# HG changeset patch
# User greg
# Date 1458305302 14400
# Node ID 147e2974b7110c8784bc673a531ff11bf9ac120d

Uploaded

diff -r 000000000000 -r 147e2974b711 TagPileup.jar
Binary file TagPileup.jar has changed
diff -r 000000000000 -r 147e2974b711 src/PileupObjects/BEDCoord.java
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/src/PileupObjects/BEDCoord.java	Fri Mar 18 08:48:22 2016 -0400
@@ -0,0 +1,138 @@
+package PileupObjects;
+
+import java.util.Comparator;
+
+public class BEDCoord {
+        private String CHROM = "";
+        private int START = 0;
+        private int STOP = 0;
+        private String DIR = "+";
+        
+        private String NAME = ".";
+        private double SCORE = 0;
+
+        private double[] Fstrand = null;
+        private double[] Rstrand = null;
+        
+        private boolean VALIDCHROM = true;
+        
+        public BEDCoord() {
+                
+        }
+        
+        public BEDCoord(String c, int sta, int sto, String di, String na) {
+                CHROM = c;
+                START = sta;
+                STOP = sto;
+                DIR = di;
+                NAME = na;
+        }
+        
+        public BEDCoord(String na, double sco) {
+                NAME = na;
+                SCORE = sco;
+        }
+        
+        public boolean getStatus() {
+                return VALIDCHROM;
+        }
+        
+        public void setStatus(boolean stat) {
+                VALIDCHROM = stat;
+        }
+        
+        public double[] getFStrand() {
+                return Fstrand;
+        }
+        
+        public double[] getRStrand() {
+                return Rstrand;
+        }
+        
+        public void setFstrand(double[] f) {
+                Fstrand = f;
+        }
+        
+        public void setRstrand(double[] r) {
+                Rstrand = r;
+        }
+        
+        public String getChrom() {
+                return CHROM;
+        }
+        
+        public void setChrom(String chr) {
+                CHROM = chr;
+        }
+        
+        public int getStart() {
+                return START;
+        }
+        
+        public void setStart(int sta) {
+                START = sta;
+        }
+        
+        public int getStop() {
+                return STOP;
+        }
+        
+        public void setStop(int sto) {
+                STOP = sto;
+        }
+        
+        public String getDir() {
+                return DIR;
+        }
+        
+        public void setDir(String di) {
+                DIR = di;
+        }
+        
+        public String getName() {
+                return NAME;
+        }
+        
+        public void setName(String na) {
+                NAME = na;
+        }
+        
+        public double getScore() {
+                return SCORE;
+        }
+        
+        public void setScore(double sco) {
+                SCORE = sco;
+        }
+        
+        public String toString() {
+                String line = CHROM + "\t" + START + "\t" + STOP + "\t" + NAME + "\t" + SCORE + "\t" + DIR;
+                return line;
+        }
+        
+        public static Comparator<BEDCoord> PeakChromComparator = new Comparator<BEDCoord>() {
+                public int compare(BEDCoord node1, BEDCoord node2) {
+                        return node1.getChrom().compareTo(node2.getChrom());
+        }
+        };
+                
+        public static Comparator<BEDCoord> PeakPositionComparator = new Comparator<BEDCoord>() {
+                public int compare(BEDCoord node1, BEDCoord node2) {
+                        int PeakStart1 = node1.getStart();
+                        int PeakStart2 = node2.getStart();
+                        if (PeakStart1 > PeakStart2) return 1;
+                        else if (PeakStart1 < PeakStart2) return -1;
+                        else return 0;
+        }
+        };
+        
+        public static Comparator<BEDCoord> ScoreComparator = new Comparator<BEDCoord>() {
+                public int compare(BEDCoord node1, BEDCoord node2) {
+                        double PeakStart1 = node1.getScore();
+                        double PeakStart2 = node2.getScore();
+                        if (PeakStart1 < PeakStart2) return 1;
+                        else if (PeakStart1 > PeakStart2) return -1;
+                        else return 0;
+        }
+        };
+}
diff -r 000000000000 -r 147e2974b711 src/PileupObjects/PileupParameters.java
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/src/PileupObjects/PileupParameters.java	Fri Mar 18 08:48:22 2016 -0400
@@ -0,0 +1,193 @@
+package PileupObjects;
+
+import java.awt.Color;
+import java.io.File;
+import java.util.ArrayList;
+
+public class PileupParameters {
+        private File OUTPUT = null;
+        private String COMPOSITE = null;
+        private int READ = 0;
+        private int STRAND = 0;
+        private int TRANS = 0;
+        private int SHIFT = 0;
+        private int BIN = 1;
+        private int SMOOTH = 0;
+        private int STDSIZE = 0;
+        private int STDNUM = 0;
+        private int CPU = 1;
+        private int OUTTYPE = 0;
+        private boolean STANDARD = false;
+        private boolean outputCOMPOSITE = false;
+        private boolean requirePE = false;
+        private double STANDRATIO = 1;
+        
+        private Color Sense = null;
+        private Color Anti = null;
+        private Color Combined = null;
+        
+        public PileupParameters() {
+                
+        }
+
+        public boolean getPErequire() {
+                return requirePE;
+        }
+        
+        public void setPErequire(boolean status) {
+                requirePE = status;
+        }
+        
+        public String getCompositeFile() {
+                return COMPOSITE;
+        }
+        
+        public void setCompositeFile(String comp) {
+                COMPOSITE = comp;
+        }
+        
+        public boolean getOutputCompositeStatus() {
+                return outputCOMPOSITE;
+        }
+        
+        public void setOutputCompositeStatus(boolean out) {
+                outputCOMPOSITE = out;
+        }
+        
+        public ArrayList<Color> getColors() {
+                ArrayList<Color> ALL = new ArrayList<Color>();
+                if(Sense != null) ALL.add(Sense);
+                if(Anti != null) ALL.add(Anti);
+                if(Combined != null) ALL.add(Combined);
+                return ALL;
+        }
+        
+        public void setSenseColor(Color s) {
+                Sense = s;
+        }
+        
+        public Color getSenseColor() {
+                return Sense;
+        }
+        
+        public void setAntiColor(Color a) {
+                Anti = a;
+        }
+        
+        public Color getAntiColor() {
+                return Anti;
+        }
+        
+        public void setCombinedColor(Color c) {
+                Combined = c;
+        }
+        
+        public Color getCombinedColor() {
+                return Combined;
+        }
+        
+        public void setRatio(double rat) {
+                STANDRATIO = rat;
+        }
+        
+        public double getRatio() {
+                return STANDRATIO;
+        }
+        
+        public void setStandard(boolean stand) {
+                STANDARD = stand;
+        }
+        
+        public boolean getStandard() {
+                return STANDARD;
+        }
+
+        public void setOutputType(int newtype) {
+                OUTTYPE = newtype;
+        }
+        
+        public int getOutputType() {
+                return OUTTYPE;
+        }
+        
+        public File getOutput() {
+                return OUTPUT;
+        }
+
+        public void setOutput(File oUTPUT) {
+                OUTPUT = oUTPUT;
+        }
+
+        public int getRead() {
+                return READ;
+        }
+
+        public void setRead(int rEAD) {
+                READ = rEAD;
+        }
+
+        public int getStrand() {
+                return STRAND;
+        }
+
+        public void setStrand(int sTRAND) {
+                STRAND = sTRAND;
+        }
+
