diff

diff --git a/.gitignore b/.gitignore
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diff --git a/Dockerfile b/Dockerfile
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diff --git a/LICENSE b/LICENSE
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diff --git a/README.md b/README.md
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diff --git a/bampairs.cpp b/bampairs.cpp
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diff --git a/bampairs.h b/bampairs.h
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diff --git a/bamreader.cpp b/bamreader.cpp
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diff --git a/bamreader.h b/bamreader.h
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diff --git a/bamtumors.cpp b/bamtumors.cpp
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diff --git a/chi.cpp b/chi.cpp
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diff --git a/chi.h b/chi.h
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diff --git a/cmds.cpp b/cmds.cpp
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diff --git a/cmds.h b/cmds.h
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new mode 100755
diff --git a/distribution.cpp b/distribution.cpp
old mode 100644
new mode 100755
index f871bd5..0fed109
--- a/distribution.cpp
+++ b/distribution.cpp
@@ -56,6 +56,7 @@ std::string normalBam;
 std::string tumorBam;
 std::string bedFile;
 std::string disFile;
+std::string modelFile;
 
 std::ifstream finH;
 std::ifstream finM;
@@ -70,6 +71,7 @@ void DisUsage(void) {
         <<"       -d   <string>   homopolymer and microsates file\n"
         <<"       -n   <string>   normal bam file\n"
         <<"       -t   <string>   tumor  bam file\n"
+        <<"       -M   <string>   model for test\n"
         <<"       -o   <string>   output distribution file\n\n"
 
         <<"       -e   <string>   bed file, optional\n"
@@ -104,6 +106,7 @@ int dGetOptions(int rgc, char *rgv[]) {
             case 'd': homoFile = rgv[++i]; break;
             case 'n': normalBam  = rgv[++i]; break;
             case 't': tumorBam  = rgv[++i]; break;
+            case 'M': modelFile = rgv[++i]; break;
             case 'o': disFile  = rgv[++i]; break;
             case 'e': bedFile  = rgv[++i]; break;
             case 'r': one_region = rgv[++i]; break;
@@ -187,7 +190,11 @@ int HomoAndMicrosateDisMsi(int argc, char *argv[]) {
         polyscan.GetHomoDistribution(sample, disFile);
     }
     if (normalBam.empty() && !tumorBam.empty()) {
-        polyscan.GetHomoTumorDistribution(sample, disFile);
+        if (modelFile.empty()) {
+            polyscan.GetHomoTumorDistribution(sample, disFile);
+        } else {
+            polyscan.GetHomoTumorDistribution(sample, disFile, modelFile);
+        }
     }
 
     std::cout << "\nTotal time consumed:  " << Cal_AllTime() << " secs\n\n";
diff --git a/distribution.h b/distribution.h
old mode 100644
new mode 100755
diff --git a/homo.cpp b/homo.cpp
old mode 100644
new mode 100755
index 238d5be..9587cfd
--- a/homo.cpp
+++ b/homo.cpp
@@ -29,10 +29,16 @@
 #include <bitset>
 #include <omp.h>
 #include <cmath>
+#include <inttypes.h>
+#include <fstream>
 
 #include "homo.h"
 #include "polyscan.h"
 #include "somatic.h"
+#include "xgboost/c_api.h"
+#include "Md5.hpp"
+
+using namespace std;
 
 extern Param param;
 extern Param paramd;
@@ -55,6 +61,7 @@ HomoSite::HomoSite()
     , highcut(0)
     , normalDis(NULL)
     , tumorDis(NULL)
+    , tumorDisNor(NULL)
     ////////////
     , normalCov( 0 )
     , tumorCov( 0 )
@@ -143,6 +150,13 @@ void HomoSite::InitialTumorDis() {
     }
 }
 
+void HomoSite::InitialTumorDisNor() {
+    tumorDisNor = new float [paramd.t_dispots];
+    for (unsigned int n=0; n<paramd.t_dispots; n++) {
+        tumorDisNor[n] = 0.0;
+    }
+}
+
 // Out distribution
 void HomoSite::OutputDis() {
     for (unsigned int j=0; j<polyscan.totalBamPairsNum; j++) {
@@ -309,7 +323,7 @@ void HomoSite::DisTumorSomatic(Sample &sample) {
         }
     }
 
-    if (tumorCov >= paramd.covCutoff){
+    if (tumorCov >= paramd.covCutoff) {
         withSufCov = true;
         comentropy = Comentropy( tumorDis[0], paramd.s_dispots);
     } else {
@@ -343,6 +357,113 @@ void HomoSite::DisTumorSomatic(Sample &sample) {
     }
 }
 
