--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/BEDTools-Version-2.14.3/src/sortBed/sortBed.cpp	Thu Nov 03 10:25:04 2011 -0400
@@ -0,0 +1,201 @@
+/*****************************************************************************
+  sortBed.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 "sortBed.h"
+
+//
+// Constructor
+//
+BedSort::BedSort(string &bedFile) {
+    _bedFile = bedFile;
+    _bed = new BedFile(bedFile);
+}
+
+//
+// Destructor
+//
+BedSort::~BedSort(void) {
+}
+
+
+void BedSort::SortBed() {
+
+    // load the "B" bed file into a map so
+    // that we can easily compare "A" to it for overlaps
+    _bed->loadBedFileIntoMapNoBin();
+
+    // loop through each chromosome and merge their BED entries
+    for (masterBedMapNoBin::iterator m = _bed->bedMapNoBin.begin(); m != _bed->bedMapNoBin.end(); ++m) {
+
+        // bedList is already sorted by start position.
+        vector<BED> bedList = m->second;
+
+        for (unsigned int i = 0; i < bedList.size(); ++i) {
+            _bed->reportBedNewLine(bedList[i]);
+        }
+    }
+}
+
+
+void BedSort::SortBedBySizeAsc() {
+
+    // load the "B" bed file into a map so
+    // that we can easily compare "A" to it for overlaps
+    _bed->loadBedFileIntoMapNoBin();
+
+    vector<BED> masterList;
+    masterList.reserve(1000000);
+
+    // loop through each chromosome and merge their BED entries
+    for (masterBedMapNoBin::iterator m = _bed->bedMapNoBin.begin(); m != _bed->bedMapNoBin.end(); ++m) {
+
+        // bedList is already sorted by start position.
+        vector<BED> bedList = m->second;
+
+        // add the entries from this chromosome to the current list
+        for (unsigned int i = 0; i < m->second.size(); ++i) {
+            masterList.push_back(m->second[i]);
+        }
+    }
+
+    // sort the master list by size (asc.)
+    sort(masterList.begin(), masterList.end(), sortBySizeAsc);
+
+    // report the entries in ascending order
+    for (unsigned int i = 0; i < masterList.size(); ++i) {
+        _bed->reportBedNewLine(masterList[i]);
+    }
+}
+
+
+void BedSort::SortBedBySizeDesc() {
+
+    // load the "B" bed file into a map so
+    // that we can easily compare "A" to it for overlaps
+    _bed->loadBedFileIntoMapNoBin();
+
+    vector<BED> masterList;
+    masterList.reserve(1000000);
+
+    // loop through each chromosome and merge their BED entries
+    for (masterBedMapNoBin::iterator m = _bed->bedMapNoBin.begin(); m != _bed->bedMapNoBin.end(); ++m) {
+
+        // bedList is already sorted by start position.
+        vector<BED> bedList = m->second;
+
+        // add the entries from this chromosome to the current list
+        for (unsigned int i = 0; i < m->second.size(); ++i) {
+            masterList.push_back(m->second[i]);
+        }
+    }
+
+    // sort the master list by size (asc.)
+    sort(masterList.begin(), masterList.end(), sortBySizeDesc);
+
+    // report the entries in ascending order
+    for (unsigned int i = 0; i < masterList.size(); ++i) {
+        _bed->reportBedNewLine(masterList[i]);
+    }
+}
+
+void BedSort::SortBedByChromThenSizeAsc() {
+
+    // load the "B" bed file into a map so
+    // that we can easily compare "A" to it for overlaps
+    _bed->loadBedFileIntoMapNoBin();
+
+    // loop through each chromosome and merge their BED entries
+    for (masterBedMapNoBin::iterator m = _bed->bedMapNoBin.begin(); m != _bed->bedMapNoBin.end(); ++m) {
+
+        // bedList is already sorted by start position.
+        vector<BED> bedList = m->second;
+        sort(bedList.begin(), bedList.end(), sortBySizeAsc);
+
+        for (unsigned int i = 0; i < bedList.size(); ++i) {
+            _bed->reportBedNewLine(bedList[i]);
+        }
+    }
+}
+
+
+void BedSort::SortBedByChromThenSizeDesc() {
+
+    // load the "B" bed file into a map so
+    // that we can easily compare "A" to it for overlaps
+    _bed->loadBedFileIntoMapNoBin();
+
+    // loop through each chromosome and merge their BED entries
+    for (masterBedMapNoBin::iterator m = _bed->bedMapNoBin.begin(); m != _bed->bedMapNoBin.end(); ++m) {
+
+        // bedList is already sorted by start position.
+        vector<BED> bedList = m->second;
+
+        sort(bedList.begin(), bedList.end(), sortBySizeDesc);
+
+        for (unsigned int i = 0; i < bedList.size(); ++i) {
+            _bed->reportBedNewLine(bedList[i]);
+        }
+    }
+}
+
+
+void BedSort::SortBedByChromThenScoreAsc() {
+
+    // load the "B" bed file into a map so
+    // that we can easily compare "A" to it for overlaps
+    _bed->loadBedFileIntoMapNoBin();
+
+    if (_bed->bedType >= 5) {
+        // loop through each chromosome and merge their BED entries
+        for (masterBedMapNoBin::iterator m = _bed->bedMapNoBin.begin(); m != _bed->bedMapNoBin.end(); ++m) {
+
+            // bedList is already sorted by start position.
+            vector<BED> bedList = m->second;
+            sort(bedList.begin(), bedList.end(), sortByScoreAsc);
+
+            for (unsigned int i = 0; i < bedList.size(); ++i) {
+                _bed->reportBedNewLine(bedList[i]);
+            }
+        }
+    }
+    else {
+        cerr << "Error: Requested a sort by score, but your BED file does not appear to be in BED 5 format or greater.  Exiting." << endl;
+        exit(1);
+    }
+}
+
+
+void BedSort::SortBedByChromThenScoreDesc() {
+
+    // load the "B" bed file into a map so
+    // that we can easily compare "A" to it for overlaps
+    _bed->loadBedFileIntoMapNoBin();
+
+    if (_bed->bedType >= 5) {
+        // loop through each chromosome and merge their BED entries
+        for (masterBedMapNoBin::iterator m = _bed->bedMapNoBin.begin(); m != _bed->bedMapNoBin.end(); ++m) {
+
+            // bedList is already sorted by start position.
+            vector<BED> bedList = m->second;
+            sort(bedList.begin(), bedList.end(), sortByScoreDesc);
+
+            for (unsigned int i = 0; i < bedList.size(); ++i) {
+                _bed->reportBedNewLine(bedList[i]);
+            }
+        }
+    }
+    else {
+        cerr << "Error: Requested a sort by score, but your BED file does not appear to be in BED 5 format or greater.  Exiting." << endl;
+        exit(1);
+    }
+}
+