+        public int getTrans() {
+                return TRANS;
+        }
+
+        public void setTrans(int tRANS) {
+                TRANS = tRANS;
+        }
+
+        public int getShift() {
+                return SHIFT;
+        }
+
+        public void setShift(int sHIFT) {
+                SHIFT = sHIFT;
+        }
+
+        public int getBin() {
+                return BIN;
+        }
+
+        public void setBin(int bIN) {
+                BIN = bIN;
+        }
+
+        public int getSmooth() {
+                return SMOOTH;
+        }
+
+        public void setSmooth(int sMOOTH) {
+                SMOOTH = sMOOTH;
+        }
+
+        public int getStdSize() {
+                return STDSIZE;
+        }
+
+        public void setStdSize(int sTDSIZE) {
+                STDSIZE = sTDSIZE;
+        }
+
+        public int getStdNum() {
+                return STDNUM;
+        }
+
+        public void setStdNum(int sTDNUM) {
+                STDNUM = sTDNUM;
+        }
+
+        public int getCPU() {
+                return CPU;
+        }
+
+        public void setCPU(int cPU) {
+                CPU = cPU;
+        }
+        
+}
diff -r 000000000000 -r 147e2974b711 src/PileupScripts/BAMUtilities.java
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/src/PileupScripts/BAMUtilities.java	Fri Mar 18 08:48:22 2016 -0400
@@ -0,0 +1,42 @@
+package PileupScripts;
+
+import java.io.File;
+import java.io.IOException;
+
+import htsjdk.samtools.AbstractBAMFileIndex;
+import htsjdk.samtools.SAMRecord;
+import htsjdk.samtools.SAMSequenceRecord;
+import htsjdk.samtools.SamReader;
+import htsjdk.samtools.SamReaderFactory;
+import htsjdk.samtools.util.CloseableIterator;
+
+public class BAMUtilities {
+        public static double calculateStandardizationRatio(File BAM) throws IOException {
+                SamReader inputSam = SamReaderFactory.makeDefault().open(BAM);
+                AbstractBAMFileIndex bai = (AbstractBAMFileIndex) inputSam.indexing().getIndex();
+                double counter = 0;
+                double totalAligned = 0;
+                double totalGenome = 0;
+                
+                for (int x = 0; x < bai.getNumberOfReferences(); x++) {
+                        SAMSequenceRecord seq = inputSam.getFileHeader().getSequence(x);
+                        totalAligned += inputSam.indexing().getIndex().getMetaData(x).getAlignedRecordCount();
+                        totalGenome += seq.getSequenceLength();
+                }
+                CloseableIterator<SAMRecord> iter = inputSam.iterator();
+                while (iter.hasNext()) {
+                        SAMRecord sr = iter.next();
+                        if(sr.getReadPairedFlag()) {
+                                if(sr.getSecondOfPairFlag()) { counter++; } //count read 2 to remove from aligned reads
+                        }
+                }
+                inputSam.close();
+                bai.close();
+                iter.close();
+                                
+                totalAligned -= counter;
+                if(totalAligned > 0) { return (totalAligned / totalGenome); }
+                else { return 1; }
+        }
+        
+}
diff -r 000000000000 -r 147e2974b711 src/PileupScripts/PileupExtract.java
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/src/PileupScripts/PileupExtract.java	Fri Mar 18 08:48:22 2016 -0400
@@ -0,0 +1,160 @@
+package PileupScripts;
+
+import htsjdk.samtools.SAMRecord;
+import htsjdk.samtools.SamReader;
+import htsjdk.samtools.SamReaderFactory;
+import htsjdk.samtools.util.CloseableIterator;
+
+import java.io.File;
+import java.util.Vector;
+
+import PileupObjects.BEDCoord;
+import PileupObjects.PileupParameters;
+
+public class PileupExtract implements Runnable{
+        PileupParameters param;
+        File BAM;
+        Vector<BEDCoord> INPUT;
+        int index;
+        int subsetsize;
+        SamReader inputSam;
+                
+        public void run() {
+                inputSam = SamReaderFactory.makeDefault().open(BAM);
+                for(int x = index; x < index + subsetsize; x++) {
+                        if(INPUT.get(x).getStatus()) { extract(INPUT.get(x)); }                
+                }
+        }
+        
+        public PileupExtract(PileupParameters p, File b, Vector<BEDCoord> i, int current, int length) {
+                param = p;
+                BAM = b;
+                INPUT = i;
+                index = current;
+                subsetsize = length;
+        }
+        
+        public void extract(BEDCoord read) {
+                double[] TAG_S1 = null;
+                double[] TAG_S2 = null;
+                int SHIFT = param.getShift();
+                int STRAND = param.getStrand();
+                
+                int BEDSTART = read.getStart();
+                int BEDSTOP = read.getStop();
+                //Correct for '-' strand BED coord so they align with '+' strand
+                if(read.getDir().equals("-")) {
+                        BEDSTART++;
+                        BEDSTOP++;
+                }
+                
+                //Correct Window Size for proper transformations
+                int WINDOW = (BEDSTOP - BEDSTART) + ((param.getBin() / 2) * 2);
+                int QUERYWINDOW = 0;
+                if(param.getTrans() == 1) {
+                        WINDOW = (BEDSTOP - BEDSTART) + (param.getBin() * param.getSmooth() * 2);
+                        QUERYWINDOW = (param.getBin() * param.getSmooth()); 
+                }
+                else if(param.getTrans() == 2) {
+                        WINDOW = (BEDSTOP - BEDSTART) + (param.getBin() * param.getStdSize() * param.getStdNum() * 2);
+                        QUERYWINDOW = (param.getBin() * param.getStdSize() * param.getStdNum()); 
+                }
+                TAG_S1 = new double[WINDOW];
+                if(STRAND == 0) TAG_S2 = new double[WINDOW];
+                
+                //SAMRecords are 1-based
+                CloseableIterator<SAMRecord> iter = inputSam.query(read.getChrom(), BEDSTART - QUERYWINDOW - SHIFT - 1, BEDSTOP + QUERYWINDOW + SHIFT + 1, false);
+                while (iter.hasNext()) {
+                        //Create the record object 
+                    //SAMRecord is 1-based
+                        SAMRecord sr = iter.next();
+                        
+                        //Must be PAIRED-END mapped, mate must be mapped, must be read1
+                        if(sr.getReadPairedFlag()) {
+                                if((sr.getProperPairFlag() && param.getPErequire()) || !param.getPErequire()) {
+                                        if((sr.getFirstOfPairFlag() && param.getRead() == 0) || (!sr.getFirstOfPairFlag() && param.getRead() == 1) || param.getRead() == 2) {
+                                                int FivePrime = sr.getUnclippedStart() - 1;
+                                                if(sr.getReadNegativeStrandFlag()) { 
+                                                        FivePrime = sr.getUnclippedEnd();
+                                                        FivePrime -= SHIFT; //SHIFT DATA HERE IF NECCESSARY
+                                                } else { FivePrime += SHIFT; }
+                                                FivePrime -= (BEDSTART - QUERYWINDOW);
+                                                
+                            //Increment Final Array keeping track of pileup
+                                                if(FivePrime >= 0 && FivePrime < TAG_S1.length) {
+                                                        if(STRAND == 0) {
+                                                                if(!sr.getReadNegativeStrandFlag() && read.getDir().equals("-")) { TAG_S2[FivePrime] += 1; }
+                                                        else if(sr.getReadNegativeStrandFlag() && read.getDir().equals("+")) { TAG_S2[FivePrime] += 1; }
+                                                        else if(!sr.getReadNegativeStrandFlag() && read.getDir().equals("+")) { TAG_S1[FivePrime] += 1; }