+std::string HomoSite::DecIntToHexStr(long long num) {
+    std::string str;
+    long long Temp = num / 16;
+    int left = num % 16;
+    if (Temp > 0)
+        str += DecIntToHexStr(Temp);
+    if (left < 10)
+        str += (left + '0');
+    else
+        str += ('a' + left - 10);
+    return str;
+}
+
+std::string HomoSite::encode(const std::string &fileName) {
+    unsigned char decrypt[16];
+    std::string decryFileName;
+    unsigned char* encrypt = (unsigned char*)fileName.c_str();
+    MD5_CTX md5;
+    MD5Init(&md5);
+    MD5Update(&md5, encrypt, (int)strlen((char *)encrypt));
+    MD5Final(&md5, decrypt);
+    for (int i = 0; i<16; i++){
+        string str = DecIntToHexStr((long long)decrypt[i]);
+        while(str.size() < 2)
+            str = "0" + str;
+        decryFileName += str;
+    }
+    return decryFileName;
+}
+
+void HomoSite::DisTumorFeature(Sample &sample, const std::string &modelPre) {
+    fstream _file;
+    bool reportSomatic;
+    std::string siteLoc;
+    std::string ModelFile;
+    std::string entryFileName;
+    const float *m_TestResults2;
+    reportSomatic = false;
+    tumorCov = 0;
+    sample.numberOftotalSites++;
+    for (unsigned int j=0; j<polyscan.totalBamTumorsNum; j++) {
+        for (unsigned int k=0; k<paramd.s_dispots; k++) {
+            tumorCov  += tumorDis[j][k];
+        }
+    }
+    if (tumorCov >= paramd.covCutoff){
+        withSufCov = true;
+        Normalization( tumorDis[0], paramd.t_dispots);
+        stringstream tmp;
+        tmp<<location;
+        string tmp_string;
+        tmp>>tmp_string;
+        siteLoc = chr + "_" + tmp_string;
+        entryFileName = encode(siteLoc);
+        ModelFile =  modelPre + "/" + entryFileName;
+        _file.open(ModelFile.c_str());
+        if (_file) {
+            sample.numberOfDataPoints++;
+            BoosterHandle handle;
+            XGBoosterCreate(NULL, 0, &handle);
+            int x = XGBoosterLoadModel(handle, ModelFile.c_str());
+            if (x != 0) {
+                cout << "Failed Loading Model" << endl;
+                exit(-1);
+            }
+            DMatrixHandle dHandle;
+            x = XGDMatrixCreateFromMat(tumorDisNor, 1, paramd.t_dispots-1, 0, &dHandle);
+            if (x != 0)
+            {
+                cout << "Failed Creating DMatrix" << endl;
+                exit(-1);
+            }
+            bst_ulong out2;
+            x = XGBoosterPredict(handle, dHandle, 0, 0, &out2, &m_TestResults2);
+            if (x != 0) {
+                cout << "Failed Predicting" << endl;
+                exit(-1);
+            }
+            if(m_TestResults2[0] > 0.3) {
+                reportSomatic = true;
+                sample.numberOfMsiDataPoints ++;
+            }
+            XGBoosterFree(handle);
+        }
+        _file.close();
+        if (reportSomatic) {
+            sample.outputSomatic << chr << "\t"
+                                << location << "\t"
+                                << fbases << "\t"
+                                << length << "\t"
+                                << bases << "\t"
+                                << ebases;
+            sample.outputSomatic << "\t" << std::fixed << m_TestResults2[0];
+            sample.outputSomatic << std::endl;
+            SomaticSite onessite;
+            onessite.chr = chr;
+            onessite.location = location;
+            onessite.length = length;
+            onessite.fbases = fbases;
+            onessite.ebases = ebases;
+            onessite.bases = bases;
+
+            sample.totalSomaticSites.push_back( onessite );
+        }
+    }
+}
+
 // distance
 double HomoSite::DistanceBetweenTwo( unsigned short * FirstOriginal, unsigned short * SecondOriginal ) {
     double SmallDouble = 0.0000000001;
@@ -436,6 +557,16 @@ double HomoSite::Comentropy( unsigned short * tumorDis, unsigned int dispots ) {
     return comentropy;
 }
 
