--- a/BEDTools-Version-2.14.3/src/annotateBed/annotateBed.cpp	Thu Nov 03 10:25:04 2011 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,209 +0,0 @@
-/*****************************************************************************
-  annotateBed.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 "annotateBed.h"
-
-// build
-BedAnnotate::BedAnnotate(const string &mainFile, const vector<string> &annoFileNames,
-            const vector<string> &annoTitles, bool sameStrand, bool diffStrand, bool reportCounts, bool reportBoth) :
-
-    _mainFile(mainFile),
-    _annoFileNames(annoFileNames),
-    _annoTitles(annoTitles),
-    _sameStrand(sameStrand),
-    _diffStrand(diffStrand),
-    _reportCounts(reportCounts),
-    _reportBoth(reportBoth)
-{
-    _bed = new BedFile(_mainFile);
-}
-
-
-// destroy and delete the open file pointers
-BedAnnotate::~BedAnnotate(void) {
-    delete _bed;
-    CloseAnnoFiles();
-}
-
-
-void BedAnnotate::OpenAnnoFiles() {
-    for (size_t i=0; i < _annoFileNames.size(); ++i) {
-        BedFile *file = new BedFile(_annoFileNames[i]);
-        file->Open();
-        _annoFiles.push_back(file);
-    }
-}
-
-
-void BedAnnotate::CloseAnnoFiles() {
-    for (size_t i=0; i < _annoFiles.size(); ++i) {
-        BedFile *file = _annoFiles[i];
-        delete file;
-        _annoFiles[i] = NULL;
-    }
-}
-
-
-void BedAnnotate::PrintHeader() {
-    // print a hash to indicate header and then write a tab
-    // for each field in the main file.
-    printf("#");
-    for (size_t i = 0; i < _bed->bedType; ++i)
-        printf("\t");
-
-    // now print the label for each file.
-    if (_reportBoth == false) {
-        for (size_t i = 0; i < _annoTitles.size(); ++i)
-            printf("%s\t", _annoTitles[i].c_str());
-        printf("\n");
-    }
-    else {
-        for (size_t i = 0; i < _annoTitles.size(); ++i)
-            printf("%s_cnt\t%s_pct", _annoTitles[i].c_str(), _annoTitles[i].c_str());
-        printf("\n");
-    }
-}
-
-
-void BedAnnotate::InitializeMainFile() {
-    // process each chromosome
-    masterBedCovListMap::iterator chromItr = _bed->bedCovListMap.begin();
-    masterBedCovListMap::iterator chromEnd = _bed->bedCovListMap.end();
-    for (; chromItr != chromEnd; ++chromItr) {
-        // for each chrom, process each bin
-        binsToBedCovLists::iterator binItr = chromItr->second.begin();
-        binsToBedCovLists::iterator binEnd = chromItr->second.end();
-        for (; binItr != binEnd; ++binItr) {
-            // initialize BEDCOVLIST in this chrom/bin
-            vector<BEDCOVLIST>::iterator bedItr = binItr->second.begin();
-            vector<BEDCOVLIST>::iterator bedEnd = binItr->second.end();
-            for (; bedItr != bedEnd; ++bedItr) {
-                // initialize the depthMaps, counts, etc. for each anno file.
-                for (size_t i = 0; i < _annoFiles.size(); ++i) {
-                    map<unsigned int, DEPTH> dummy;
-                    bedItr->depthMapList.push_back(dummy);
-                    bedItr->counts.push_back(0);
-                    bedItr->minOverlapStarts.push_back(INT_MAX);
-                }
-            }
-        }
-    }
-}
-
-
-void BedAnnotate::AnnotateBed() {
-
-    // load the "main" bed file into a map so
-    // that we can easily compare each annoFile to it for overlaps
-    _bed->loadBedCovListFileIntoMap();
-    // open the annotations files for processing;
-    OpenAnnoFiles();
-    // initialize counters, depths, etc. for the main file
-    InitializeMainFile();
-
-    // annotate the main file with the coverage from the annotation files.