+                                                        else if(sr.getReadNegativeStrandFlag() && read.getDir().equals("-")) { TAG_S1[FivePrime] += 1;}
+                                                        } else {
+                                                                TAG_S1[FivePrime] += 1;
+                                                        }
+                                                }
+                                        }
+                                }
+                        } else if(param.getRead() == 0 || param.getRead() == 2) {
+                                //Also outputs if not paired-end since by default it is read-1
+                                int FivePrime = sr.getUnclippedStart() - 1;
+                                if(sr.getReadNegativeStrandFlag()) { 
+                                        FivePrime = sr.getUnclippedEnd();
+                                        FivePrime -= SHIFT; //SHIFT DATA HERE IF NECCESSARY
+                                } else { FivePrime += SHIFT; }
+                                FivePrime -= (BEDSTART - QUERYWINDOW);
+                                
+                                //Increment Final Array keeping track of pileup
+                                if(FivePrime >= 0 && FivePrime < TAG_S1.length) {
+                                        if(STRAND == 0) {
+                                                if(!sr.getReadNegativeStrandFlag() && read.getDir().equals("-")) { TAG_S2[FivePrime] += 1; }
+                                                else if(sr.getReadNegativeStrandFlag() && read.getDir().equals("+")) { TAG_S2[FivePrime] += 1; }
+                                                else if(!sr.getReadNegativeStrandFlag() && read.getDir().equals("+")) { TAG_S1[FivePrime] += 1; }
+                                                else if(sr.getReadNegativeStrandFlag() && read.getDir().equals("-")) { TAG_S1[FivePrime] += 1;}
+                                        } else {
+                                                TAG_S1[FivePrime] += 1;
+                                        }
+                                }
+                        }
+                }
+                iter.close();
+                
+                if(read.getDir().equals("-")) {
+                        TAG_S1 = TransformArray.reverseTran(TAG_S1);
+                        TAG_S2 = TransformArray.reverseTran(TAG_S2);
+                }
+                
+                //Perform Binning here
+                double[] binF = new double[TAG_S1.length];
+                double[] binR = null;
+                if(TAG_S2 != null) binR = new double[TAG_S2.length]; 
+                
+                for(int j = 0; j < TAG_S1.length; j++) {
+                        for(int k = j - (param.getBin() / 2); k <= j + (param.getBin() / 2); k++) {
+                                if(k < 0) k = 0;
+                                if(k >= TAG_S1.length) k = j + (param.getBin() / 2) + 1;
+                                else  {
+                                        binF[k] += TAG_S1[j];
+                                        if(binR != null) binR[k] += TAG_S2[j];
+                                }
+                        }
+                }
+                double[] finalF = new double[TAG_S1.length / param.getBin()];
+                double[] finalR = null;
+                if(TAG_S2 != null) finalR = new double[TAG_S2.length / param.getBin()];
+                
+                for(int x = (param.getBin() / 2); x < TAG_S1.length - (param.getBin() / 2); x += param.getBin()) {
+                        finalF[(x - (param.getBin() / 2)) / param.getBin()] = TAG_S1[x];
+                        if(TAG_S2 != null) finalR[(x - (param.getBin() / 2)) / param.getBin()] = TAG_S2[x];
+                }
+                
+                //Perform Tag Standardization Here
+                if(param.getStandard()) {
+                        for(int i = 0; i < finalF.length; i++) {
+                                if(finalF != null) finalF[i] /= param.getRatio();
+                                if(finalR != null) finalR[i] /= param.getRatio();
+                        }
+                }
+                
+                read.setFstrand(finalF);
+                read.setRstrand(finalR);
+        }
+}
diff -r 000000000000 -r 147e2974b711 src/PileupScripts/TransformArray.java
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/src/PileupScripts/TransformArray.java	Fri Mar 18 08:48:22 2016 -0400
@@ -0,0 +1,53 @@
+package PileupScripts;
+
+public class TransformArray {
+        
+        public static double[] reverseTran(double[] orig) {
+                if(orig != null) {
+                        double[] reverse = new double[orig.length];                
+                        for(int x = orig.length - 1; x >= 0; x--) {
+                                reverse[orig.length - 1 - x] = orig[x];
+                        }
+                        return reverse;
+                }
+                return null;
+        }
+        
+        public static double[] smoothTran(double[] orig, int win) {
+                int window = win / 2;
+                double[] Sarray = new double[orig.length];
+                for(int x = 0; x < orig.length; x++) {
+                        double score = 0;
+                        double weight = 0;
+                        for(int y = x - window; y <= x + window; y++) {
+                                if(y < 0) y = -1;
+                                else if(y < orig.length) {
+                                        score += orig[y];
+                                        weight++;
+                                } else y = x + window + 1;
+                        }
+                        if(weight != 0) Sarray[x] = score / weight;
+                }
+                return Sarray;
+        }
+        
+        public static double[] gaussTran(double[] orig, int size, int num) {
+                double[] Garray = new double[orig.length];
+                int window = size * num;
+                double SDSize = (double)size;
+                for(int x = 0; x < orig.length; x++) {
+                 double score = 0;
+                 double weight = 0;
+                 for(int y = x - window; y <= x + window; y++) {
+                        if(y < 0) y = -1;
+                        else if(y < orig.length) {
+                                double HEIGHT = Math.exp(-1 * Math.pow((y - x), 2) / (2 * Math.pow(SDSize, 2)));
+                                score += (HEIGHT * orig[y]);
+                                weight += HEIGHT;
+                        } else y = x + window + 1;
+                 }
+                 if(weight != 0) Garray[x] = score / weight;
+                }
+                return Garray;
+         }
+}
diff -r 000000000000 -r 147e2974b711 src/TagPileup.java
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/src/TagPileup.java	Fri Mar 18 08:48:22 2016 -0400
@@ -0,0 +1,508 @@
+import java.awt.Color;
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.IOException;
+import java.io.PrintStream;
+import java.sql.Timestamp;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Date;
+import java.util.Scanner;
+import java.util.Vector;
+import java.util.concurrent.ExecutorService;
+import java.util.concurrent.Executors;
+
+import PileupObjects.BEDCoord;
+import PileupObjects.PileupParameters;
+import PileupScripts.BAMUtilities;
+import PileupScripts.PileupExtract;
+import PileupScripts.TransformArray;
+import htsjdk.samtools.AbstractBAMFileIndex;
+import htsjdk.samtools.SamReader;
+import htsjdk.samtools.SamReaderFactory;
+
+public class TagPileup {
+        //Global Transformations
+        private static boolean TAGSEQUAL = false; //set tags to be equal
+        private static int SHIFT = 0; //shift from 5' to 3'
+        private static int BINSIZE = 1; //bin tags, useful for mammalian or larger windows
+        
+        //Composite Transformations
+        private static int SMOOTHWINDOW = 0;
+        
+        //Read parameters
+        private static int STRAND = 0; //0 - strand sep, 1 - strand combined