+void HomoSite::Normalization( unsigned short * tumorDis, unsigned int dispots ) {
+    double sum = 0;
+    for (int i = 0; i < dispots; i++){
+        sum += tumorDis[i];
+    }
+    for (int j = 0; j < dispots; j++){
+	    tumorDisNor[j] = tumorDis[j]/sum;
+    }
+}
+
 void HomoSite::ComputeGenotype( unsigned short * NormalReadCount ) {
     unsigned int Offset, CoverageCutoff, first, second, Sum;
     Offset = 1; CoverageCutoff = paramd.covCutoff;
@@ -496,3 +627,11 @@ void HomoSite::ReleaseTumorMemory() {
     }
     delete [] tumorDis;
 }
+
+void HomoSite::ReleaseTumorMemoryNor() {
+    for (unsigned int k=0; k<polyscan.totalBamTumorsNum; k++) {
+        delete []  tumorDis[k]; 
+    }
+    delete [] tumorDis;
+    delete [] tumorDisNor;
+}
diff --git a/homo.h b/homo.h
old mode 100644
new mode 100755
index 4abbac9..3561315
--- a/homo.h
+++ b/homo.h
@@ -73,6 +73,7 @@ public:
     // distribution
     unsigned short **normalDis;
     unsigned short **tumorDis;
+    float *tumorDisNor;
 
     ////// genotyping //////
     unsigned normalCov;
@@ -89,22 +90,30 @@ public:
 
     inline void InitType(){ genotype[0] = genotype[1] = -2; };
 
+    //decrypt file name
+    std::string encode(const std::string &fileName);
+    std::string DecIntToHexStr(long long num);
+
     void TransferString();
     void InitialDis();
     void InitialTumorDis();
+    void InitialTumorDisNor();
     void OutputDis();
     void OutputTumorDis();
     void ReleaseMemory();
     void ReleaseTumorMemory();
+    void ReleaseTumorMemoryNor();
     //void PouroutDis(std::ofstream &fout);
     void PouroutDis(Sample &sample);
     void PourTumoroutDis(Sample &sample);
     void DisGenotyping(Sample &sample);
     void DisTumorSomatic(Sample &sample);
+    void DisTumorFeature(Sample &sample, const std::string &modelPre);
     //// genotyping ///
     void BoolsInitial();
     double DistanceBetweenTwo( unsigned short * FirstOriginal, unsigned short * SecondOriginal );
     double Comentropy( unsigned short * tumorDis, unsigned int dispots );
+    void Normalization( unsigned short * tumorDis, unsigned int dispots );
     void ComputeGenotype( unsigned short * NormalReadCount );
 
     protected:
diff --git a/makefile b/makefile
old mode 100644
new mode 100755
index 31ccb3f..6aaaf0e
--- a/makefile
+++ b/makefile
@@ -1,26 +1,28 @@
 CXX=g++
 SAMTOOLS_ROOT=vendor/samtools-0.1.19
+XGBOOST_ROOT=vendor/xgboost
 
-
+STATIC_LIST=vendor/xgboost/lib/libxgboost.a vendor/xgboost/dmlc-core/libdmlc.a vendor/xgboost/rabit/lib/librabit.a
 CXXFLAGS+=    -O2 -fopenmp
 LDFLAGS+=    -L${SAMTOOLS_ROOT}
 LIBS+=    -lm -lbam -lz -lpthread
-INCLUDES+=    -I${SAMTOOLS_ROOT}
-SOURCE = cmds scan distribution refseq polyscan param utilities homo window bamreader sample chi somatic
+INCLUDES+=    -I${SAMTOOLS_ROOT} -I${XGBOOST_ROOT}/include -I${XGBOOST_ROOT}/dmlc-core/include -I${XGBOOST_ROOT}/rabit/include
+SOURCE = cmds scan distribution refseq polyscan param utilities homo window bamreader sample chi somatic Md5 
 OBJS= $(patsubst %,%.o,$(SOURCE))
 
 %.o:%.cpp
 	        $(CXX) $(CXXFLAGS) $(INCLUDES) -c $< -o $@
 
-all: samtools msisensor
-
-samtools:
-	        $(MAKE) -C ${SAMTOOLS_ROOT}
+all: msisensor 
 
