From 0b3f2511e7b895c261997384f7747e941da88492 Mon Sep 17 00:00:00 2001
From: Aaron <aaronquinlan@gmail.com>
Date: Thu, 23 Jun 2011 15:06:17 -0400
Subject: [PATCH] Pushed tagBam to GitHub
---
Makefile | 1 +
src/tagBam/Makefile | 51 ++++++++++++++
src/tagBam/tagBam.cpp | 108 +++++++++++++++++++++++++++++
src/tagBam/tagBam.h | 74 ++++++++++++++++++++
src/tagBam/tagBamMain.cpp | 141 ++++++++++++++++++++++++++++++++++++++
5 files changed, 375 insertions(+)
create mode 100644 src/tagBam/Makefile
create mode 100644 src/tagBam/tagBam.cpp
create mode 100644 src/tagBam/tagBam.h
create mode 100644 src/tagBam/tagBamMain.cpp
diff --git a/Makefile b/Makefile
index 8e1fa0b4..4ee8b3e1 100644
--- a/Makefile
+++ b/Makefile
@@ -37,6 +37,7 @@ SUBDIRS = $(SRC_DIR)/annotateBed \
$(SRC_DIR)/slopBed \
$(SRC_DIR)/sortBed \
$(SRC_DIR)/subtractBed \
+ $(SRC_DIR)/tagBam \
$(SRC_DIR)/unionBedGraphs \
$(SRC_DIR)/windowBed
diff --git a/src/tagBam/Makefile b/src/tagBam/Makefile
new file mode 100644
index 00000000..b2dbcc4c
--- /dev/null
+++ b/src/tagBam/Makefile
@@ -0,0 +1,51 @@
+UTILITIES_DIR = ../utils/
+OBJ_DIR = ../../obj/
+BIN_DIR = ../../bin/
+
+# -------------------
+# define our includes
+# -------------------
+INCLUDES = -I$(UTILITIES_DIR)/bedFile/ \
+ -I$(UTILITIES_DIR)/version/ \
+ -I$(UTILITIES_DIR)/gzstream/ \
+ -I$(UTILITIES_DIR)/genomeFile/ \
+ -I$(UTILITIES_DIR)/lineFileUtilities/ \
+ -I$(UTILITIES_DIR)/fileType/ \
+ -I$(UTILITIES_DIR)/BamTools/include \
+ -I$(UTILITIES_DIR)/BamTools-Ancillary
+# ----------------------------------
+# define our source and object files
+# ----------------------------------
+SOURCES= tagBamMain.cpp tagBam.cpp
+OBJECTS= $(SOURCES:.cpp=.o)
+_EXT_OBJECTS=bedFile.o lineFileUtilities.o gzstream.o fileType.o
+EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS))
+BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
+PROGRAM= tagBam
+
+
+all: $(PROGRAM)
+
+.PHONY: all
+
+$(PROGRAM): $(BUILT_OBJECTS) $(EXT_OBJECTS)
+ @echo " * linking $(PROGRAM)"
+ @$(CXX) $(LDFLAGS) $(CXXFLAGS) -o $(BIN_DIR)/$@ $^ $(LIBS) -L$(UTILITIES_DIR)/BamTools/lib/ -lbamtools
+
+$(BUILT_OBJECTS): $(SOURCES)
+ @echo " * compiling" $(*F).cpp
+ @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
+
+$(EXT_OBJECTS):
+ @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/bedFile/
+ @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/lineFileUtilities/
+ @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/gzstream/
+ @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/BamTools/
+ @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/BamTools-Ancillary/
+ @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/fileType/
+
+clean:
+ @echo "Cleaning up."