+        private static int READ = 0; //0 - read 1, 1 - read 2, 2 - combined
+        private static boolean PE_STATUS = false; //require read 1 and 2 to be properly paired
+        
+        //Run parameters
+        private static int CPU = 1;
+        private static boolean OUTPUT_HEATMAP = true;
+        private static boolean OUTPUT_COMP = true;
+        
+        private static File BAM = null;
+        private static File BAI = null;
+        private static File BED = null;
+        private static Vector<BEDCoord> INPUT = null;
+        
+        private static String HPATH = null;
+        private static String CNAME = null;
+        private static PileupParameters PARAM = null;
+        private static PrintStream COMPOSITE = null;
+        private static PrintStream OUT_S1 = null;
+        private static PrintStream OUT_S2 = null;
+        
+        public static void main(String[] args) throws IOException {
+                loadConfig(args);
+
+                System.out.println("\n" + getTimeStamp() + "\nLoading BED Coordinates..");
+                INPUT = loadCoord(BED);
+                System.out.println("BED Coordinates Loaded\n" + getTimeStamp());
+                
+                //Validate BED coordinates exist in BAM file
+                validateBED();
+                
+                System.out.println("\n" + getTimeStamp() + "\nParsing Tags...");
+                run();
+                System.out.println("Tags Parsed\n" + getTimeStamp());
+        }
+        
+        //Get size of largest array for composite generation
+        public static int getMaxBEDSize(Vector<BEDCoord> sites) {
+                int maxSize = 0;
+                for(int x = 0; x < sites.size(); x++) {
+                        int SIZE = sites.get(x).getFStrand().length;
+                        if(SIZE > maxSize) {
+                                maxSize = SIZE;
+                        }
+                }
+                return maxSize;
+        }
+        
+        //Validate BED coordinates exist within BAM file and satisfy BED format
+        public static void validateBED() throws IOException {
+                //Get chromosome IDs
+                SamReader inputSam = SamReaderFactory.makeDefault().open(BAM);
+                AbstractBAMFileIndex bai = (AbstractBAMFileIndex) inputSam.indexing().getIndex();
+                ArrayList<String> chrom = new ArrayList<String>();
+                for(int x = 0; x < bai.getNumberOfReferences(); x++) {
+                        chrom.add(inputSam.getFileHeader().getSequence(x).getSequenceName());
+                }
+                inputSam.close();
+                bai.close();
+                
+                ArrayList<Integer> indexFail = new ArrayList<Integer>();
+                int FAILcount = 0;
+                for(int x = 0; x < INPUT.size(); x++) {
+                        //check for existence of chromosome in BAM file
+                        if(!chrom.contains(INPUT.get(x).getChrom())) {
+                                INPUT.get(x).setStatus(false);
+                                indexFail.add(new Integer(x));
+                                FAILcount++;
+                        }
+                        //check that the start is smaller than the stop
+                        if(INPUT.get(x).getStart() > INPUT.get(x).getStop()) {
+                                INPUT.get(x).setStatus(false);
+                                indexFail.add(new Integer(x));
+                                FAILcount++;
+                        }
+                }
+                if(FAILcount == INPUT.size()) {
+                        System.err.println("No BED Coordinates exist within BAM file!!!");
+                        printUsage();
+                        System.exit(1);
+                }
+                //Remove failed indexes to more efficiently use CPUs
+                for(int x = indexFail.size() - 1; x >= 0; x--) {
+                        INPUT.remove(indexFail.get(x).intValue());
+                }
+        }
+        
+        public static void run() throws IOException {
+                if(PARAM.getOutputCompositeStatus()) {
+                        try { 
+                                if(CNAME != null) { COMPOSITE = new PrintStream(CNAME); }
+                                else { COMPOSITE = new PrintStream("composite.out"); }
+                        } catch (FileNotFoundException e) {        e.printStackTrace(); }
+                }
+                
+                //Code to standardize tags sequenced to genome size (1 tag / 1 bp)
+                if(PARAM.getStandard()) { PARAM.setRatio(BAMUtilities.calculateStandardizationRatio(BAM)); }
+                                                        
+                        if(PARAM.getOutputType() != 0) {
+                                if(STRAND == 0) {
+                                        try {
+                                                if(HPATH != null) {
+                                                        OUT_S1 = new PrintStream(HPATH + File.separator + generateFileName(BED.getName(), BAM.getName(), 0));
+                                                        OUT_S2 = new PrintStream(HPATH + File.separator + generateFileName(BED.getName(), BAM.getName(), 1));
+                                                } else {
+                                                        OUT_S1 = new PrintStream(generateFileName(BED.getName(), BAM.getName(), 0));
+                                                        OUT_S2 = new PrintStream(generateFileName(BED.getName(), BAM.getName(), 1));
+                                                }                                                
+                                        } catch (FileNotFoundException e) {        e.printStackTrace(); }
+                                } else {
+                                        try {
+                                                if(HPATH != null) { OUT_S1 = new PrintStream(HPATH + File.separator + generateFileName(BED.getName(), BAM.getName(), 2)); }
+                                                else { OUT_S1 = new PrintStream(generateFileName(BED.getName(), BAM.getName(), 2)); }
+                                        } catch (FileNotFoundException e) {        e.printStackTrace(); }
+                                }
+                        }
+                                        
+                        //Split up job and send out to threads to process                                
+                        ExecutorService parseMaster = Executors.newFixedThreadPool(CPU);
+                        if(INPUT.size() < CPU) CPU = INPUT.size();
+                        int subset = 0;
+                        int currentindex = 0;
+                        for(int x = 0; x < CPU; x++) {
+                                currentindex += subset;
+                                if(CPU == 1) subset = INPUT.size();
+                                else if(INPUT.size() % CPU == 0) subset = INPUT.size() / CPU;
+                                else {
+                                        int remainder = INPUT.size() % CPU;
+                                        if(x < remainder ) subset = (int)(((double)INPUT.size() / (double)CPU) + 1);
+                                        else subset = (int)(((double)INPUT.size() / (double)CPU));
+                                }
+                                PileupExtract extract = new PileupExtract(PARAM, BAM, INPUT, currentindex, subset);
+                                parseMaster.execute(extract);
+                        }
+                        parseMaster.shutdown();
+                        while (!parseMaster.isTerminated()) {
+                        }
+                                        
+                        //double[] AVG_S1 = new double[INPUT.get(0).getFStrand().length];
+                        double[] AVG_S1 = new double[getMaxBEDSize(INPUT)];
+                        double[] AVG_S2 = null;
+                        if(STRAND == 0) AVG_S2 = new double[AVG_S1.length];
+                        double[] DOMAIN = new double[AVG_S1.length];
+        