-msisensor: $(OBJS)
-	        $(CXX) $^ $(CXXFLAGS) $(LDFLAGS) $(LIBS) -o $@ 
+msisensor: 
+		$(MAKE) -C ${SAMTOOLS_ROOT}
+		$(MAKE) -C ${XGBOOST_ROOT}
+		$(MAKE) $(OBJS)
+		$(CXX) $(OBJS) $(STATIC_LIST) $(CXXFLAGS) $(LDFLAGS) $(LIBS) $(INCLUDES) -o $@
 
 clean:
 	        rm -f *.o msisensor
-			        $(MAKE) -C ${SAMTOOLS_ROOT} clean
+		$(MAKE) -C ${SAMTOOLS_ROOT} clean
+		$(MAKE) -C ${XGBOOST_ROOT} clean
 
diff --git a/param.cpp b/param.cpp
old mode 100644
new mode 100755
index 7bb7435..eefd938
--- a/param.cpp
+++ b/param.cpp
@@ -93,6 +93,7 @@ Param::Param()
     , HomoOnly(0)
     , MicrosateOnly(0)
     , s_dispots(100)
+    , t_dispots(35)
     , MaxMicrosate(5)
     , Repeats(3)
     , numberThreads(1)
diff --git a/param.h b/param.h
old mode 100644
new mode 100755
index bb4354e..14efacd
--- a/param.h
+++ b/param.h
@@ -81,6 +81,7 @@ public:
     unsigned int numberThreads;
     // statistic var
     unsigned int s_dispots; 
+    unsigned int t_dispots;
     unsigned int PercentPairs;
     unsigned int PercentPairsNumber;
     unsigned int HomoCoverage;
diff --git a/polyscan.cpp b/polyscan.cpp
old mode 100644
new mode 100755
index e375013..ec9eca3
--- a/polyscan.cpp
+++ b/polyscan.cpp
@@ -29,6 +29,7 @@
 #include <bitset>
 #include <map>
 #include <omp.h>
+#include <string>
 
 #include "utilities.h"
 #include "polyscan.h"
@@ -36,6 +37,8 @@
 #include "param.h"
 #include "sample.h"
 
+using namespace std;
+
 extern Param paramd;
 extern bit8_t alphabet[];
 extern bit8_t rev_alphabet[];
@@ -436,4 +439,20 @@ void PolyScan::GetHomoTumorDistribution( Sample &oneSample, const std::string &p
     oneSample.VerboseInfo();
 
 }
+void PolyScan::GetHomoTumorDistribution( Sample &oneSample, const std::string &prefix, const std::string &prefixM ) {
+    oneSample.iniTumorDisOutput(prefix);
+    std::vector< SPLIT_READ > readsInWindow;
+    for (int i=0; i< totalWindowsNum; i++) {
+        totalWindows[i].InitialTumorDisWNor(); 
+        totalWindows[i].GetTumorDistribution(readsInWindow);
+        totalWindows[i].PourTumoroutDisW(oneSample);
+        totalWindows[i].PouroutTumorFeature(oneSample, prefixM);
+        totalWindows[i].ClearTumorDisNor();
+        readsInWindow.clear();
+        std::cout << "window: " << i << " done...:" <<  totalWindows[i]._chr << ":" << totalWindows[i]._start << "-" << totalWindows[i]._end << std::endl;
+    }
+    oneSample.pourOutMsiScore();
+    oneSample.closeOutStream();
+    oneSample.VerboseInfo();
+}
 
diff --git a/polyscan.h b/polyscan.h
old mode 100644
new mode 100755
index 2e38b7c..2c87395
--- a/polyscan.h
+++ b/polyscan.h
@@ -93,6 +93,7 @@ class PolyScan
         void releaseDistributions(); 
         void GetHomoDistribution( Sample &oneSample, const std::string &prefix );
         void GetHomoTumorDistribution( Sample &oneSample, const std::string &prefix );
+        void GetHomoTumorDistribution( Sample &oneSample, const std::string &prefix, const std::string &prefixM);
 
 protected:
 
diff --git a/refseq.cpp b/refseq.cpp
old mode 100644
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diff --git a/refseq.h b/refseq.h
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diff --git a/sample.cpp b/sample.cpp
old mode 100644
new mode 100755
index ea2e05b..58adabd
--- a/sample.cpp
+++ b/sample.cpp
@@ -31,6 +31,7 @@
 #include <iomanip>
 
 #include "sample.h"
+#include "homo.h"
 #include "param.h"
 
 extern Param paramd;
@@ -38,6 +39,7 @@ extern Param paramd;
 Sample::Sample()
     : outputPrefix( "test" )
     , output( NULL )
+    , modelPrefix( "" )
    //, outputPSomatic( NULL )
     , outputSomatic( NULL )
     , outputGermline( NULL )
@@ -137,6 +139,7 @@ void Sample::calculateFDR() {
     }
 }
 