-    for (size_t annoIndex = 0; annoIndex < _annoFiles.size(); ++annoIndex) {
-        // grab the current annotation file.
-        BedFile *anno = _annoFiles[annoIndex];
-        int lineNum = 0;
-        BED a, nullBed;
-        BedLineStatus bedStatus;
-
-        // process each entry in the current anno file
-        while ((bedStatus = anno->GetNextBed(a, lineNum)) != BED_INVALID) {
-            if (bedStatus == BED_VALID) {
-                _bed->countListHits(a, annoIndex, _sameStrand, _diffStrand);
-                a = nullBed;
-            }
-        }
-    }
-
-    // report the annotations of the main file from the anno file.
-    ReportAnnotations();
-    // close the annotations files;
-    CloseAnnoFiles();
-}
-
-
-void BedAnnotate::ReportAnnotations() {
-
-    if (_annoTitles.size() > 0) {
-        PrintHeader();
-    }
-
-    // process each chromosome
-    masterBedCovListMap::const_iterator chromItr = _bed->bedCovListMap.begin();
-    masterBedCovListMap::const_iterator chromEnd = _bed->bedCovListMap.end();
-    for (; chromItr != chromEnd; ++chromItr) {
-        // for each chrom, process each bin
-        binsToBedCovLists::const_iterator binItr = chromItr->second.begin();
-        binsToBedCovLists::const_iterator binEnd = chromItr->second.end();
-        for (; binItr != binEnd; ++binItr) {
-            // for each chrom & bin, compute and report
-            // the observed coverage for each feature
-            vector<BEDCOVLIST>::const_iterator bedItr = binItr->second.begin();
-            vector<BEDCOVLIST>::const_iterator bedEnd = binItr->second.end();
-            for (; bedItr != bedEnd; ++bedItr) {
-                // print the main BED entry.
-                _bed->reportBedTab(*bedItr);
-
-                // now report the coverage from each annotation file.
-                for (size_t i = 0; i < _annoFiles.size(); ++i) {
-                    unsigned int totalLength = 0;
-                    int zeroDepthCount = 0; // number of bases with zero depth
-                    int depth          = 0; // tracks the depth at the current base
-
-                    // the start is either the first base in the feature OR
-                    // the leftmost position of an overlapping feature. e.g. (s = start):
-                    // A    ----------
-                    // B    s    ------------
-                    int start          = min(bedItr->minOverlapStarts[i], bedItr->start);
-
-                    map<unsigned int, DEPTH>::const_iterator depthItr;
-                    map<unsigned int, DEPTH>::const_iterator depthEnd;
-
-                    // compute the coverage observed at each base in the feature marching from start to end.
-                    for (CHRPOS pos = start+1; pos <= bedItr->end; pos++) {
-                        // map pointer grabbing the starts and ends observed at this position
-                        depthItr = bedItr->depthMapList[i].find(pos);
-                        depthEnd = bedItr->depthMapList[i].end();
-
-                        // increment coverage if starts observed at this position.
-                        if (depthItr != depthEnd)
-                            depth += depthItr->second.starts;
-                        // update zero depth
-                        if ((pos > bedItr->start) && (pos <= bedItr->end) && (depth == 0))
-                            zeroDepthCount++;
-                        // decrement coverage if ends observed at this position.
-                        if (depthItr != depthEnd)
-                            depth = depth - depthItr->second.ends;
-                    }
-                    // Summarize the coverage for the current interval,
-                    CHRPOS length     = bedItr->end - bedItr->start;
-                    totalLength       += length;
-                    int nonZeroBases   = (length - zeroDepthCount);
-                    float fractCovered = (float) nonZeroBases / length;
-                    if (_reportCounts == false && _reportBoth == false)
-                        printf("%f\t", fractCovered);
-                    else if (_reportCounts == true && _reportBoth == false)
-                        printf("%d\t", bedItr->counts[i]);
-                    else if (_reportCounts == false && _reportBoth == true)
-                        printf("%d\t%f\t", bedItr->counts[i], fractCovered);
-                }
-                // print newline for next feature.
-                printf("\n");
-            }
-        }
-    }
-}
-
-