+                        //Account for the shifted oversized window produced by binning and smoothing
+                        int OUTSTART = 0;
+                        if(PARAM.getTrans() == 1) { OUTSTART = PARAM.getSmooth(); }
+                        else if(PARAM.getTrans() == 2) { OUTSTART = (PARAM.getStdSize() * PARAM.getStdNum()); }
+                                                                        
+                        if(PARAM.getOutputType() == 2) {
+                                if(OUT_S1 != null) OUT_S1.print("YORF\tNAME");
+                                if(OUT_S2 != null) OUT_S2.print("YORF\tNAME");
+                                                                                        
+                                for(int i = OUTSTART; i < AVG_S1.length - OUTSTART; i++) {
+                                        int index = i - OUTSTART;
+                                        if(OUT_S1 != null) OUT_S1.print("\t" + index);
+                                        if(OUT_S2 != null) OUT_S2.print("\t" + index);
+                                }
+                                if(OUT_S1 != null) OUT_S1.println();
+                                if(OUT_S2 != null) OUT_S2.println();
+                        }
+                                        
+                        //Output individual sites
+                        for(int i = 0; i < INPUT.size(); i++) {
+                                double[] tempF = INPUT.get(i).getFStrand();
+                                double[] tempR = INPUT.get(i).getRStrand();
+                                if(OUT_S1 != null) OUT_S1.print(INPUT.get(i).getName());
+                                if(OUT_S2 != null) OUT_S2.print(INPUT.get(i).getName());
+                                
+                                if(PARAM.getOutputType() == 2) {
+                                        if(OUT_S1 != null) OUT_S1.print("\t" + INPUT.get(i).getName());
+                                        if(OUT_S2 != null) OUT_S2.print("\t" + INPUT.get(i).getName());
+                                }
+                                
+                                for(int j = 0; j < tempF.length; j++) {
+                                        if(j >= OUTSTART && j < tempF.length - OUTSTART) {
+                                                if(OUT_S1 != null) OUT_S1.print("\t" + tempF[j]);
+                                                if(OUT_S2 != null) OUT_S2.print("\t" + tempR[j]);
+                                        }
+                                        AVG_S1[j] += tempF[j];
+                                        if(AVG_S2 != null) AVG_S2[j] += tempR[j];
+                                }
+                                if(OUT_S1 != null) OUT_S1.println();
+                                if(OUT_S2 != null) OUT_S2.println();
+                        }
+        
+                        //Calculate average and domain here
+                        int temp = (int) (((double)AVG_S1.length / 2.0) + 0.5);
+                        for(int i = 0; i < AVG_S1.length; i++) {
+                                DOMAIN[i] = (double)((temp - (AVG_S1.length - i)) * PARAM.getBin()) + 1;
+                                AVG_S1[i] /= INPUT.size();
+                                if(AVG_S2 != null) AVG_S2[i] /= INPUT.size();
+                        }
+                        
+                        //Transform average given transformation parameters
+                        if(PARAM.getTrans() == 1) { 
+                                AVG_S1 = TransformArray.smoothTran(AVG_S1, PARAM.getSmooth());
+                                if(AVG_S2 != null) AVG_S2 = TransformArray.smoothTran(AVG_S2, PARAM.getSmooth());
+                        } else if(PARAM.getTrans() == 2) {
+                                AVG_S1 = TransformArray.gaussTran(AVG_S1, PARAM.getStdSize(), PARAM.getStdNum());
+                                if(AVG_S2 != null) AVG_S2 = TransformArray.gaussTran(AVG_S2, PARAM.getStdSize(), PARAM.getStdNum());
+                        }
+                                        
+                        //Trim average here and output to statistics pane
+                        double[] AVG_S1_trim = new double[AVG_S1.length - (OUTSTART * 2)];
+                        double[] AVG_S2_trim = null;
+                        if(STRAND == 0) AVG_S2_trim = new double[AVG_S1_trim.length];
+                        double[] DOMAIN_trim = new double[AVG_S1_trim.length];
+                        for(int i = OUTSTART; i < AVG_S1.length - OUTSTART; i++) {
+                                if(AVG_S2 != null) {
+                                        AVG_S2_trim[i - OUTSTART] = AVG_S2[i];
+                                }
+                                AVG_S1_trim[i - OUTSTART] = AVG_S1[i];
+                                DOMAIN_trim[i - OUTSTART] = DOMAIN[i];
+                        }
+                        AVG_S1 = AVG_S1_trim;
+                        AVG_S2 = AVG_S2_trim;
+                        DOMAIN = DOMAIN_trim;
+                                        
+                        //Output composite data to tab-delimited file
+                        if(COMPOSITE != null) {
+                                for(int a = 0; a < DOMAIN.length; a++) {
+                                        COMPOSITE.print("\t" + DOMAIN[a]);
+                                }
+                                COMPOSITE.println();
+                                if(STRAND == 0) {
+                                        COMPOSITE.print(generateFileName(BED.getName(), BAM.getName(), 0));
+                                        for(int a = 0; a < AVG_S1.length; a++) {
+                                                COMPOSITE.print("\t" + AVG_S1[a]);
+                                        }
+                                        COMPOSITE.println();
+                                        COMPOSITE.print(generateFileName(BED.getName(), BAM.getName(), 1));
+                                        for(int a = 0; a < AVG_S2.length; a++) {
+                                                COMPOSITE.print("\t" + AVG_S2[a]);
+                                        }
+                                        COMPOSITE.println();
+                                } else {
+                                        COMPOSITE.print(generateFileName(BED.getName(), BAM.getName(), 2));
+                                        for(int a = 0; a < AVG_S1.length; a++) {
+                                                COMPOSITE.print("\t" + AVG_S1[a]);
+                                        }
+                                        COMPOSITE.println();
+                                }                        
+                        }
+                                                                                
+                        if(OUT_S1 != null && PARAM.getOutputType() == 2) { OUT_S1.close(); }
+                        if(OUT_S2 != null && PARAM.getOutputType() == 2) { OUT_S2.close(); }
+        }
+        
+        public static String generateFileName(String bed, String bam, int strandnum) {
+                String[] bedname = bed.split("\\.");
+                String[] bamname = bam.split("\\.");
+                
+                String strand = "sense";
+                if(strandnum == 1) strand = "anti";
+                else if(strandnum == 2) strand = "combined";
+                String read = "read1";
+                if(PARAM.getRead() == 1) read = "read2";
+                else if(PARAM.getRead() == 2) read = "readc";
+                
+                String filename = bedname[0] + "_" + bamname[0] + "_" + read + "_" + strand + ".tabular";
+                return filename;
+        }
+        
+    public static Vector<BEDCoord> loadCoord(File INPUT) throws FileNotFoundException {
+                Scanner scan = new Scanner(INPUT);
+                Vector<BEDCoord> c = new Vector<BEDCoord>();
+                while (scan.hasNextLine()) {
+                        String[] temp = scan.nextLine().split("\t");
+                        if(temp.length > 2) { 