+
 // report somatics && FDR
 void Sample::pourOutSomaticFDR() {
     for ( std::vector< SomaticSite >::iterator _it = totalSomaticSites.begin(); _it != totalSomaticSites.end(); ++_it ) {
diff --git a/sample.h b/sample.h
old mode 100644
new mode 100755
index af672a0..0a6410e
--- a/sample.h
+++ b/sample.h
@@ -44,6 +44,7 @@ public:
     ~Sample();
 
     std::string outputPrefix;
+    std::string modelPrefix;
 
     std::ofstream output;
     //std::ofstream outputPSomatic;
diff --git a/scan.cpp b/scan.cpp
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diff --git a/vendor/samtools-0.1.19/samtools.1 b/vendor/samtools-0.1.19/samtools.1
old mode 100644
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diff --git a/vendor/samtools-0.1.19/win32/xcurses.h b/vendor/samtools-0.1.19/win32/xcurses.h
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diff --git a/vendor/samtools-0.1.19/win32/zconf.h b/vendor/samtools-0.1.19/win32/zconf.h
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diff --git a/vendor/samtools-0.1.19/win32/zlib.h b/vendor/samtools-0.1.19/win32/zlib.h
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diff --git a/window.cpp b/window.cpp
old mode 100644
new mode 100755
index 957b5bd..b8e29b3
--- a/window.cpp
+++ b/window.cpp
@@ -71,6 +71,15 @@ void Window::InitialTumorDisW() {
     }
 };
 
+void Window::InitialTumorDisWNor() {
+    HomoSite *p = NULL;
+    for (unsigned short i=0; i<_siteCount; i++) {
+        p = _startSite + i;
+        p->InitialTumorDis();
+        p->InitialTumorDisNor();
+    }
+};
+
 void Window::ClearDis() {
     HomoSite *p = NULL;
     for (unsigned short i=0; i<_siteCount; i++) {
@@ -87,6 +96,15 @@ void Window::ClearTumorDis() {
     }
 };
 
+void Window::ClearTumorDisNor() {
+    HomoSite *p = NULL;
+    for (unsigned short i=0; i<_siteCount; i++) {
+        p = _startSite + i;
+        //p->ReleaseTumorMemory();
+        p->ReleaseTumorMemoryNor();
+    }
+};
+
 void Window::OutputDisW() {
     HomoSite *p = NULL;
     for (unsigned short i=0; i<_siteCount; i++) {
@@ -127,7 +145,7 @@ void Window::DisGenotypingW(Sample &oneSample) {
     }
 };
 
-void Window:: PouroutTumorSomatic(Sample &oneSample) {
+void Window::PouroutTumorSomatic(Sample &oneSample) {
     HomoSite *p = NULL;
     for (unsigned short i=0; i<_siteCount; i++){
         p = _startSite + i;
@@ -135,6 +153,14 @@ void Window:: PouroutTumorSomatic(Sample &oneSample) {
     }
 };
 
+void Window::PouroutTumorFeature(Sample &oneSample, const std::string &modelPrefix) {
+    HomoSite *p = NULL;
+    for (unsigned short i=0; i<_siteCount; i++){
+        p = _startSite + i;
+        p->DisTumorFeature(oneSample, modelPrefix);
+    }
+};
+
 // change start
 void Window::ChangeStart() {
     if ((_start - MAX_SPAN_SIZE) < 0) {
diff --git a/window.h b/window.h
old mode 100644
new mode 100755
index 44442c5..37d82d0
--- a/window.h
+++ b/window.h
@@ -50,15 +50,18 @@ public:
     int _end;
     unsigned short _siteCount;
     std::string _chr;
+    std::string modelPrefix;
     HomoSite *_startSite;
     HomoSite *_endSite;
 
     void InitialDisW(); 
     void InitialTumorDisW();
+    void InitialTumorDisWNor();
     void OutputDisW();
     void OutputTumorDisW();
     void ClearDis();
     void ClearTumorDis();
+    void ClearTumorDisNor();
     void ChangeStart(); 
     void GetDistribution(std::vector <SPLIT_READ> &readsInWindow);
     void GetTumorDistribution(std::vector <SPLIT_READ> &readsInWindow);
@@ -70,6 +73,7 @@ public:
     void PourTumoroutDisW(Sample &oneSample);
     void DisGenotypingW(Sample &oneSample);
     void PouroutTumorSomatic(Sample &oneSample);
+    void PouroutTumorFeature(Sample &oneSample, const std::string &modelPrefix);
 
 protected:
     //xxxxxx