.h"
diff --git a/src/bedToIgv/Makefile b/src/bedToIgv/Makefile
index b6c8a689b7f51fb219b4192cc0bc5a68303ee5f1..bdd1969b4eb4914d7b0aeac5e0d9a67a821d402c 100644
--- a/src/bedToIgv/Makefile
+++ b/src/bedToIgv/Makefile
@@ -6,7 +6,7 @@ BIN_DIR = ../../bin/
# define our includes
# -------------------
INCLUDES = -I$(UTILITIES_DIR)/bedFile/ \
- -I$(UTILITIES_DIR)/genomeFile/ \
+ -I$(UTILITIES_DIR)/GenomeFile/ \
-I$(UTILITIES_DIR)/lineFileUtilities/ \
-I$(UTILITIES_DIR)/gzstream/ \
-I$(UTILITIES_DIR)/fileType/ \
diff --git a/src/bedToIgv/bedToIgv.cpp b/src/bedToIgv/bedToIgv.cpp
index 41ace10bd53de0371fe381e6be98a73c2658e2e4..26b33d6e30e8ed06d7a6f2776fef058bc191f914 100644
--- a/src/bedToIgv/bedToIgv.cpp
+++ b/src/bedToIgv/bedToIgv.cpp
@@ -11,7 +11,7 @@
******************************************************************************/
#include "lineFileUtilities.h"
#include "bedFile.h"
-#include "genomeFile.h"
+#include "GenomeFile.h"
#include "version.h"
#include <vector>
diff --git a/src/bedpeToBam/Makefile b/src/bedpeToBam/Makefile
index 9df3c21fb0e9954f0fdfbf60359611258969d488..625234fc69328ecc278ca9acfdf22c9b3fbaf6ae 100644
--- a/src/bedpeToBam/Makefile
+++ b/src/bedpeToBam/Makefile
@@ -9,7 +9,7 @@ INCLUDES = -I$(UTILITIES_DIR)/bedFile/ \
-I$(UTILITIES_DIR)/bedFilePE/ \
-I$(UTILITIES_DIR)/version/ \
-I$(UTILITIES_DIR)/gzstream/ \
- -I$(UTILITIES_DIR)/genomeFile/ \
+ -I$(UTILITIES_DIR)/GenomeFile/ \
-I$(UTILITIES_DIR)/lineFileUtilities/ \
-I$(UTILITIES_DIR)/fileType/ \
-I$(UTILITIES_DIR)/BamTools/include \
diff --git a/src/bedpeToBam/bedpeToBam.cpp b/src/bedpeToBam/bedpeToBam.cpp
index 0e6ef2e4e1419e8998f10e650ecfc0b8de18047a..9a31081b83c418f022029b2812502574466ee1fa 100644
--- a/src/bedpeToBam/bedpeToBam.cpp
+++ b/src/bedpeToBam/bedpeToBam.cpp
@@ -11,7 +11,7 @@
******************************************************************************/
#include "lineFileUtilities.h"
#include "bedFilePE.h"
-#include "genomeFile.h"
+#include "GenomeFile.h"
#include "version.h"
diff --git a/src/bedtools.cpp b/src/bedtools.cpp
index 11ff3a6296074279dbebadd59aef1ed1af611255..c0e98d3c155150b34bd878a5d4e2cca4f58aa312 100644
--- a/src/bedtools.cpp
+++ b/src/bedtools.cpp
@@ -45,6 +45,7 @@ int closest_main(int argc, char* argv[]); //
int cluster_main(int argc, char* argv[]); //
int complement_main(int argc, char* argv[]);//
int coverage_main(int argc, char* argv[]); //
+int regress_test_main(int argc, char **argv); //
int expand_main(int argc, char* argv[]);//
int fastafrombed_main(int argc, char* argv[]);//
int flank_main(int argc, char* argv[]); //
@@ -59,6 +60,7 @@ int map_main(int argc, char* argv[]); //
int merge_main(int argc, char* argv[]); //
int multibamcov_main(int argc, char* argv[]);//
int multiintersect_main(int argc, char* argv[]);//
+int nek_sandbox1_main(int argc, char* argv[]);//
int nuc_main(int argc, char* argv[]);//
int pairtobed_main(int argc, char* argv[]);//
int pairtopair_main(int argc, char* argv[]);//
@@ -136,9 +138,8 @@ int main(int argc, char *argv[])
else if (sub_cmd == "makewindows") return windowmaker_main(argc-1, argv+1);
else if (sub_cmd == "groupby") return groupby_main(argc-1, argv+1);
else if (sub_cmd == "expand") return expand_main(argc-1, argv+1);
-
-
-
+ else if (sub_cmd == "neksb1") return nek_sandbox1_main(argc-1, argv+1);
+ else if (sub_cmd == "regresstest") return regress_test_main(argc, argv); //this command does need all the orig args.
// help
else if (sub_cmd == "-h" || sub_cmd == "--help" ||
sub_cmd == "-help")
@@ -230,7 +231,7 @@ int bedtools_help(void)
cout << "[ BAM focused tools ]" << endl;
cout << " multicov " << "Counts coverage from multiple BAMs at specific intervals.\n";
cout << " tag " << "Tag BAM alignments based on overlaps with interval files.\n";
-
+
cout << endl;
cout << "[ Statistical relationships ]" << endl;
cout << " jaccard " << "Calculate the Jaccard statistic b/w two sets of intervals.\n";
diff --git a/src/complementBed/Makefile b/src/complementBed/Makefile
index 8b80c316002bb11494e821e8352354a8d933cadf..30f70b2c3b49f39ef38a6d232687ca5717ecb8bc 100644
--- a/src/complementBed/Makefile
+++ b/src/complementBed/Makefile
@@ -6,7 +6,7 @@ BIN_DIR = ../../bin/
# define our includes
# -------------------
INCLUDES = -I$(UTILITIES_DIR)/bedFile/ \
- -I$(UTILITIES_DIR)/genomeFile/ \
+ -I$(UTILITIES_DIR)/GenomeFile/ \
-I$(UTILITIES_DIR)/lineFileUtilities/ \
-I$(UTILITIES_DIR)/gzstream/ \
-I$(UTILITIES_DIR)/fileType/ \
diff --git a/src/complementBed/complementBed.h b/src/complementBed/complementBed.h
index 29a6f3345eb521615a3ee4b3f2aa1844b2ed04ab..a6603899222a221ad1fb1f4ab9a37cd2d67eccb5 100644
--- a/src/complementBed/complementBed.h
+++ b/src/complementBed/complementBed.h
@@ -10,7 +10,7 @@
Licenced under the GNU General Public License 2.0 license.
******************************************************************************/
#include "bedFile.h"
-#include "genomeFile.h"
+#include "GenomeFile.h"
#include <vector>
#include <bitset>
diff --git a/src/flankBed/Makefile b/src/flankBed/Makefile
index e8ef3e49f26ad9ad3c944007a0dfd8e8d53b5943..ad3f0a1838d7d63282f3c07b7c088839d1d35254 100644
--- a/src/flankBed/Makefile
+++ b/src/flankBed/Makefile
@@ -6,7 +6,7 @@ BIN_DIR = ../../bin/
# define our includes
# -------------------
INCLUDES = -I$(UTILITIES_DIR)/bedFile/ \
- -I$(UTILITIES_DIR)/genomeFile/ \
+ -I$(UTILITIES_DIR)/GenomeFile/ \
-I$(UTILITIES_DIR)/lineFileUtilities/ \
-I$(UTILITIES_DIR)/gzstream/ \
-I$(UTILITIES_DIR)/fileType/ \
diff --git a/src/flankBed/flankBed.h b/src/flankBed/flankBed.h
index f344f60f18686f84f796618a4ad1659a52430189..995d13a04dd67d1082f0b762a39d840cbd3db6d9 100644
--- a/src/flankBed/flankBed.h
+++ b/src/flankBed/flankBed.h
@@ -11,7 +11,7 @@
******************************************************************************/
#include "bedFile.h"
-#include "genomeFile.h"
+#include "GenomeFile.h"
#include <vector>
#include <iostream>
diff --git a/src/genomeCoverageBed/Makefile b/src/genomeCoverageBed/Makefile
index 8936fffc8d921254f1fa906a76a6507103ceb983..83e5563ef869ce7f0385de3cd5906db580442ebd 100644
--- a/src/genomeCoverageBed/Makefile
+++ b/src/genomeCoverageBed/Makefile
@@ -7,7 +7,7 @@ BIN_DIR = ../../bin/
# -------------------
INCLUDES = -I$(UTILITIES_DIR)/bedFile/ \
-I$(UTILITIES_DIR)/gzstream/ \
- -I$(UTILITIES_DIR)/genomeFile/ \
+ -I$(UTILITIES_DIR)/GenomeFile/ \
-I$(UTILITIES_DIR)/lineFileUtilities/ \
-I$(UTILITIES_DIR)/fileType/ \
-I$(UTILITIES_DIR)/BamTools/include \
diff --git a/src/genomeCoverageBed/genomeCoverageBed.h b/src/genomeCoverageBed/genomeCoverageBed.h
index f2a877fd097a0a86bdc381e687ebd86151ecda16..09df91c64deae3e925014542c404bbd5ea759023 100644
--- a/src/genomeCoverageBed/genomeCoverageBed.h
+++ b/src/genomeCoverageBed/genomeCoverageBed.h
@@ -10,7 +10,7 @@ aaronquinlan@gmail.com
Licenced under the GNU General Public License 2.0 license.