+                                if(!temp[0].contains("track") && !temp[0].contains("#")) {
+                                        String name = "";
+                                        if(temp.length > 3) { name = temp[3]; }
+                                        else { name = temp[0] + "_" + temp[1] + "_" + temp[2]; }
+                                        if(Integer.parseInt(temp[1]) >= 0) {
+                                                if(temp.length > 4) { 
+                                                        if(temp[5].equals("+")) { c.add(new BEDCoord(temp[0], Integer.parseInt(temp[1]), Integer.parseInt(temp[2]), "+", name)); }
+                                                        else { c.add(new BEDCoord(temp[0], Integer.parseInt(temp[1]), Integer.parseInt(temp[2]), "-", name)); }
+                                                } else { c.add(new BEDCoord(temp[0], Integer.parseInt(temp[1]), Integer.parseInt(temp[2]), "+", name)); }
+
+                                        } else {
+                                                System.out.println("Invalid Coordinate in File!!!\n" + Arrays.toString(temp));
+                                        }
+                                }
+                        }
+                }
+                scan.close();
+                return c;
+    }
+
+        public static void loadConfig(String[] command){
+                for (int i = 0; i < command.length; i++) {
+                        switch (command[i].charAt((1))) {
+                                case 'b':
+                                        BAM = new File(command[i + 1]);
+                                        i++;
+                                        break;
+                                case 'i':
+                                        BAI = new File(command[i + 1]);
+                                        i++;
+                                        break;
+                                case 'c':
+                                        BED = new File(command[i + 1]);
+                                        i++;
+                                        break;
+                                case 's':
+                                        SHIFT = Integer.parseInt(command[i + 1]);
+                                        i++;
+                                        break;
+                                case 'n':
+                                        BINSIZE = Integer.parseInt(command[i + 1]);
+                                        i++;
+                                        break;
+                                case 'e':
+                                        TAGSEQUAL = Boolean.parseBoolean(command[i + 1]); 
+                                        i++;
+                                        break;
+                                case 'r':
+                                        READ = Integer.parseInt(command[i + 1]);
+                                        i++;
+                                        break;
+                                case 'a':
+                                        STRAND = Integer.parseInt(command[i + 1]);
+                                        i++;
+                                        break;
+                                case 'p':
+                                        PE_STATUS = Boolean.parseBoolean(command[i + 1]);
+                                        i++;
+                                        break;
+                                case 't':
+                                        CPU = Integer.parseInt(command[i + 1]);
+                                        i++;
+                                        break;
+                                case 'w':
+                                        SMOOTHWINDOW = Integer.parseInt(command[i + 1]);
+                                        i++;
+                                        break;
+                                case 'h':
+                                        OUTPUT_HEATMAP = Boolean.parseBoolean(command[i + 1]);
+                                        i++;
+                                        break;
+                                case 'm':
+                                        OUTPUT_COMP = Boolean.parseBoolean(command[i + 1]);
+                                        i++;
+                                        break;
+                                case 'o':
+                                        HPATH = command[i + 1];
+                                        i++;
+                                        break;
+                                case 'x':
+                                        CNAME = command[i + 1];
+                                        i++;
+                                        break;
+                        }
+                }
+                if(BAM == null) {
+                        System.err.println("No BAM File loaded!!!\n");
+                        printUsage();
+                        System.exit(1);
+                } else if(BAI == null) {
+                        System.err.println("No BAI Index File loaded!!!\n");
+                        printUsage();
+                        System.exit(1);
+                }else if(BED == null) {
+                        System.err.println("No BED File loaded!!!\n");
+                        printUsage();
+                        System.exit(1);
+                }
+                
+                if(BINSIZE < 1) {
+                        System.err.println("Invalid Bin Size!!! Must be larger than 0 bp");
+                        printUsage();
+                        System.exit(1);
+                } else if(READ < 0 || READ > 2) {
+                        System.err.println("Invalid Read to Examine!!! Select 0-2");
+                        printUsage();
+                        System.exit(1);
+                } else if(CPU < 1) {
+                        System.err.println("Invalid Number of CPU's!!! Must use at least 1");
+                        printUsage();
+                        System.exit(1);
+                } else if(SMOOTHWINDOW < 0) {
+                        System.err.println("Invalid Smoothing Window Size!!! Must be larger than 0 bp");
+                        printUsage();
+                        System.exit(1);
+                } 
+
+                //Load up parameters for the pileup into single object
+                PARAM = new PileupParameters();
+                               
+            //Initialize global transformation parameters
+            PARAM.setShift(SHIFT); //SHIFT can be negative
+            PARAM.setBin(BINSIZE);
+            PARAM.setStandard(TAGSEQUAL);
+            
+            //Initialize read parameters
+            PARAM.setRead(READ);
+            PARAM.setPErequire(PE_STATUS);
+            if(STRAND == 0) {
+                    PARAM.setStrand(0);
+                    PARAM.setSenseColor(Color.BLUE);
+                    PARAM.setAntiColor(Color.RED);
+            } else {
+                    PARAM.setStrand(1);
+                    PARAM.setCombinedColor(new Color(0, 100, 0));
+            }
+            
+            //Initialize run parameters
+            PARAM.setCPU(CPU);
+            if(SMOOTHWINDOW > 0) {
+                    PARAM.setTrans(1);
+                    PARAM.setSmooth(SMOOTHWINDOW);
+            } else { PARAM.setTrans(0); }
+            
+            if(!OUTPUT_HEATMAP) { PARAM.setOutputType(0); }
+            else { PARAM.setOutputType(2); }
+            if(!OUTPUT_HEATMAP && !OUTPUT_COMP) { PARAM.setOutput(null); }
+            else { PARAM.setOutput(new File(System.getProperty("user.dir"))); }
+            
+            PARAM.setOutputCompositeStatus(OUTPUT_COMP);
+            
+                System.out.println("-----------------------------------------\nCommand Line Arguments:");
+                System.out.println("BAM file: " + BAM);
+                System.out.println("BAI file: " + BAI);
+                System.out.println("BED file: " + BED);
+                
+                System.out.println("\nGlobal transformations:");