+ @rm -f $(OBJ_DIR)/* $(BIN_DIR)/*
+
+.PHONY: clean
diff --git a/src/tagBam/tagBam.cpp b/src/tagBam/tagBam.cpp
new file mode 100644
index 00000000..3a65db8d
--- /dev/null
+++ b/src/tagBam/tagBam.cpp
@@ -0,0 +1,108 @@
+/*****************************************************************************
+ tagBam.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 "tagBam.h"
+
+// build
+TagBam::TagBam(const string &bamFile, const vector<string> &annoFileNames,
+ const vector<string> &annoLables, bool forceStrand) :
+
+ _bamFile(bamFile),
+ _annoFileNames(annoFileNames),
+ _annoLabels(annoLables),
+ _forceStrand(forceStrand)
+{}
+
+
+// destroy and delete the open file pointers
+TagBam::~TagBam(void) {
+ delete _bed;
+ CloseAnnoFiles();
+}
+
+
+void TagBam::OpenAnnoFiles() {
+ for (size_t i=0; i < _annoFileNames.size(); ++i) {
+ BedFile *file = new BedFile(_annoFileNames[i]);
+ file->loadBedFileIntoMap();
+ _annoFiles.push_back(file);
+ }
+}
+
+
+void TagBam::CloseAnnoFiles() {
+ for (size_t i=0; i < _annoFiles.size(); ++i) {
+ BedFile *file = _annoFiles[i];
+ delete file;
+ _annoFiles[i] = NULL;
+ }
+}
+
+bool TagBam::FindOneOrMoreOverlap(const BED &a, BedFile *bedFile) {
+ return bedFile->FindOneOrMoreOverlapsPerBin(a.chrom, a.start, a.end, a.strand,
+ _forceStrand, 0);
+}
+
+void TagBam::Tag() {
+
+ // open the annotations files for processing;
+ OpenAnnoFiles();
+
+ // open the BAM file
+ BamReader reader;
+ BamWriter writer;
+ reader.Open(_bamFile);
+ // get header & reference information
+ string bamHeader = reader.GetHeaderText();
+ RefVector refs = reader.GetReferenceData();
+
+ // 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);
+
+ // rip through the BAM file and test for overlaps with each annotation file.
+ BamAlignment al;
+ while (reader.GetNextAlignment(al)) {
+ if (al.IsMapped() == true) {
+ BED a;
+ a.chrom = refs.at(al.RefID).RefName;
+ a.start = al.Position;
+ a.end = al.GetEndPosition(false, false);
+ if (al.IsReverseStrand()) a.strand = "-";
+ a.strand = "+";
+
+ ostringstream annotations;
+ // annotate the BAM file based on overlaps with the annotation files.
+ for (size_t i = 0; i < _annoFiles.size(); ++i)
+ {
+ // grab the current annotation file.
+ BedFile *anno = _annoFiles[i];
+ // add the label for this annotation file to tag if there is overlap
+ if (FindOneOrMoreOverlap(a, anno)) {
+ annotations << _annoLabels[i] << ";";
+ }
+ }
+ // were there any overlaps with which to make a tag?
+ if (annotations.str().size() > 0) {
+ al.AddTag("YB", "Z", annotations.str().substr(0, annotations.str().size() - 1)); // get rid of the last ";"
+ }
+ writer.SaveAlignment(al);
+ }
+ }
+ reader.Close();
+
+ // close the annotations files;
+ CloseAnnoFiles();
+}
diff --git a/src/tagBam/tagBam.h b/src/tagBam/tagBam.h
new file mode 100644
index 00000000..85ada900
--- /dev/null
+++ b/src/tagBam/tagBam.h
@@ -0,0 +1,74 @@
+/*****************************************************************************
+ tagBam.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 TAGBAM_H
+#define TAGBAM_H
+
+#include "bedFile.h"
+
+#include "version.h"
+#include "api/BamReader.h"
+#include "api/BamWriter.h"
+#include "api/BamAux.h"
+#include "BamAncillary.h"
+using namespace BamTools;
+
+#include "bedFile.h"
+#include <vector>
+#include <algorithm>
+#include <iostream>
+#include <iomanip>
+#include <fstream>
+#include <stdlib.h>
+
+using namespace std;
+
+//************************************************
+// Class methods and elements
+//************************************************
+class TagBam {
+
+public:
+
+ // constructor
+ TagBam(const string &bamFile, const vector<string> &annoFileNames,
+ const vector<string> &annoLabels, bool forceStrand);
+
+ // destructor
+ ~TagBam(void);
+
+ // annotate the BAM file with all of the annotation files.
+ void Tag();
+
+private:
+
+ // input files.
+ string _bamFile;
+ vector<string> _annoFileNames;
+ vector<string> _annoLabels;
+
+ // instance of a bed file class.
+ BedFile *_bed;
+ vector<BedFile*> _annoFiles;
+
+ // do we care about strandedness when tagging?