******************************************************************************/
#include "bedFile.h"
-#include "genomeFile.h"
+#include "GenomeFile.h"
#include "BlockedIntervals.h"
#include "api/BamReader.h"
diff --git a/src/intersectBed/Makefile b/src/intersectBed/Makefile
deleted file mode 100644
index 33fc0917468234c31d91530ead52684104abc4cf..0000000000000000000000000000000000000000
--- a/src/intersectBed/Makefile
+++ /dev/null
@@ -1,39 +0,0 @@
-UTILITIES_DIR = ../utils/
-OBJ_DIR = ../../obj/
-BIN_DIR = ../../bin/
-
-# -------------------
-# define our includes
-# -------------------
-INCLUDES = -I$(UTILITIES_DIR)/bedFile/ \
- -I$(UTILITIES_DIR)/gzstream/ \
- -I$(UTILITIES_DIR)/genomeFile/ \
- -I$(UTILITIES_DIR)/lineFileUtilities/ \
- -I$(UTILITIES_DIR)/fileType/ \
- -I$(UTILITIES_DIR)/BamTools/include \
- -I$(UTILITIES_DIR)/BlockedIntervals \
- -I$(UTILITIES_DIR)/BamTools-Ancillary \
- -I$(UTILITIES_DIR)/chromsweep \
- -I$(UTILITIES_DIR)/version/
-
-# ----------------------------------
-# define our source and object files
-# ----------------------------------
-SOURCES= intersectMain.cpp intersectBed.cpp intersectBed.h
-OBJECTS= intersectMain.o intersectBed.o
-BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
-PROGRAM= intersectBed
-
-all: $(BUILT_OBJECTS)
-
-.PHONY: all
-
-$(BUILT_OBJECTS): $(SOURCES)
- @echo " * compiling" $(*F).cpp
- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(DFLAGS) $(INCLUDES)
-
-clean:
- @echo "Cleaning up."
- @rm -f $(OBJ_DIR)/intersectMain.o $(OBJ_DIR)/intersectBed.o
-
-.PHONY: clean
diff --git a/src/intersectBed/intersectBed.cpp b/src/intersectBed/intersectBed.cpp
deleted file mode 100644
index 5d115abf9169c2b2c8021cb76d2fd2c3951eb339..0000000000000000000000000000000000000000
--- a/src/intersectBed/intersectBed.cpp
+++ /dev/null
@@ -1,401 +0,0 @@
-/*****************************************************************************
- intersectBed.cpp
-
- (c) 2009 - Aaron Quinlan
- Hall Laboratory
- Department of Biochemistry and Molecular Genetics
- University of Virginia
- aaronquinlan@gmail.com
-
- Licenced under the GNU General Public License 2.0 license.
-******************************************************************************/
-#include "lineFileUtilities.h"
-#include "intersectBed.h"
-
-/************************************
-Helper functions
-************************************/
-bool BedIntersect::processHits(const BED &a, const vector<BED> &hits) {
- bool hitsFound = false;
- if (_printable == true) {
- // -wao the user wants to force the reporting of 0 overlap
- if (hits.size() == 0) {
- if (_writeAllOverlap) {
- _bedA->reportBedTab(a);
- _bedB->reportNullBedTab();
- printf("0\n");
- }
- else if (_leftJoin) {
- _bedA->reportBedTab(a);
- _bedB->reportNullBedNewLine();
- }
- }
- else {
- vector<BED>::const_iterator h = hits.begin();
- vector<BED>::const_iterator hitsEnd = hits.end();
- for (; h != hitsEnd; ++h) {
- CHRPOS s = max(a.start, h->start);
- CHRPOS e = min(a.end, h->end);
- int overlapBases = (e - s);
- ReportOverlapDetail(overlapBases, a, *h, s, e);
- hitsFound = true;
- }
- }
- }
- else {
- ReportOverlapSummary(a, hits.size());
- }
- return hitsFound;
-}
-
-
-/*
- Constructor
-*/
-BedIntersect::BedIntersect(string bedAFile, string bedBFile,
- bool anyHit, bool writeA,
- bool writeB, bool writeOverlap,
- bool writeAllOverlap, float overlapFraction,
- bool noHit, bool leftJoin,
- bool writeCount, bool sameStrand,
- bool diffStrand, bool reciprocal,
- bool obeySplits, bool bamInput,
- bool bamOutput, bool isUncompressedBam,
- bool sortedInput, bool printHeader)
-{
- _bedAFile = bedAFile;
- _bedBFile = bedBFile;
- _anyHit = anyHit;
- _noHit = noHit;
- _leftJoin = leftJoin;
- _writeA = writeA;
- _writeB = writeB;
- _writeOverlap = writeOverlap;
- _writeAllOverlap = writeAllOverlap;
- _writeCount = writeCount;
- _overlapFraction = overlapFraction;
- _sameStrand = sameStrand;
- _diffStrand = diffStrand;
- _reciprocal = reciprocal;
- _obeySplits = obeySplits;
- _bamInput = bamInput;
- _bamOutput = bamOutput;
- _isUncompressedBam = isUncompressedBam;
- _sortedInput = sortedInput;
- _printHeader = printHeader;
-
- // should we print each overlap, or does the user want summary information?
- _printable = true;
- if (_anyHit || _noHit || _writeCount)
- _printable = false;
-
- if (_bamInput == false)
- IntersectBed();
- else
- IntersectBam(bedAFile);
-}
-
-
-/*
- Destructor
-*/
-BedIntersect::~BedIntersect(void) {
-}
-
-
-bool BedIntersect::FindOverlaps(const BED &a, vector<BED> &hits) {
- bool hitsFound = false;
-
- // collect and report the sufficient hits
- _bedB->allHits(a.chrom, a.start, a.end, a.strand,
- hits, _sameStrand, _diffStrand,
- _overlapFraction, _reciprocal);
- hitsFound = processHits(a, hits);
- return hitsFound;
-}
-
-
-bool BedIntersect::FindBlockedOverlaps(const BED &a,
- const vector<BED> &a_blocks,
- const vector<BED> &hits,
- bool a_is_bam)
-{
- int a_footprint = GetTotalBlockLength(a_blocks);
- // container to store the set of raw hits
- // that actually overlap the A blocks
- bedVector valid_hits;
- valid_hits.reserve(hits.size());
-
- // 1. Loop through each raw hit (outer loop)
- // 2. Break the raw hit into it;s blocks
- // and see of one of the hit blocks (inner loop)
- // overlaps one of a's blocks (inner, inner loop)
- // 3. If so, mark the hit as valid and add it to the valid_set.
- // Otherwise, the hit only overlapped the span of a and not
- // the individual blocks. Thus, it doesn't count.
- bedVector::const_iterator hItr = hits.begin();
- bedVector::const_iterator hEnd = hits.end();
- for (; hItr != hEnd; ++hItr) {
- // break the hit into blocks
- bedVector hitBlocks;
- GetBedBlocks(*hItr, hitBlocks);
- int b_footprint = GetTotalBlockLength(hitBlocks);
- // test to see if there is a valid hit with one of the blocks
- bool valid_hit = false;
- int total_overlap = 0;
- bedVector::const_iterator hbItr = hitBlocks.begin();
- bedVector::const_iterator hbEnd = hitBlocks.end();
- for (; hbItr != hbEnd; ++hbItr) {
- // look for overlaps between this hit/block and each block in a
- bedVector::const_iterator a_blockItr = a_blocks.begin();
- bedVector::const_iterator a_blockEnd = a_blocks.end();
- for (; a_blockItr != a_blockEnd; ++a_blockItr) {
- int hs = max(a_blockItr->start, hbItr->start);
- int he = min(a_blockItr->end, hbItr->end);
- int overlap = he - hs;
- if (overlap > 0) {
- valid_hit = true;
- total_overlap += overlap;
- }
- }
- }
- if (valid_hit) {
- // require sufficient overlap fraction (reciprocal or otherwise)
- // w.r.t to the "footprint" (i.e., the total length of each block)
- if ( ((float) total_overlap
- /
- (float) a_footprint) > _overlapFraction)
- {
- if (_reciprocal && ((float) total_overlap /
- (float) b_footprint) > _overlapFraction)
- {
- valid_hits.push_back(*hItr);
- }
- else if (!_reciprocal) {
- valid_hits.push_back(*hItr);
- }
- }
- }
- }
- if (!a_is_bam) {
- return processHits(a, valid_hits);
- }
- else
- return !valid_hits.empty();
-}
-
-
-void BedIntersect::ReportOverlapDetail(int overlapBases, const BED &a,
- const BED &b, CHRPOS s, CHRPOS e)
-{
- // default. simple intersection only
- if (_writeA == false && _writeB == false &&
- _writeOverlap == false && _leftJoin == false)
- {
- _bedA->reportBedRangeNewLine(a,s,e);
- }
- // -wa -wb write the original A and B
- else if ((_writeA == true && _writeB == true) || _leftJoin == true) {
- _bedA->reportBedTab(a);
- _bedB->reportBedNewLine(b);
- }
- // -wa write just the original A
- else if (_writeA == true) {
- _bedA->reportBedNewLine(a);
- }
- // -wb write the intersected portion of A and the original B
- else if (_writeB == true) {
- _bedA->reportBedRangeTab(a,s,e);
- _bedB->reportBedNewLine(b);
- }
- // -wo write the original A and B plus the no. of overlapping bases.