+                System.out.println("5' to 3' Tag Shift (bp):\t" + SHIFT);
+                System.out.println("Bin Size (bp):\t\t\t" + BINSIZE);
+                System.out.println("Set Tags to be equal:\t\t" + TAGSEQUAL);
+                System.out.println("\nRead parameters:");
+                System.out.println("Reads to Examine:\t\t" + READ);
+                System.out.println("Require Proper PE:\t\t" + PE_STATUS);
+                System.out.println("Combine Strands:\t\t" + STRAND);
+                System.out.println("\nRun parameters:");
+                System.out.println("CPUs to use:\t\t\t" + CPU);
+                System.out.println("Composite smoothing window (bp):" + SMOOTHWINDOW);
+                System.out.println("Output heatmap:\t\t\t" + OUTPUT_HEATMAP);
+                System.out.println("Output path for heatmap:\t" + HPATH);
+                System.out.println("Output composite:\t\t" + OUTPUT_COMP);
+                System.out.println("Output filename for composite:\t" + CNAME);
+
+        }
+        
+        public static void printUsage() {
+                System.err.println("Usage: java -jar TagPileup.jar -b [BAMFile] -c [BEDFile] [Options]");
+                System.err.println("-----------------------------------------");
+                System.err.println("\nRequired Parameter:");
+                System.err.println("BAM File:\t\t\t-b\tBAM file");
+                System.err.println("BAI File:\t\t\t-i\tBAI file");
+                System.err.println("BED File:\t\t\t-c\tBED file");
+                System.err.println("\nOptional Parameters:");
+                System.err.println("\nGlobal transformations:");
+                System.err.println("5' to 3' Tag Shift (bp):\t-s\t0 (default)");
+                System.err.println("Bin Size (bp):\t\t\t-n\t1 (default)");
+                System.err.println("Set Tags to be equal:\t\t-e\tfalse (default), true");
+                System.err.println("\nRead parameters:");
+                System.err.println("Reads to Examine:\t\t-r\t0 - Read 1 (default), 1 - Read 2, 2 - Combined");
+                System.err.println("Require Proper PE:\t\t-p\tfalse (default), true");
+                System.err.println("Combine Strands:\t\t-a\t0 - Strand seperate (default), 1 - Strand combined");
+                System.err.println("\nRun parameters:");
+                System.err.println("CPUs to use:\t\t\t-t\t1 (default)");
+                System.err.println("Composite smoothing window (bp):-w\t0 (default)");
+                System.err.println("Output heatmap:\t\t\t-h\ttrue (default), false");
+                System.err.println("Output composite:\t\t-m\ttrue (default), false");
+                System.err.println("Output path for heatmap:\t-o\tDefault local path");
+                System.err.println("Output filename for composite:\t-x\tcomposite.out (default)");
+        }
+        
+        private static String getTimeStamp() {
+                Date date= new Date();
+                String time = new Timestamp(date.getTime()).toString();
+                return time;
+        }
+}
diff -r 000000000000 -r 147e2974b711 tag_pileup_frequency.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tag_pileup_frequency.xml	Fri Mar 18 08:48:22 2016 -0400
@@ -0,0 +1,111 @@
+<tool id="tag_pileup_frequency" name="Tag pileup frequency" version="1.0.0">
+    <description></description>
+    <command>
+        <![CDATA[
+            mkdir -p output &&
+            ln -f -s "${input1.metadata.bam_index}" "${input1}.bai" &&
+            java -jar $__tool_directory__/TagPileup.jar
+            -b "$input1"
+            -i "${input1}.bai"
+            -c "$input2"
+            -s $tag_shift
+            -n $bin_size
+            -e $tags_equal
+            -r $reads
+            -p $proper_pe
+            -a $combine_strands
+            -t "\${GALAXY_SLOTS:-4}"
+            -w $composite_smoothing_window
+            -m "true"
+            -x "$output1"
+            -h $output_heatmap
+            #if str($output_heatmap) == "true":
+                -o output
+            #end if
+            1>/dev/null
+        ]]>
+    </command>
+    <inputs>
+        <param name="input1" type="data" format="bam" label="BAM file" />
+        <param name="input2" type="data" format="bed" label="Bed file" />
+        <param name="tag_shift" type="integer" value="0" min="0" label="5' to 3' Tag Shift (bp)" />
+        <param name="bin_size" type="integer" value="1" min="1" label="Bin Size (bp)" />
+        <param  name="tags_equal" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Set Tags to be equal?" />
+        <param  name="reads" type="select" label="Reads to examine" help="Selecting combined requires paired-end BAM input">
+            <option value="0" selected="True">Read1</option>
+            <option value="1">Read2</option>
+            <option value="2">combined</option>
+        </param>
+        <param  name="proper_pe" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Require proper PE?" help="Requires paired-end BAM input"/>
+        <param  name="combine_strands" type="select" label="Combine strands?">
+            <option value="0" selected="True">No</option>
+            <option value="1">Yes</option>
+        </param>
+        <param name="composite_smoothing_window" type="integer" value="0" min="0" label="Composite smoothing window (bp)" />
+        <param name="output_heatmap" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Output frequencies heatmap?" />
+    </inputs>
+    <outputs>
+        <collection name="heatmaps" type="list" label="Heatmap frequencies: ${tool.name} on ${on_string}">
+            <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="output" ext="tabular" visible="false" />
+            <filter>output_heatmap == true</filter>
+        </collection>
+        <data name="output1" format="tabular"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input1" value="input.bam" ftype="bam"/>
+            <param name="input2" value="input.bed" ftype="bed"/>
+            <param name="tag_shift" value="0" />
+            <param name="bin_size" value="1" />
+            <param name="tags_equal" value="false" />
+            <param name="reads" value="0" />
+            <param name="proper_pe" value="false" />
+            <param name="combine_strands" value="0" />
+            <param name="composite_smoothing_window" value="0" />
+            <param name="output_heatmap" value="true" />
+            <output name="output1" file="output1.tabular" ftype="tabular"/>
+            <output_collection name="heatmaps" type="list">
+                <element name="dataset_2_dataset_1_read1_anti.tabular" file="input2_input1_read1_anti.tabular" ftype="tabular" compare="contains"/>
+                <element name="dataset_2_dataset_1_read1_sense.tabular" file="input2_input1_read1_sense.tabular" ftype="tabular" compare="contains"/>
+            </output_collection>
+        </test>
+    </tests>
+    <help>
+
+**What it does**
+
+Generates a frequency pileup of the 5' ends of aligned reads in a BAM file relative to reference points in a BED file.
+
+-----
+
+**Options**
+
+**Global transformations**
+
+ - **5' to 3' tag shift (bp)** - moves all tags from the 5' to the 3' direction given a specified distance in base pairs.
+ - **Bin Size (bp)** - bins tags together into specified size, useful for lower resolution data or for especially wide reference windows.
+ - **Set Tags to be equal** - standardizes tag count to be equal to genome size, useful for replicate comparisons.
+
+**Read parameters**
+
+ - **Reads to Examine** - output data for Read1, Read2, or combined (only for paired end BAM files).
+ - **Require Proper PE** - require output reads to be properly paired (only for paired end BAM files).
+ - **Combine Strands** - examine reads on a forward/reverse basis (strand separate) or ignoring read orientation (strand combined).
+
+**Run parameters**
+
+ - **Composite smoothing window (bp)** - sliding window to smooth composite frequencies.
+ - **Output frequencies for heatmap** - generate an additional dataset collection containing frequencies that can be used to generate a heatmap plot.