+ bool _forceStrand;
+
+ // private function for reporting coverage information
+ void ReportAnnotations();
+
+ void OpenAnnoFiles();
+
+ void CloseAnnoFiles();
+
+ bool FindOneOrMoreOverlap(const BED &a, BedFile *bedFile);
+};
+#endif /* TAGBAM_H */
diff --git a/src/tagBam/tagBamMain.cpp b/src/tagBam/tagBamMain.cpp
new file mode 100644
index 00000000..f66ae83b
--- /dev/null
+++ b/src/tagBam/tagBamMain.cpp
@@ -0,0 +1,141 @@
+/*****************************************************************************
+ annotateMain.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 "tagBam.h"
+#include "version.h"
+
+using namespace std;
+
+// define the version
+#define PROGRAM_NAME "tagBam"
+
+// define our parameter checking macro
+#define PARAMETER_CHECK(param, paramLen, actualLen) (strncmp(argv[i], param, min(actualLen, paramLen))== 0) && (actualLen == paramLen)
+
+// function declarations
+void ShowHelp(void);
+
+int main(int argc, char* argv[]) {
+
+ // our configuration variables
+ bool showHelp = false;
+
+ // input file
+ string bamFile;
+
+ // parm flags
+ bool forceStrand = false;
+ bool haveBam = false;
+ bool haveFiles = false;
+ bool haveLabels = false;
+
+ // list of annotation files / names
+ vector<string> inputFiles;
+ vector<string> inputLabels;
+
+ // 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) ShowHelp();
+
+ // 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("-i", 2, parameterLength)) {
+ if ((i+1) < argc) {
+ haveBam = true;
+ bamFile = argv[i + 1];
+ i++;
+ }
+ }
+ else if(PARAMETER_CHECK("-files", 6, parameterLength)) {
+ if ((i+1) < argc) {
+ haveFiles = true;
+ i = i+1;
+ string file = argv[i];
+ while (file[0] != '-' && i < argc) {
+ inputFiles.push_back(file);
+ i++;
+ if (i < argc)
+ file = argv[i];
+ }
+ i--;
+ }
+ }
+ else if(PARAMETER_CHECK("-tags", 5, parameterLength)) {
+ if ((i+1) < argc) {
+ haveLabels = true;
+ i = i+1;
+ string label = argv[i];
+ while (label[0] != '-' && i < argc) {
+ inputLabels.push_back(label);
+ i++;
+ if (i < argc)
+ label = argv[i];
+ }
+ i--;
+ }
+ }
+ else if (PARAMETER_CHECK("-s", 2, parameterLength)) {
+ forceStrand = true;
+ }
+ else {
+ cerr << endl << "*****ERROR: Unrecognized parameter: " << argv[i] << " *****" << endl << endl;
+ showHelp = true;
+ }
+ }
+
+ // make sure we have both input files
+ if (!haveBam || !haveFiles || !haveLabels) {
+ cerr << endl << "*****" << endl << "*****ERROR: Need -i, -files, and -labels. " << endl << "*****" << endl;
+ showHelp = true;
+ }
+
+ if (!showHelp) {
+ TagBam *ba = new TagBam(bamFile, inputFiles, inputLabels, forceStrand);
+ ba->Tag();
+ delete ba;
+ return 0;
+ }
+ else {
+ ShowHelp();
+ }
+}
+
+void ShowHelp(void) {
+
+ cerr << endl << "Program: " << PROGRAM_NAME << " (v" << VERSION << ")" << endl;
+
+ cerr << "Author: Aaron Quinlan (aaronquinlan@gmail.com)" << endl;
+
+ cerr << "Summary: Annotates a BAM file based on overlaps with multiple BED/GFF/VCF files" << endl;
+ cerr << "\t on the intervals in -i." << endl << endl;
+
+ cerr << "Usage: " << PROGRAM_NAME << " [OPTIONS] -i <BAM> -files FILE1 FILE2 .. FILEn -labels LAB1 LAB2 ,,, LABn" << endl << endl;
+
+ cerr << "Options: " << endl;
+
+ cerr << "\t-s\t" << "Force strandedness. That is, only tag alignments that have the same" << endl;
+ cerr << "\t\tstrand as a feature in the annotation file(s)." << endl << endl;
+
+ exit(1);
+}
--
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