- else if (_writeOverlap == true) {
- _bedA->reportBedTab(a);
- _bedB->reportBedTab(b);
- if (b.zeroLength == false) printf("%d\n", overlapBases);
- else printf("0\n");
- }
-}
-
-
-void BedIntersect::ReportOverlapSummary(const BED &a, const int &numOverlapsFound) {
- // -u just report the fact that there was >= 1 overlaps
- if (_anyHit && (numOverlapsFound >= 1)) {
- _bedA->reportBedNewLine(a);
- }
- // -c report the total number of features overlapped in B
- else if (_writeCount) {
- _bedA->reportBedTab(a);
- printf("%d\n", numOverlapsFound);
- }
- // -v report iff there were no overlaps
- else if (_noHit && (numOverlapsFound == 0)) {
- _bedA->reportBedNewLine(a);
- }
-}
-
-
-void BedIntersect::IntersectBed() {
-
- // create new BED file objects for A and B
- _bedA = new BedFile(_bedAFile);
- _bedB = new BedFile(_bedBFile);
-
- if (_sortedInput == false) {
- // load the "B" file into a map in order to
- // compare each entry in A to it in search of overlaps.
- _bedB->loadBedFileIntoMap();
-
- vector<BED> hits;
- hits.reserve(100);
- BED a;
-
- // open the "A" file, process each BED entry and searh for overlaps.
- _bedA->Open();
- // report A's header first if asked.
- if (_printHeader == true) {
- _bedA->PrintHeader();
- }
- while (_bedA->GetNextBed(a)) {
- if (_bedA->_status == BED_VALID) {
- // treat the BED as a single "block"
- if (_obeySplits == false)
- FindOverlaps(a, hits);
- // split the BED12 into blocks and look for
- // overlaps in each discrete block
- else {
- // find the hits that overlap with the
- // full span of the blocked BED
- _bedB->allHits(a.chrom, a.start, a.end, a.strand,
- hits, _sameStrand, _diffStrand,
- 0.0, false);
- // break a into discrete blocks, as we need to
- // measure overlap with the individual blocks,
- // not the full span.
- bedVector a_blocks;
- GetBedBlocks(a, a_blocks);
- // find the overlaps between the block in A and B
- // last parm is false as a is not a BAM entry
- FindBlockedOverlaps(a, a_blocks, hits, false);
- }
- hits.clear();
- }
- }
- _bedA->Close();
- }
- else {
- // use the chromsweep algorithm to detect overlaps on the fly.
- ChromSweep sweep = ChromSweep(_bedA, _bedB,
- _sameStrand, _diffStrand,
- _overlapFraction, _reciprocal,
- false, _printHeader);
-
- pair<BED, vector<BED> > hit_set;
- hit_set.second.reserve(10000);
- while (sweep.Next(hit_set)) {
- if (_obeySplits == false) {
- processHits(hit_set.first, hit_set.second);
- }
- else {
- bedVector a_blocks;
- GetBedBlocks(hit_set.first, a_blocks);
- FindBlockedOverlaps(hit_set.first, a_blocks,
- hit_set.second, false);
- }
- }
- }
-}
-
-
-void BedIntersect::IntersectBam(string bamFile) {
-
- // load the "B" bed file into a map so
- // that we can easily compare "A" to it for overlaps
- _bedB = new BedFile(_bedBFile);
- _bedB->loadBedFileIntoMap();
-
- // create a dummy BED A file for printing purposes if not
- // using BAM output.
- if (_bamOutput == false) {
- _bedA = new BedFile(_bedAFile);
- _bedA->bedType = 12;
- }
- // open the BAM file
- BamReader reader;
- BamWriter writer;
- if (!reader.Open(bamFile)) {
- cerr << "Failed to open BAM file " << bamFile << endl;
- exit(1);
- }
-
- // get header & reference information
- string bamHeader = reader.GetHeaderText();
- RefVector refs = reader.GetReferenceData();
- // open a BAM output to stdout if we are writing BAM
- if (_bamOutput == true) {
- // set compression mode
- BamWriter::CompressionMode compressionMode = BamWriter::Compressed;
- if ( _isUncompressedBam ) compressionMode = BamWriter::Uncompressed;
- writer.SetCompressionMode(compressionMode);
- // open our BAM writer
- writer.Open("stdout", bamHeader, refs);
- }
- vector<BED> hits;
- // reserve some space
- hits.reserve(100);
- BamAlignment bam;
- // get each set of alignments for each pair.
- while (reader.GetNextAlignment(bam)) {
-
- // save an unaligned read if -v
- if (!bam.IsMapped()) {
- if ((_noHit == true) && (_bamOutput == true))
- writer.SaveAlignment(bam);
- continue;
- }
- // break alignment into discrete blocks,
- bedVector bed_blocks;
- string chrom = refs.at(bam.RefID).RefName;
- GetBamBlocks(bam, chrom, bed_blocks, false, true);
- // create a basic BED entry from the BAM alignment
- BED bed;
- MakeBedFromBam(bam, chrom, bed_blocks, bed);
- bool overlapsFound = false;
- if ((_bamOutput == true) && (_obeySplits == false))
- {
- overlapsFound = _bedB->anyHits(bed.chrom, bed.start, bed.end,
- bed.strand, _sameStrand, _diffStrand,
- _overlapFraction, _reciprocal);
- }
- else if ( ((_bamOutput == true) && (_obeySplits == true)) ||
- ((_bamOutput == false) && (_obeySplits == true)) )
- {
- // find the hits that overlap with the full span of the blocked BED
- _bedB->allHits(bed.chrom, bed.start, bed.end, bed.strand,
- hits, _sameStrand, _diffStrand,
- _overlapFraction, _reciprocal);
- // find the overlaps between the block in A and B
- overlapsFound =
- FindBlockedOverlaps(bed, bed_blocks, hits, _bamOutput);
- }
- else if ((_bamOutput == false) && (_obeySplits == false))
- {
- FindOverlaps(bed, hits);
- }
- // save the BAM alignment if overlap reqs. were met
- if (_bamOutput == true) {
- if ((overlapsFound == true) && (_noHit == false))
- writer.SaveAlignment(bam);
- else if ((overlapsFound == false) && (_noHit == true))
- writer.SaveAlignment(bam);
- }
- hits.clear();
- }
-
- // close the relevant BAM files.
- reader.Close();
- if (_bamOutput == true) {
- writer.Close();
- }
-}
-
diff --git a/src/intersectBed/intersectBed.h b/src/intersectBed/intersectBed.h
deleted file mode 100644
index 5a10a81db0d276cda62613114934368bad04eb27..0000000000000000000000000000000000000000
--- a/src/intersectBed/intersectBed.h
+++ /dev/null
@@ -1,102 +0,0 @@
-/*****************************************************************************
- intersectBed.h
-
- (c) 2009 - Aaron Quinlan
- Hall Laboratory
- Department of Biochemistry and Molecular Genetics
- University of Virginia
- aaronquinlan@gmail.com
-
- Licenced under the GNU General Public License 2.0 license.
-******************************************************************************/
-#ifndef INTERSECTBED_H
-#define INTERSECTBED_H
-
-#include "bedFile.h"
-#include "chromsweep.h"
-#include "api/BamReader.h"
-#include "api/BamWriter.h"
-#include "api/BamAux.h"
-#include "BlockedIntervals.h"
-#include "BamAncillary.h"
-using namespace BamTools;
-
-
-#include <vector>
-#include <iostream>
-#include <fstream>
-#include <stdlib.h>
-using namespace std;
-
-
-
-class BedIntersect {
-
-public:
-
- // constructor
- BedIntersect(string bedAFile, string bedBFile, bool anyHit,
- bool writeA, bool writeB, bool writeOverlap, bool writeAllOverlap,
- float overlapFraction, bool noHit, bool leftJoin, bool writeCount, bool sameStrand, bool diffStrand,
- bool reciprocal, bool obeySplits, bool bamInput, bool bamOutput, bool isUncompressedBam,
- bool sortedInput, bool printHeader);
-
- // destructor
- ~BedIntersect(void);
-
-private:
-
- //------------------------------------------------
- // private attributes
- //------------------------------------------------
- string _bedAFile;
- string _bedBFile;
-
- bool _writeA; // should the original A feature be reported?
- bool _writeB; // should the original B feature be reported?
- bool _writeOverlap;
- bool _writeAllOverlap;
-
- bool _sameStrand;
- bool _diffStrand;
- bool _reciprocal;
- float _overlapFraction;
-
- bool _anyHit;
- bool _noHit;
- bool _leftJoin;
- bool _writeCount; // do we want a count of the number of overlaps in B?
- bool _obeySplits;
- bool _bamInput;
- bool _bamOutput;
- bool _isUncompressedBam;
- bool _sortedInput;
- bool _printable;
- bool _printHeader;
-
- // instance of a bed file class.
- BedFile *_bedA, *_bedB;
-
- //------------------------------------------------
- // private methods
- //------------------------------------------------
- void IntersectBed(istream &bedInput);
-
- void IntersectBed();
-
- void IntersectBam(string bamFile);
-
- bool processHits(const BED &a, const vector<BED> &hits);
-
- bool FindOverlaps(const BED &a, vector<BED> &hits);
-
- bool FindBlockedOverlaps(const BED &a, const vector<BED> &a_blocks,
- const vector<BED> &hits, bool a_is_bam);
-
- void ReportOverlapDetail(int overlapBases, const BED &a, const BED &b, CHRPOS s, CHRPOS e);
-
- void ReportOverlapSummary(const BED &a, const int &numOverlapsFound);
-
-};
-
-#endif /* INTERSECTBED_H */
diff --git a/src/intersectBed/intersectMain.cpp b/src/intersectBed/intersectMain.cpp
deleted file mode 100644
index be3991a4daee23db5729cb96b520206301773fe4..0000000000000000000000000000000000000000
--- a/src/intersectBed/intersectMain.cpp
+++ /dev/null
@@ -1,327 +0,0 @@
-/*****************************************************************************
- intersectMain.cpp
-
- (c) 2009 - Aaron Quinlan
- Hall Laboratory
- Department of Biochemistry and Molecular Genetics
- University of Virginia
- aaronquinlan@gmail.com
-
- Licenced under the GNU General Public License 2.0 license.