+
+    </help>
+    <citations>
+        <citation type="bibtex">
+            @unpublished{None,
+            author = {Lai, William},
+            title = {None},
+            year = {None},
+            eprint = {None},
+            url = {http://www.huck.psu.edu/content/research/independent-centers-excellence/center-for-eukaryotic-gene-regulation}
+        }</citation>
+    </citations>
+</tool>
diff -r 000000000000 -r 147e2974b711 test-data/input.bam
Binary file test-data/input.bam has changed
diff -r 000000000000 -r 147e2974b711 test-data/input.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input.bed	Fri Mar 18 08:48:22 2016 -0400
@@ -0,0 +1,41 @@
+chr17	958782	958824	chr17_951114_951309_1:0:0_1:0:0_d50af/2	37	+
+chr17	1820041	1820100	chr17_1810548_1810721_1:0:0_0:0:0_519fb/1	37	-
+chr17	1849174	1849232	chr17_1839787_1839971_1:0:0_0:0:0_4c72d/1	37	+
+chr17	2778100	2778159	chr17_2768150_2768389_2:0:0_0:0:0_d422b/1	37	-
+chr17	3205460	3205518	chr17_3195095_3195290_2:0:0_1:0:0_b31e3/1	37	-
+chr17	4509384	4509441	chr17_4498414_4498642_2:0:0_1:1:0_f20f8/2	37	+
+chr17	9677386	9677444	chr17_9676629_9676795_2:0:0_2:0:0_e997/2	37	+
+chr17	10089099	10089157	chr17_10088345_10088511_1:0:0_0:0:0_3a7a2/2	37	+
+chr17	12974352	12974399	chr17_51669566_51669767_1:0:0_4:0:0_4fa93/1	23	+
+chr17	13430901	13430960	chr17_13429910_13430116_0:0:0_1:1:0_7c74f/2	37	+
+chr17	15885434	15885477	chr17_15882376_15882562_3:0:0_1:0:0_8ca48/2	37	+
+chr17	20624853	20624912	chr17_20622248_20622418_1:0:0_1:0:0_9f20f/1	37	-
+chr17	27071126	27071171	chr17_75470822_75470987_3:0:0_2:0:0_4c20e/1	23	-
+chr17	27913463	27913508	chr17_27909785_27909976_3:0:0_4:0:0_7f1ea/2	25	-
+chr17	34920830	34920869	chr17_33286571_33286762_2:0:0_3:0:0_dc02a/1	25	+
+chr17	39322684	39322742	chr17_39321131_39321340_1:0:0_1:0:0_db376/2	37	-
+chr17	39810522	39810581	chr17_39810082_39810271_0:0:0_0:0:0_7eb08/2	37	+
+chr17	39810524	39810583	chr17_39809904_39810133_1:0:0_0:0:0_8c2b/1	37	-
+chr17	39960509	39960568	chr17_39959909_39960118_2:0:0_0:0:0_36d84/2	37	-
+chr17	43542321	43542379	chr17_43542841_43543044_0:0:0_1:0:0_bda98/1	37	-
+chr17	45800655	45800713	chr17_45803004_45803206_2:0:0_0:0:2_41429/1	37	+
+chr17	46313026	46313081	chr17_46315776_46315986_1:0:0_0:0:0_e4beb/2	23	+
+chr17	47124773	47124830	chr17_47127410_47127618_0:0:0_3:0:0_768f2/1	37	-
+chr17	48697937	48697995	chr17_48708043_48708274_1:0:0_1:0:0_1a6/1	37	-
+chr17	48697939	48697997	chr17_48708227_48708422_1:0:0_1:0:0_d70c1/2	37	+
+chr17	52847681	52847739	chr17_52851082_52851314_1:0:0_1:0:0_6a280/2	37	-
+chr17	54474562	54474618	chr17_54477683_54477878_2:0:0_1:0:0_c9f4/1	37	-
+chr17	56652426	56652468	chr17_56655628_56655799_1:0:0_1:0:0_28a86/2	37	-
+chr17	60951987	60952045	chr17_60960117_60960339_0:1:0_1:0:0_ea16c/2	37	+
+chr17	61271205	61271247	chr17_61279152_61279329_1:0:0_1:0:0_477ec/2	37	-
+chr17	64901295	64901353	chr17_64907182_64907353_0:0:0_1:0:0_188c2/1	37	-
+chr17	64901313	64901371	chr17_64907182_64907371_0:0:0_1:0:0_50fa5/2	37	-
+chr17	65065434	65065475	chr17_65071347_65071553_0:0:0_1:0:0_5e8bb/2	37	-
+chr17	66772270	66772328	chr17_66777686_66777888_1:0:0_1:0:0_fcea/2	37	-
+chr17	68614271	68614328	chr17_68621038_68621213_0:0:0_1:1:0_3ebaf/2	37	-
+chr17	69072334	69072383	chr17_1119124_1119366_1:0:0_1:0:0_736b9/1	25	+
+chr17	74122686	74122743	chr17_74128589_74128844_1:0:0_1:0:0_b61d8/2	37	+
+chr17	76184542	76184601	chr17_76191086_76191297_0:0:0_2:0:0_5f28c/1	37	+
+chr17	76518424	76518474	chr17_76526501_76526684_2:0:0_0:0:0_95fe3/2	25	+
+chr17	76518826	76518878	chr17_76524679_76524888_0:0:0_0:0:0_8f754/1	37	-
+chr17	76941019	76941064	chr17_55336589_55336803_2:0:0_5:0:0_4a6cb/1	23	+
diff -r 000000000000 -r 147e2974b711 test-data/input2_input1_read1_anti.tabular
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input2_input1_read1_anti.tabular	Fri Mar 18 08:48:22 2016 -0400
@@ -0,0 +1,15 @@
+YORF	NAME	0	1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	16	17	18	19	20	21	22	23	24	25	26	27	28	29	30	31	32	33	34	35	36	37	38	39	40	41	42	43	44	45	46	47	48	49	50	51	52	53	54	55	56	57	58
+chr17_951114_951309_1:0:0_1:0:0_d50af/2	chr17_951114_951309_1:0:0_1:0:0_d50af/2	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0
+chr17_1810548_1810721_1:0:0_0:0:0_519fb/1	chr17_1810548_1810721_1:0:0_0:0:0_519fb/1	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0
+chr17_1839787_1839971_1:0:0_0:0:0_4c72d/1	chr17_1839787_1839971_1:0:0_0:0:0_4c72d/1	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0
+chr17_2768150_2768389_2:0:0_0:0:0_d422b/1	chr17_2768150_2768389_2:0:0_0:0:0_d422b/1	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0
+chr17_3195095_3195290_2:0:0_1:0:0_b31e3/1	chr17_3195095_3195290_2:0:0_1:0:0_b31e3/1	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0
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+chr17_27909785_27909976_3:0:0_4:0:0_7f1ea/2	chr17_27909785_27909976_3:0:0_4:0:0_7f1ea/2	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0
diff -r 000000000000 -r 147e2974b711 test-data/input2_input1_read1_sense.tabular
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input2_input1_read1_sense.tabular	Fri Mar 18 08:48:22 2016 -0400
@@ -0,0 +1,15 @@
+YORF	NAME	0	1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	16	17	18	19	20	21	22	23	24	25	26	27	28	29	30	31	32	33	34	35	36	37	38	39	40	41	42	43	44	45	46	47	48	49	50	51	52	53	54	55	56	57	58
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diff -r 000000000000 -r 147e2974b711 test-data/output1.tabular
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output1.tabular	Fri Mar 18 08:48:22 2016 -0400
@@ -0,0 +1,3 @@
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