-******************************************************************************/
-#include "intersectBed.h"
-#include "version.h"
-
-using namespace std;
-
-// define our program name
-#define PROGRAM_NAME "bedtools intersect"
-
-
-// define our parameter checking macro
-#define PARAMETER_CHECK(param, paramLen, actualLen) (strncmp(argv[i], param, min(actualLen, paramLen))== 0) && (actualLen == paramLen)
-
-// function declarations
-void intersect_help(void);
-
-int intersect_main(int argc, char* argv[]) {
-
- // our configuration variables
- bool showHelp = false;
-
- // input files
- string bedAFile;
- string bedBFile;
-
- // input arguments
- float overlapFraction = 1E-9;
-
- bool haveBedA = false;
- bool haveBedB = false;
- bool noHit = false;
- bool leftJoin = false;
- bool anyHit = false;
- bool writeA = false;
- bool writeB = false;
- bool writeCount = false;
- bool writeOverlap = false;
- bool writeAllOverlap = false;
- bool haveFraction = false;
- bool reciprocalFraction = false;
- bool sameStrand = false;
- bool diffStrand = false;
- bool obeySplits = false;
- bool inputIsBam = false;
- bool outputIsBam = true;
- bool uncompressedBam = false;
- bool sortedInput = false;
- bool printHeader = false;
-
- // check to see if we should print out some help
- if(argc <= 1) showHelp = true;
-
- for(int i = 1; i < argc; i++) {
- int parameterLength = (int)strlen(argv[i]);
-
- if((PARAMETER_CHECK("-h", 2, parameterLength)) ||
- (PARAMETER_CHECK("--help", 5, parameterLength))) {
- showHelp = true;
- }
- }
-
- if(showHelp) intersect_help();
-
- // do some parsing (all of these parameters require 2 strings)
- for(int i = 1; i < argc; i++) {
-
- int parameterLength = (int)strlen(argv[i]);
-
- if(PARAMETER_CHECK("-a", 2, parameterLength)) {
- if ((i+1) < argc) {
- haveBedA = true;
- outputIsBam = false;
- bedAFile = argv[i + 1];
- i++;
- }
- }
- else if(PARAMETER_CHECK("-abam", 5, parameterLength)) {
- if ((i+1) < argc) {
- haveBedA = true;
- inputIsBam = true;
- bedAFile = argv[i + 1];
- i++;
- }
- }
- else if(PARAMETER_CHECK("-b", 2, parameterLength)) {
- if ((i+1) < argc) {
- haveBedB = true;
- bedBFile = argv[i + 1];
- i++;
- }
- }
- else if(PARAMETER_CHECK("-bed", 4, parameterLength)) {
- outputIsBam = false;
- }
- else if(PARAMETER_CHECK("-u", 2, parameterLength)) {
- anyHit = true;
- }
- else if(PARAMETER_CHECK("-f", 2, parameterLength)) {
- if ((i+1) < argc) {
- haveFraction = true;
- overlapFraction = atof(argv[i + 1]);
- i++;
- }
- }
- else if(PARAMETER_CHECK("-wa", 3, parameterLength)) {
- writeA = true;
- }
- else if(PARAMETER_CHECK("-wb", 3, parameterLength)) {
- writeB = true;
- }
- else if(PARAMETER_CHECK("-wo", 3, parameterLength)) {
- writeOverlap = true;
- }
- else if(PARAMETER_CHECK("-wao", 4, parameterLength)) {
- writeAllOverlap = true;
- writeOverlap = true;
- }
- else if(PARAMETER_CHECK("-c", 2, parameterLength)) {
- writeCount = true;
- }
- else if(PARAMETER_CHECK("-r", 2, parameterLength)) {
- reciprocalFraction = true;
- }
- else if (PARAMETER_CHECK("-v", 2, parameterLength)) {
- noHit = true;
- }
- else if (PARAMETER_CHECK("-s", 2, parameterLength)) {
- sameStrand = true;
- }
- else if (PARAMETER_CHECK("-S", 2, parameterLength)) {
- diffStrand = true;
- }
- else if (PARAMETER_CHECK("-split", 6, parameterLength)) {
- obeySplits = true;
- }
- else if (PARAMETER_CHECK("-loj", 4, parameterLength)) {
- leftJoin = true;
- }
- else if(PARAMETER_CHECK("-ubam", 5, parameterLength)) {
- uncompressedBam = true;
- }
- else if(PARAMETER_CHECK("-sorted", 7, parameterLength)) {
- sortedInput = true;
- }
- else if(PARAMETER_CHECK("-header", 7, parameterLength)) {
- printHeader = true;
- }
- else {
- cerr << endl << "*****ERROR: Unrecognized parameter: " << argv[i] << " *****" << endl << endl;
- showHelp = true;
- }
- }
-
- // make sure we have both input files
- if (!haveBedA || !haveBedB) {
- cerr << endl << "*****" << endl << "*****ERROR: Need -a and -b files. " << endl << "*****" << endl;
- showHelp = true;
- }
-
- if (anyHit && noHit) {
- cerr << endl << "*****" << endl << "*****ERROR: Request either -u OR -v, not both." << endl << "*****" << endl;
- showHelp = true;
- }
-
- if (writeB && writeCount) {
- cerr << endl << "*****" << endl << "*****ERROR: Request either -wb OR -c, not both." << endl << "*****" << endl;
- showHelp = true;
- }
-
- if (writeCount && writeOverlap) {
- cerr << endl << "*****" << endl << "*****ERROR: Request either -wb OR -wo, not both." << endl << "*****" << endl;
- showHelp = true;
- }
-
- if (writeA && writeOverlap) {
- cerr << endl << "*****" << endl << "*****ERROR: Request either -wa OR -wo, not both." << endl << "*****" << endl;
- showHelp = true;
- }
-
- if (writeB && writeOverlap) {
- cerr << endl << "*****" << endl << "*****ERROR: Request either -wb OR -wo, not both." << endl << "*****" << endl;
- showHelp = true;
- }
-
- if (reciprocalFraction && !haveFraction) {
- cerr << endl << "*****" << endl << "*****ERROR: If using -r, you need to define -f." << endl << "*****" << endl;
- showHelp = true;
- }
-
- if (anyHit && writeCount) {
- cerr << endl << "*****" << endl << "*****ERROR: Request either -u OR -c, not both." << endl << "*****" << endl;
- showHelp = true;
- }
-
- if (anyHit && writeB) {
- cerr << endl << "*****" << endl << "*****ERROR: Request either -u OR -wb, not both." << endl << "*****" << endl;
- showHelp = true;
- }
-
- if (anyHit && writeOverlap) {
- cerr << endl << "*****" << endl << "*****ERROR: Request either -u OR -wo, not both." << endl << "*****" << endl;
- showHelp = true;
- }
-
- if (sameStrand && diffStrand) {
- cerr << endl << "*****" << endl << "*****ERROR: Request either -s OR -S, not both." << endl << "*****" << endl;
- showHelp = true;
- }
-
- if (inputIsBam && writeB && outputIsBam) {
- cerr << endl << "*****" << endl << "*****WARNING: -wb is ignored with -abam" << endl << "*****" << endl;
- }
-
- if (inputIsBam && leftJoin) {
- cerr << endl << "*****" << endl << "*****WARNING: -loj is ignored with -abam" << endl << "*****" << endl;
- }
-
- if (outputIsBam && (writeCount || writeOverlap || writeAllOverlap))
- {
- outputIsBam = false;
- }
-
- if (!showHelp) {
-
- BedIntersect *bi = new BedIntersect(bedAFile, bedBFile, anyHit, writeA, writeB, writeOverlap,
- writeAllOverlap, overlapFraction, noHit, leftJoin, writeCount, sameStrand, diffStrand,
- reciprocalFraction, obeySplits, inputIsBam, outputIsBam, uncompressedBam,
- sortedInput, printHeader);
- delete bi;
- return 0;
- }
- else {
- intersect_help();
- return 0;
- }
-}
-
-void intersect_help(void) {
-
- cerr << "\nTool: bedtools intersect (aka intersectBed)" << endl;
- cerr << "Version: " << VERSION << "\n";
- cerr << "Summary: Report overlaps between two feature files." << endl << endl;
-
- cerr << "Usage: " << PROGRAM_NAME << " [OPTIONS] -a <bed/gff/vcf> -b <bed/gff/vcf>" << endl << endl;
-
- cerr << "Options: " << endl;
-
- cerr << "\t-abam\t" << "The A input file is in BAM format. Output will be BAM as well. Replaces -a." << endl << endl;
-
- cerr << "\t-ubam\t" << "Write uncompressed BAM output. Default writes compressed BAM." << endl << endl;
-
- cerr << "\t-bed\t" << "When using BAM input (-abam), write output as BED. The default" << endl;
- cerr << "\t\tis to write output in BAM when using -abam." << endl << endl;
-
- cerr << "\t-wa\t" << "Write the original entry in A for each overlap." << endl << endl;
-
- cerr << "\t-wb\t" << "Follow the A entry with the original "
- << "entry in B for each overlap." << endl;
- cerr << "\t\t- Useful for knowing _what_ A overlaps. Restricted by -f and -r." << endl << endl;
-
- cerr << "\t-loj\t" << "Perform a \"left outer join\". That is, for each feature in A" << endl;
- cerr << "\t\treport each overlap with B. If no overlaps are found, " << endl;
- cerr << "\t\treport a NULL feature for B." << endl << endl;
-
- cerr << "\t-wo\t" << "Write the original A and B entries plus the number of base" << endl;
- cerr << "\t\tpairs of overlap between the two features." << endl;
- cerr << "\t\t- Overlaps restricted by -f and -r." << endl;
- cerr << "\t\t Only A features with overlap are reported." << endl << endl;
-
- cerr << "\t-wao\t" << "Write the original A and B entries plus the number of base" << endl;
- cerr << "\t\tpairs of overlap between the two features." << endl;
- cerr << "\t\t- Overlapping features restricted by -f and -r." << endl;
- cerr << "\t\t However, A features w/o overlap are also reported" << endl;
- cerr << "\t\t with a NULL B feature and overlap = 0." << endl << endl;
-
- cerr << "\t-u\t" << "Write the original A entry _once_ if _any_ overlaps found in B." << endl;
- cerr << "\t\t- In other words, just report the fact >=1 hit was found." << endl;
- cerr << "\t\t- Overlaps restricted by -f and -r." << endl << endl;
-
- cerr << "\t-c\t" << "For each entry in A, report the number of overlaps with B." << endl;
- cerr << "\t\t- Reports 0 for A entries that have no overlap with B." << endl;
- cerr << "\t\t- Overlaps restricted by -f and -r." << endl << endl;
-
- cerr << "\t-v\t" << "Only report those entries in A that have _no overlaps_ with B." << endl;
- cerr << "\t\t- Similar to \"grep -v\" (an homage)." << endl << endl;
-
- cerr << "\t-f\t" << "Minimum overlap required as a fraction of A." << endl;
- cerr << "\t\t- Default is 1E-9 (i.e., 1bp)." << endl;
- cerr << "\t\t- FLOAT (e.g. 0.50)" << endl << endl;
-
- cerr << "\t-r\t" << "Require that the fraction overlap be reciprocal for A and B." << endl;
- cerr << "\t\t- In other words, if -f is 0.90 and -r is used, this requires" << endl;
- cerr << "\t\t that B overlap 90% of A and A _also_ overlaps 90% of B." << endl << endl;
-
- cerr << "\t-s\t" << "Require same strandedness. That is, only report hits in B" << endl;
- cerr << "\t\tthat overlap A on the _same_ strand." << endl;
- cerr << "\t\t- By default, overlaps are reported without respect to strand." << endl << endl;
-
- cerr << "\t-S\t" << "Require different strandedness. That is, only report hits in B" << endl;
- cerr << "\t\tthat overlap A on the _opposite_ strand." << endl;
- cerr << "\t\t- By default, overlaps are reported without respect to strand." << endl << endl;
-
- cerr << "\t-split\t" << "Treat \"split\" BAM or BED12 entries as distinct BED intervals." << endl << endl;
-
- cerr << "\t-sorted\t" << "Use the \"chromsweep\" algorithm for sorted (-k1,1 -k2,2n) input" << endl << endl;
-
- cerr << "\t-header\t" << "Print the header from the A file prior to results." << endl << endl;
-
- cerr << "Notes: " << endl;
- cerr << "\t(1) When a BAM file is used for the A file, the alignment is retained if overlaps exist," << endl;
- cerr << "\tand exlcuded if an overlap cannot be found. If multiple overlaps exist, they are not" << endl;
- cerr << "\treported, as we are only testing for one or more overlaps." << endl << endl;
-
- // end the program here
- exit(1);
-
-}
diff --git a/src/multiIntersectBed/Makefile b/src/multiIntersectBed/Makefile
index 6ebf6050d40b1e163a12a2b521680eccffb20df5..e43e7554964982ed756417d078d3bb882831bfd4 100644
--- a/src/multiIntersectBed/Makefile
+++ b/src/multiIntersectBed/Makefile
@@ -7,7 +7,7 @@ BIN_DIR = ../../bin/
# -------------------
INCLUDES = -I$(UTILITIES_DIR)/bedFile/ \
-I$(UTILITIES_DIR)/lineFileUtilities/ \
- -I$(UTILITIES_DIR)/genomeFile/ \
+ -I$(UTILITIES_DIR)/GenomeFile/ \
-I$(UTILITIES_DIR)/gzstream/ \
-I$(UTILITIES_DIR)/fileType/ \
-I$(UTILITIES_DIR)/Point/ \
diff --git a/src/multiIntersectBed/multiIntersectBed.h b/src/multiIntersectBed/multiIntersectBed.h
index 949cea1b7d86a96800f79bf9f5c73e917df5939e..fb757a8bcf4a06e78265d73c8eef99460c5d58ac 100644
--- a/src/multiIntersectBed/multiIntersectBed.h
+++ b/src/multiIntersectBed/multiIntersectBed.h
@@ -17,7 +17,7 @@
#include <vector>
#include <string>
#include "bedFile.h"
-#include "genomeFile.h"
+#include "GenomeFile.h"
#include "Point.h"
class MultiIntersectBed
diff --git a/src/multiIntersectBed/multiIntersectBedMain.cpp b/src/multiIntersectBed/multiIntersectBedMain.cpp
index 3ac39d15db49530cb98147a90938cce9d11c7765..5b8d1b2724df8732aeb7cf4b73c61e5de31c33eb 100644
--- a/src/multiIntersectBed/multiIntersectBedMain.cpp
+++ b/src/multiIntersectBed/multiIntersectBedMain.cpp
@@ -19,7 +19,7 @@
#include <getopt.h>
#include <libgen.h> //for basename()
-#include "genomeFile.h"
+#include "GenomeFile.h"
#include "multiIntersectBed.h"
#include "version.h"
diff --git a/src/randomBed/Makefile b/src/randomBed/Makefile
index 3a9ee898ad36288629e4df0e269aca9ff82e96b5..2c795c2477909489f30708e888c4debd789d37d2 100644
--- a/src/randomBed/Makefile
+++ b/src/randomBed/Makefile
@@ -5,7 +5,7 @@ BIN_DIR = ../../bin/
# -------------------
# define our includes
# -------------------
-INCLUDES = -I$(UTILITIES_DIR)/genomeFile/ \
+INCLUDES = -I$(UTILITIES_DIR)/GenomeFile/ \
-I$(UTILITIES_DIR)/BamTools/include \
-I$(UTILITIES_DIR)/version/
diff --git a/src/randomBed/randomBed.h b/src/randomBed/randomBed.h
index f922a38eb4f1d5226b11868b91ef29bb995c4510..4002c1986b2101124ec8f10e2a3af1c5cbb7de8b 100644
--- a/src/randomBed/randomBed.h
+++ b/src/randomBed/randomBed.h
@@ -9,7 +9,7 @@
Licenced under the GNU General Public License 2.0 license.
******************************************************************************/
-#include "genomeFile.h"
+#include "GenomeFile.h"
#include <vector>
#include <iostream>
diff --git a/src/shuffleBed/Makefile b/src/shuffleBed/Makefile
index 2f945715cff8508e0167776f96e6b658064f4493..a85f2df607778018ecec266f2dc574f9f806c558 100644
--- a/src/shuffleBed/Makefile
+++ b/src/shuffleBed/Makefile
@@ -7,7 +7,7 @@ BIN_DIR = ../../bin/
# -------------------
INCLUDES = -I$(UTILITIES_DIR)/bedFile/ \
-I$(UTILITIES_DIR)/bedFilePE/ \
- -I$(UTILITIES_DIR)/genomeFile/ \
+ -I$(UTILITIES_DIR)/GenomeFile/ \
-I$(UTILITIES_DIR)/lineFileUtilities/ \
-I$(UTILITIES_DIR)/gzstream/ \
-I$(UTILITIES_DIR)/fileType/ \
diff --git a/src/shuffleBed/shuffleBed.h b/src/shuffleBed/shuffleBed.h
index 2623c174106ab75e2355947069659a0856a40b2c..e80b11ecfe629f2659ce9c7e5889c165b22ce213 100644
--- a/src/shuffleBed/shuffleBed.h
+++ b/src/shuffleBed/shuffleBed.h
@@ -11,7 +11,7 @@
******************************************************************************/
#include "bedFile.h"
#include "bedFilePE.h"
-#include "genomeFile.h"
+#include "GenomeFile.h"
#include <vector>
#include <iostream>
diff --git a/src/slopBed/Makefile b/src/slopBed/Makefile
index ebdaba35b406d4e4dae8eadef89f7319df88313d..d63d924733f1db248f531ebab1ce968b8a76c982 100644
--- a/src/slopBed/Makefile
+++ b/src/slopBed/Makefile
@@ -6,7 +6,7 @@ BIN_DIR = ../../bin/
# define our includes
# -------------------
INCLUDES = -I$(UTILITIES_DIR)/bedFile/ \
- -I$(UTILITIES_DIR)/genomeFile/ \
+ -I$(UTILITIES_DIR)/GenomeFile/ \
-I$(UTILITIES_DIR)/lineFileUtilities/ \
-I$(UTILITIES_DIR)/gzstream/ \
-I$(UTILITIES_DIR)/fileType/ \
diff --git a/src/slopBed/slopBed.h b/src/slopBed/slopBed.h
index 7de0afd728cce49b85f31f0ec60c1f2efbcd4001..1fd1aba2ccc5de333734dc345f1a35fa2f41fdc6 100644
--- a/src/slopBed/slopBed.h
+++ b/src/slopBed/slopBed.h
@@ -11,7 +11,7 @@
******************************************************************************/
#include "bedFile.h"
-#include "genomeFile.h"
+#include "GenomeFile.h"
#include <vector>
#include <iostream>
diff --git a/src/unionBedGraphs/Makefile b/src/unionBedGraphs/Makefile
index 1d255d067ad7d1d8739bdd4d3c3f43d8a561e6cc..b0c0d8d688319293fd812abd4ed731839aed52aa 100755
--- a/src/unionBedGraphs/Makefile
+++ b/src/unionBedGraphs/Makefile
@@ -7,7 +7,7 @@ BIN_DIR = ../../bin/
# -------------------
INCLUDES = -I$(UTILITIES_DIR)/bedGraphFile/ \
-I$(UTILITIES_DIR)/lineFileUtilities/ \
- -I$(UTILITIES_DIR)/genomeFile/ \
+ -I$(UTILITIES_DIR)/GenomeFile/ \
-I$(UTILITIES_DIR)/gzstream/ \
-I$(UTILITIES_DIR)/fileType/ \
-I$(UTILITIES_DIR)/Point/ \
diff --git a/src/unionBedGraphs/unionBedGraphs.h b/src/unionBedGraphs/unionBedGraphs.h
index 25cbe4e73994343ee149f60b9c9cb83925d04d95..c0f5929e4fbe6a70d686ab71d46bcd69c58fd0b1 100644
--- a/src/unionBedGraphs/unionBedGraphs.h
+++ b/src/unionBedGraphs/unionBedGraphs.h
@@ -16,7 +16,7 @@
#include <vector>
#include <string>
#include "bedGraphFile.h"
-#include "genomeFile.h"
+#include "GenomeFile.h"
#include "Point.h"
class UnionBedGraphs
diff --git a/src/unionBedGraphs/unionBedGraphsMain.cpp b/src/unionBedGraphs/unionBedGraphsMain.cpp
index 6411adffbe69f543feb6ea33612a2c6ee20faa21..46d36184d5f6cc88d15312c72f95461122a41cba 100644
--- a/src/unionBedGraphs/unionBedGraphsMain.cpp
+++ b/src/unionBedGraphs/unionBedGraphsMain.cpp
@@ -19,7 +19,7 @@
#include <getopt.h>
#include <libgen.h> //for basename()
-#include "genomeFile.h"
+#include "GenomeFile.h"
#include "unionBedGraphs.h"
#include "version.h"
diff --git a/src/utils/BamTools-Ancillary/Makefile b/src/utils/BamTools-Ancillary/Makefile
index a0024c1bb0df614c274423ec4c1428e30cc98710..8d64745eff9c594a1e88c88f877c95af491995f4 100644
--- a/src/utils/BamTools-Ancillary/Makefile
+++ b/src/utils/BamTools-Ancillary/Makefile
@@ -12,7 +12,7 @@ INCLUDES = -I$(UTILITIES_DIR)/BamTools/include \
# define our source and object files
# ----------------------------------
SOURCES= BamAncillary.cpp BamAncillary.h
-OBJECTS= BamAncillary.o
+OBJECTS= $(SOURCES:.cpp=.o)
BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
all: $(BUILT_OBJECTS)
@@ -27,4 +27,4 @@ clean:
@echo "Cleaning up."
@rm -f $(OBJ_DIR)/* $(BIN_DIR)/*
-.PHONY: clean
+.PHONY: clean
\ No newline at end of file
diff --git a/src/utils/BamTools/src/api/BamAlignment.h b/src/utils/BamTools/src/api/BamAlignment.h
index a2349ea9ce9b254066450dc953b99925a8f03b56..fb1e8722d9fc70bbc118552e209fba44ef2dbc07 100644
--- a/src/utils/BamTools/src/api/BamAlignment.h
+++ b/src/utils/BamTools/src/api/BamAlignment.h
@@ -139,7 +139,9 @@ struct API_EXPORT BamAlignment {
unsigned int& numBytesParsed) const;
// internal data
- private:
+ public: //had to change this from private.
+ //needed to expose some members of support data that
+ //were otherwise inaccessible when using only core alignments.
struct BamAlignmentSupportData {
@@ -163,6 +165,7 @@ struct API_EXPORT BamAlignment {
BamAlignmentSupportData SupportData;
friend class Internal::BamReaderPrivate;
friend class Internal::BamWriterPrivate;
+ friend class BamFileReader;
mutable std::string ErrorString; // mutable to allow updates even in logically const methods
//! \endinternal
diff --git a/src/utils/BamTools/src/api/BamReader.cpp b/src/utils/BamTools/src/api/BamReader.cpp
index ae2adec94e498dadc97115807ab0d52dbe178804..b92c71355aca2fa8be427e59f2778e97b0d9e4fd 100644
--- a/src/utils/BamTools/src/api/BamReader.cpp
+++ b/src/utils/BamTools/src/api/BamReader.cpp
@@ -259,6 +259,11 @@ bool BamReader::Open(const std::string& filename) {
return d->Open(filename);
}
+bool BamReader::OpenStream(std::istream* stream) {
+ return d->OpenStream(stream);
+}
+
+
/*! \fn bool BamReader::OpenIndex(const std::string& indexFilename)
\brief Opens a BAM index file.
diff --git a/src/utils/BamTools/src/api/BamReader.h b/src/utils/BamTools/src/api/BamReader.h
index fb9064d9994d08a4c2afe177b2ca205c1841da4c..5660040ca4e9647e7fc1fe59789782e6bfde8c1c 100644
--- a/src/utils/BamTools/src/api/BamReader.h
+++ b/src/utils/BamTools/src/api/BamReader.h
@@ -46,6 +46,8 @@ class API_EXPORT BamReader {
bool Jump(int refID, int position = 0);
// opens a BAM file
bool Open(const std::string& filename);
+ bool OpenStream(std::istream* stream);
+
// returns internal file pointer to beginning of alignment data
bool Rewind(void);
// sets the target region of interest
diff --git a/src/utils/BamTools/src/api/internal/bam/BamReader_p.cpp b/src/utils/BamTools/src/api/internal/bam/BamReader_p.cpp
index 75d727928bb6757c49f033ea938e2fa4e81a5f20..70782a76117e78247eb690b2ff1f24bc547cd20c 100644
--- a/src/utils/BamTools/src/api/internal/bam/BamReader_p.cpp
+++ b/src/utils/BamTools/src/api/internal/bam/BamReader_p.cpp
@@ -388,6 +388,35 @@ bool BamReaderPrivate::Open(const string& filename) {
}
}
+bool BamReaderPrivate::OpenStream(std::istream* stream) {
+
+ try {
+
+ // make sure we're starting with fresh state
+ Close();
+
+ // open BgzfStream
+ m_stream.OpenStream(stream, IBamIODevice::ReadOnly);
+
+ // load BAM metadata
+ LoadHeaderData();
+ LoadReferenceData();
+
+ // store "filename" & offset of first alignment
+ m_filename = "stream"; // or whatever
+ m_alignmentsBeginOffset = m_stream.Tell();
+
+ // return success
+ return true;
+
+ } catch ( BamException& e ) {
+ const string error = e.what();
+ const string message = string("could not open input stream: \n\t") + error;
+ SetErrorString("BamReader::Open", message);
+ return false;
+ }
+}
+
bool BamReaderPrivate::OpenIndex(const std::string& indexFilename) {
if ( m_randomAccessController.OpenIndex(indexFilename, this) )
diff --git a/src/utils/BamTools/src/api/internal/bam/BamReader_p.h b/src/utils/BamTools/src/api/internal/bam/BamReader_p.h
index e8db646e28034eaf20095b31a1fda2b3cd30a8a2..3164d6fc82af19da8983b3325544a62d605d1939 100644
--- a/src/utils/BamTools/src/api/internal/bam/BamReader_p.h
+++ b/src/utils/BamTools/src/api/internal/bam/BamReader_p.h
@@ -47,6 +47,7 @@ class BamReaderPrivate {
const std::string Filename(void) const;
bool IsOpen(void) const;
bool Open(const std::string& filename);
+ bool OpenStream(std::istream* stream);
bool Rewind(void);
bool SetRegion(const BamRegion& region);
diff --git a/src/utils/BamTools/src/api/internal/io/BamDeviceFactory_p.cpp b/src/utils/BamTools/src/api/internal/io/BamDeviceFactory_p.cpp
index f9c7694ec179e0265c7468dacd98cb097b72a621..a1fdd3d12633762780764f0ea44ddc92da7e8d8d 100644
--- a/src/utils/BamTools/src/api/internal/io/BamDeviceFactory_p.cpp
+++ b/src/utils/BamTools/src/api/internal/io/BamDeviceFactory_p.cpp
@@ -12,6 +12,8 @@
#include "api/internal/io/BamFtp_p.h"
#include "api/internal/io/BamHttp_p.h"
#include "api/internal/io/BamPipe_p.h"
+#include "api/internal/io/StdStreamDevice_p.h"
+
using namespace BamTools;
using namespace BamTools::Internal;
@@ -35,3 +37,9 @@ IBamIODevice* BamDeviceFactory::CreateDevice(const string& source) {
// otherwise assume a "normal" file
return new BamFile(source);
}
+
+IBamIODevice* BamDeviceFactory::CreateDevice(std::istream *stream) {
+ // compile-time sanity check
+ BT_ASSERT_X( stream, "BamDeviceFactory::CreateDevice - null input stream");
+ return new StdStreamDevice(stream);
+}
diff --git a/src/utils/BamTools/src/api/internal/io/BamDeviceFactory_p.h b/src/utils/BamTools/src/api/internal/io/BamDeviceFactory_p.h
index 1d48533d8687773384b4582f2e006a07612890eb..00bb07d1be4c4b0ca3ac84a04b7240ad61e242bb 100644
--- a/src/utils/BamTools/src/api/internal/io/BamDeviceFactory_p.h
+++ b/src/utils/BamTools/src/api/internal/io/BamDeviceFactory_p.h
@@ -29,6 +29,7 @@ namespace Internal {
class BamDeviceFactory {
public:
static IBamIODevice* CreateDevice(const std::string& source);
+ static IBamIODevice* CreateDevice(std::istream *stream);
};
} // namespace Internal
diff --git a/src/utils/BamTools/src/api/internal/io/BgzfStream_p.cpp b/src/utils/BamTools/src/api/internal/io/BgzfStream_p.cpp
index 7f73d67fea9c43fd387523fce4ade4c49ed3dc5b..fe90e5f877a897cd475a31f7195acdb013e989fc 100644
--- a/src/utils/BamTools/src/api/internal/io/BgzfStream_p.cpp
+++ b/src/utils/BamTools/src/api/internal/io/BgzfStream_p.cpp
@@ -286,6 +286,28 @@ void BgzfStream::Open(const string& filename, const IBamIODevice::OpenMode mode)
}
}
+void BgzfStream::OpenStream(std::istream* stream, const IBamIODevice::OpenMode mode) {
+
+ // close current device if necessary
+ Close();
+ BT_ASSERT_X( (m_device == 0), "BgzfStream::Open() - unable to properly close previous IO device" );
+
+ // run-time sanity check
+ if ( stream == NULL )
+ throw BamException("BgzfStream::Open", "null input stream");
+
+ // retrieve new IO device for std::stream*
+ m_device = BamDeviceFactory::CreateDevice(stream);
+ BT_ASSERT_X( m_device, "BgzfStream::Open() - unable to create IO device from stream" );
+
+ // if device fails to open
+ if ( !m_device->Open(mode) ) {
+ const string deviceError = m_device->GetErrorString();
+ const string message = string("could not open BGZF stream: \n\t") + deviceError;
+ throw BamException("BgzfStream::Open", message);
+ }
+}
+
// reads BGZF data into a byte buffer
size_t BgzfStream::Read(char* data, const size_t dataLength) {
@@ -345,6 +367,8 @@ void BgzfStream::ReadBlock(void) {
// read block header from file
char header[Constants::BGZF_BLOCK_HEADER_LENGTH];
+ memset(header, 0, Constants::BGZF_BLOCK_HEADER_LENGTH);
+
int64_t numBytesRead = m_device->Read(header, Constants::BGZF_BLOCK_HEADER_LENGTH);
// check for device error
diff --git a/src/utils/BamTools/src/api/internal/io/BgzfStream_p.h b/src/utils/BamTools/src/api/internal/io/BgzfStream_p.h
index 47b360904740420ff919748a07fdf09756c6e111..9297820b9bc7d4a9c031fe7414bb8bb253ed687f 100644
--- a/src/utils/BamTools/src/api/internal/io/BgzfStream_p.h
+++ b/src/utils/BamTools/src/api/internal/io/BgzfStream_p.h
@@ -45,6 +45,8 @@ class BgzfStream {
bool IsOpen(void) const;
// opens the BGZF file
void Open(const std::string& filename, const IBamIODevice::OpenMode mode);
+
+ void OpenStream(std::istream* stream, const IBamIODevice::OpenMode mode);
// reads BGZF data into a byte buffer
size_t Read(char* data, const size_t dataLength);
// seek to position in BGZF file
diff --git a/src/utils/BamTools/src/api/internal/io/NetUnix_p.h b/src/utils/BamTools/src/api/internal/io/NetUnix_p.h
index f06c4df72f01910c42ef13ed39f7d83768965088..8cf75f8d300464eac4c06ca864e7caa535722d72 100644
--- a/src/utils/BamTools/src/api/internal/io/NetUnix_p.h
+++ b/src/utils/BamTools/src/api/internal/io/NetUnix_p.h
@@ -23,7 +23,6 @@
#ifndef _WIN32 // <-- source files only include the proper Net*_p.h, but this is a double-check
#include <arpa/inet.h>
-#include <netinet/in.h>
#include <sys/ioctl.h>
#include <sys/socket.h>
#include <sys/stat.h>
diff --git a/src/utils/BamTools/src/api/internal/io/StdStreamDevice_p.h b/src/utils/BamTools/src/api/internal/io/StdStreamDevice_p.h
new file mode 100644
index 0000000000000000000000000000000000000000..a957c2645572f23bb37f3120a94e594115e32591
--- /dev/null
+++ b/src/utils/BamTools/src/api/internal/io/StdStreamDevice_p.h
@@ -0,0 +1,54 @@
+/*
+ * StdStreamDevice_p.h
+ *
+ * Created on: Apr 24, 2013
+ * Author: nek3d
+ */
+
+#ifndef STDSTREAMDEVICE_P_H_
+#define STDSTREAMDEVICE_P_H_
+
+//NOTE: The stream management methods in this class are placeholders. The class is not intended to manage a
+// a stream. Rather, it is intended to accept a stream that is managed elsewhere, and allow that stream to
+//be used with bamtools.
+
+#include "api/IBamIODevice.h"
+#include <cstring> //for strlen
+#include <istream>
+
+namespace BamTools {
+namespace Internal {
+
+class StdStreamDevice : public IBamIODevice {
+
+ // ctor & dtor
+ public:
+ StdStreamDevice(std::istream *stream) : m_stream(stream) {
+ IBamIODevice::m_mode = IBamIODevice::ReadOnly;
+ }
+ ~StdStreamDevice() {}
+
+ // IBamIODevice implementation
+ public:
+ void Close(void) {}
+ bool IsOpen(void) const { return true; } // assume stream passed in is always open.
+ bool IsRandomAccess(void) const { return false; }
+ bool Open(const IBamIODevice::OpenMode mode) { return true; } //stream is assumed opened by caller.
+ int64_t Read(char* data, const unsigned int numBytes) {
+ m_stream->read(data, numBytes);
+ return (int64_t)(numBytes);
+ }
+ bool Seek(const int64_t& position, const int origin = SEEK_SET) { return false; }
+
+ //Not sure what Tell and Write should do for streams.
+ int64_t Tell(void) const { return 0; }
+ int64_t Write(const char* data, const unsigned int numBytes) { return 0; }
+
+ private:
+ std::istream* m_stream;
+};
+
+} // namespace Internal
+} // namespace BamTools
+
+#endif /* STDSTREAMDEVICE_P_H_ */
diff --git a/src/utils/fileType/Makefile b/src/utils/fileType/Makefile
index 91585d5ed8b7d7f5e1ed2268f980fa5924e841d5..50ed87b54bbe2e5cec0e4a45d7b420dfbb82deae 100644
--- a/src/utils/fileType/Makefile
+++ b/src/utils/fileType/Makefile
@@ -4,26 +4,28 @@ UTILITIES_DIR = ../../utils/
# -------------------
# define our includes
# -------------------
-INCLUDES =
+INCLUDES = -I$(UTILITIES_DIR)/BamTools/include/ \
+ -I$(UTILITIES_DIR)/general
# ----------------------------------
# define our source and object files
# ----------------------------------
-SOURCES= fileType.cpp fileType.h
-OBJECTS= $(SOURCES:.cpp=.o)
-_EXT_OBJECTS=
-EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS))
+SOURCES= fileType.cpp fileType.h FileRecordTypeChecker.cpp FileRecordTypeChecker.h
+OBJECTS= fileType.o FileRecordTypeChecker.o
+#_EXT_OBJECTS=ParseTools.o QuickString.o
+#EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS))
BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
+all: $(BUILT_OBJECTS)
+
+.PHONY: all
+
$(BUILT_OBJECTS): $(SOURCES)
@echo " * compiling" $(*F).cpp
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
-$(EXT_OBJECTS):
- @$(MAKE) --no-print-directory -C $(INCLUDES)
-
clean:
@echo "Cleaning up."
- @rm -f $(OBJ_DIR)/* $(BIN_DIR)/*
+ @rm -f $(OBJ_DIR)/fileType.o $(OBJ_DIR)/FileRecordTypeChecker.o
.PHONY: clean
\ No newline at end of file
diff --git a/src/utils/fileType/fileType.cpp b/src/utils/fileType/fileType.cpp
index 431782acf826f6884bd4b7c559fc3615c1ad091d..0b05acb18ffa42d7df6c33630f6bedc0d9d48b19 100644
--- a/src/utils/fileType/fileType.cpp
+++ b/src/utils/fileType/fileType.cpp
@@ -38,7 +38,9 @@ bool isRegularFile(const string& filename) {
returns TRUE if the file has a GZIP header.
Should only be run on regular files.
*/
-bool isGzipFile(istream *file) {
+bool isGzipFile(istream *file) {
+ //see http://www.gzip.org/zlib/rfc-gzip.html#file-format
+
/*
11-Sep-2011:
We now only peek at the first byte and test for GZIPiness.
@@ -52,19 +54,18 @@ bool isGzipFile(istream *file) {
// unsigned char cm;
} gzip_header;
- /*
- 26-Dec-2012:
- Just peek at the first byte instead of reading it so that we don't
- affect the istream's failbit. This modification was wisely proposed
- by John Marshall in response to Issue 30:
- https://github.com/arq5x/bedtools/issues/30
- */
-
- // Check to see if the first byte matches expectations for a
- // GZIP header.
- // Deatils: http://www.gzip.org/zlib/rfc-gzip.html#file-format
- if (file->peek() != 0x1f)
+ if (!file->read((char*)&gzip_header, sizeof(gzip_header))) {
return false;
- else
+ }
+
+ if ( gzip_header.id1 == 0x1f )
+// &&
+// gzip_header.id2 == 0x8b
+// &&
+// gzip_header.cm == 8 )
+ {
return true;
+ }
+ file->putback(gzip_header.id1);
+ return false;
}
diff --git a/src/utils/genomeFile/Makefile b/src/utils/genomeFile/Makefile
deleted file mode 100644
index 680343c4edef69838cbacc54580fab1096a34490..0000000000000000000000000000000000000000
--- a/src/utils/genomeFile/Makefile
+++ /dev/null
@@ -1,32 +0,0 @@
-OBJ_DIR = ../../../obj/
-BIN_DIR = ../../../bin/
-UTILITIES_DIR = ../
-# -------------------
-# define our includes
-# -------------------
-INCLUDES = -I$(UTILITIES_DIR)/lineFileUtilities/ \
- -I$(UTILITIES_DIR)/fileType/ \
- -I$(UTILITIES_DIR)/BamTools/include/
-
-# ----------------------------------
-# define our source and object files
-# ----------------------------------
-SOURCES= genomeFile.cpp genomeFile.h
-OBJECTS= $(SOURCES:.cpp=.o)
-_EXT_OBJECTS=lineFileUtilities.o fileType.o
-EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS))
-BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
-
-$(BUILT_OBJECTS): $(SOURCES)
- @echo " * compiling" $(*F).cpp
- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES) -L$(BT_ROOT)/lib
-
-$(EXT_OBJECTS):
- @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/lineFileUtilities/
- @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/fileType/
-
-clean:
- @echo "Cleaning up."
- @rm -f $(OBJ_DIR)/* $(BIN_DIR)/*
-
-.PHONY: clean
diff --git a/src/utils/genomeFile/genomeFile.cpp b/src/utils/genomeFile/genomeFile.cpp
deleted file mode 100644
index b84948e6604776b55794cf3000e396e928ff0cb4..0000000000000000000000000000000000000000
--- a/src/utils/genomeFile/genomeFile.cpp
+++ /dev/null
@@ -1,121 +0,0 @@
-/*****************************************************************************
- genomeFile.cpp
-
- (c) 2009 - Aaron Quinlan
- Hall Laboratory
- Department of Biochemistry and Molecular Genetics
- University of Virginia
- aaronquinlan@gmail.com
-
- Licensed under the GNU General Public License 2.0 license.
-******************************************************************************/
-#include "lineFileUtilities.h"
-#include "genomeFile.h"
-
-
-GenomeFile::GenomeFile(const string &genomeFile) {
- _genomeFile = genomeFile;
- loadGenomeFileIntoMap();
-}
-
-GenomeFile::GenomeFile(const RefVector &genome) {
- for (size_t i = 0; i < genome.size(); ++i) {
- string chrom = genome[i].RefName;
- int length = genome[i].RefLength;
-
- _chromSizes[chrom] = length;
- _chromList.push_back(chrom);
- }
-}
-
-// Destructor
-GenomeFile::~GenomeFile(void) {
-}
-
-
-void GenomeFile::loadGenomeFileIntoMap() {
-
- string genomeLine;
- int lineNum = 0;
- vector<string> genomeFields; // vector for a GENOME entry
-
- // open the GENOME file for reading
- ifstream genome(_genomeFile.c_str(), ios::in);
- if ( !genome ) {
- cerr << "Error: The requested genome file (" << _genomeFile << ") could not be opened. Exiting!" << endl;
- exit (1);
- }
-
- while (getline(genome, genomeLine)) {
-
- Tokenize(genomeLine,genomeFields); // load the fields into the vector
- lineNum++;
-
- // ignore a blank line
- if (genomeFields.size() > 0) {
- if (genomeFields[0].find("#") != 0) {
- // we need at least 2 columns
- if (genomeFields.size() >= 2) {
- char *p2End;
- long c2;
- // make sure the second column is numeric.
- c2 = strtol(genomeFields[1].c_str(), &p2End, 10);
-
- // strtol will set p2End to the start of the string if non-integral, base 10
- if (p2End != genomeFields[1].c_str()) {
- string chrom = genomeFields[0];
- int size = atoi(genomeFields[1].c_str());
- _chromSizes[chrom] = size;
- _chromList.push_back(chrom);
- _startOffsets.push_back(_genomeLength);
- _genomeLength += size;
- }
- }
- else {
- cerr << "Less than the req'd two fields were encountered in the genome file (" << _genomeFile << ")";
- cerr << " at line " << lineNum << ". Exiting." << endl;
- exit (1);
- }
- }
- }
- genomeFields.clear();
- }
-}
-
-pair<string, uint32_t> GenomeFile::projectOnGenome(uint32_t genome_pos) {
- // search for the chrom that the position belongs on.
- // add 1 to genome position b/c of zero-based, half open.
- vector<uint32_t>::const_iterator low =
- lower_bound(_startOffsets.begin(), _startOffsets.end(), genome_pos + 1);
-
- // use the iterator to identify the appropriate index
- // into the chrom name and start vectors
- int i = int(low-_startOffsets.begin());
- string chrom = _chromList[i - 1];
- uint32_t start = genome_pos - _startOffsets[i - 1];
- return make_pair(chrom, start);
-}
-
-uint32_t GenomeFile::getChromSize(const string &chrom) {
- chromToSizes::const_iterator chromIt = _chromSizes.find(chrom);
- if (chromIt != _chromSizes.end())
- return _chromSizes[chrom];
- else
- return -1; // chrom not found.
-}
-
-uint32_t GenomeFile::getGenomeSize(void) {
- return _genomeLength;
-}
-
-vector<string> GenomeFile::getChromList() {
- return _chromList;
-}
-
-int GenomeFile::getNumberOfChroms() {
- return _chromList.size();
-}
-
-string GenomeFile::getGenomeFileName() {
- return _genomeFile;
-}
diff --git a/src/utils/genomeFile/genomeFile.h b/src/utils/genomeFile/genomeFile.h
deleted file mode 100644
index a71d61ec0ff6b191abdbff78b0f85628da4ecdbc..0000000000000000000000000000000000000000
--- a/src/utils/genomeFile/genomeFile.h
+++ /dev/null
@@ -1,72 +0,0 @@
-/*****************************************************************************
- genomeFile.h
-
- (c) 2009 - Aaron Quinlan
- Hall Laboratory
- Department of Biochemistry and Molecular Genetics
- University of Virginia
- aaronquinlan@gmail.com
-
- Licensed under the GNU General Public License 2.0 license.
-******************************************************************************/
-#ifndef GENOMEFILE_H
-#define GENOMEFILE_H
-
-#include <map>
-#include <string>
-#include <iostream>
-#include <sstream>
-#include <fstream>
-#include <cstring>
-#include <cstdio>
-#include <algorithm> // for bsearch lower_bound()
-#include "api/BamReader.h"
-#include "api/BamAux.h"
-using namespace BamTools;
-
-using namespace std;
-
-
-// typedef for mapping b/w chrom name and it's size in b.p.
-typedef map<string, int, std::less<string> > chromToSizes;
-
-
-class GenomeFile {
-
-public:
-
- // Constructor using a file
- GenomeFile(const string &genomeFile);
-
- // Constructor using a vector of BamTools RefVector
- GenomeFile(const RefVector &genome);
-
- // Destructor
- ~GenomeFile(void);
-
- // load a GENOME file into a map keyed by chrom. value is size of chrom.
- void loadGenomeFileIntoMap();
-
- pair<string, uint32_t> projectOnGenome(uint32_t genome_pos);
-
- uint32_t getChromSize(const string &chrom); // return the size of a chromosome
- uint32_t getGenomeSize(void); // return the total size of the geonome
- vector<string> getChromList(); // return a list of chrom names
- int getNumberOfChroms(); // return the number of chroms
- string getGenomeFileName(); // return the name of the genome file
-
-
-
-
-private:
- string _genomeFile;
- chromToSizes _chromSizes;
- vector<string> _chromList;
-
- // projecting chroms into a single coordinate system
- uint32_t _genomeLength;
- vector<uint32_t> _startOffsets;
-
-};
-
-#endif /* GENOMEFILE_H */
diff --git a/src/windowMaker/Makefile b/src/windowMaker/Makefile
index b51e487be536abb6b3b29b8d723d502c39c236ab..35c6ca3524721b8fa90489b58c3cbbae747dcda0 100644
--- a/src/windowMaker/Makefile
+++ b/src/windowMaker/Makefile
@@ -5,7 +5,7 @@ BIN_DIR = ../../bin/
# -------------------
# define our includes
# -------------------
-INCLUDES = -I$(UTILITIES_DIR)/genomeFile/ \
+INCLUDES = -I$(UTILITIES_DIR)/GenomeFile/ \
-I$(UTILITIES_DIR)/bedFile/ \
-I$(UTILITIES_DIR)/gzstream/ \
-I$(UTILITIES_DIR)/fileType/ \
diff --git a/src/windowMaker/windowMaker.h b/src/windowMaker/windowMaker.h
index b06b46ec337766073f324d797f6d58cb96080630..3c7d14fa7f2cc67c763d457e31796a0bc9576ffe 100644
--- a/src/windowMaker/windowMaker.h
+++ b/src/windowMaker/windowMaker.h
@@ -9,7 +9,7 @@ aaronquinlan@gmail.com
Licenced under the GNU General Public License 2.0 license.
******************************************************************************/
-#include "genomeFile.h"
+#include "GenomeFile.h"
#include "bedFile.h"
using namespace std;