added files and changed readme

RAHenriksen · Apr 8, 2024 · 35958fd · 35958fd
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diff --git a/Chr22_024_36_68_0097.sorted.MD.bam b/Chr22_024_36_68_0097.sorted.MD.bam
diff --git a/Chr22_024_36_68_0097_eps10.sorted.MD.bam b/Chr22_024_36_68_0097_eps10.sorted.MD.bam
diff --git a/Chr22_024_36_68_0097_eps10.sorted.MD.coord.bam b/Chr22_024_36_68_0097_eps10.sorted.MD.coord.bam
diff --git a/Chr22_024_36_68_0097_eps10.sorted.MD.coord.bam.bai b/Chr22_024_36_68_0097_eps10.sorted.MD.coord.bam.bai
diff --git a/README.md b/README.md
@@ -9,13 +9,13 @@ git clone https://github.com/RAHenriksen/ngsBriggs.git
 
 git clone https://github.com/samtools/htslib.git
 
-cd htslib; make; cd ../NGSNGS; make HTSSRC=../htslib
+cd htslib; make; cd ../ngsBriggs; make HTSSRC=../htslib
 
 * Use systemwide installation of htslib
 
 git clone https://github.com/RAHenriksen/ngsBriggs.git
 
-cd NGSNGS; make
+cd ngsBriggs; make
 
 **NOTE:** Newer version of htslib which includes bam_set1 is required
 
@@ -47,6 +47,13 @@ Usage
 	-> -nthreads: Choose the number of threads to speed up the recalibration process.
 
 Example
-./ngsbriggs -bam /projects/korneliussen/people/wql443/NGSNGS/HgSimTest1.bam -ref /projects/korneliussen/people/wql443/NGSNGS/Test_Examples/Mycobacterium_leprae.fa.gz -model b
+
+Inference of Briggs parameters
+
+Inference of Briggs parameters with epsilon
+./ngsbriggs -bam Chr22_024_36_68_0097_eps10.sorted.MD.bam -ref chr22.fa -eps 0.1 -model nb
+
+Decontamination with epsilon
+./ngsbriggs -bam Chr22_024_36_68_0097_eps10.sorted.MD.coord.bam -model nb -eps 0.1 -ibam Chr22_024_36_68_0097_eps10.sorted.MD.coord.bam -obam Chr22_024_36_68_0097_eps10.sorted.MD.scores.bam -isrecal 1 -ibed chr22.bed -chr chr22 -nthread 1
 
 ~~~~
diff --git a/chr22.bed b/chr22.bed
@@ -0,0 +1 @@
+chr22	1	51304566
diff --git a/chr22.fa b/chr22.fa
diff --git a/chr22.fa.fai b/chr22.fa.fai
@@ -0,0 +1 @@
+chr22	51304566	7	60	61
diff --git a/ngsBriggs.cpp b/ngsBriggs.cpp
@@ -193,11 +193,11 @@ int main(int argc, char **argv){
 
     fprintf(stderr,"\nThe misincorporting matrix is as follows:\n");
     fprintf(stderr,"Dir.\tPos.\tFreqCT\tFreqGA\n");
-    for (int i=0; i<MAXLENGTH;i++){
+    for (int i=0; i<5;i++){
         fprintf(stderr,"5'\t%d\t",i+1);
         fprintf(stderr,"%f\t%f\n",freqCT[i],freqGA[2*MAXLENGTH-1-i]);
     }
-    for (int i=0; i<MAXLENGTH;i++){
+    for (int i=0; i<5;i++){
         fprintf(stderr,"3'\t%d\t",i+1);
         fprintf(stderr,"%f\t%f\n",freqCT[2*MAXLENGTH-1-i],freqGA[i]);
     }

diff --git a/ngsbriggs b/ngsbriggs
diff --git a/profile.cpp b/profile.cpp
@@ -58,11 +58,6 @@ void wrapper(const bam1_t *b,const char * reconstructedReference,const std::vect
     }
 }
 
-int usage(FILE *fp,int val){
-  fprintf(stderr,"./metadamage pmd [options]\n");
-  return 0;
-}
-
 float **getmatrix(size_t x,size_t y){
   float **ret = new float*[x];
   for(int i=0;i<x;i++){

diff --git a/profile.h b/profile.h
@@ -67,7 +67,6 @@ typedef struct{
 }mydata2;
 
 void wrapper(const bam1_t *b,const char * reconstructedReference,const std::vector<int> &  reconstructedReferencePos,const int & minQualBase, int MAXLENGTH,float **mm5p,float **mm3p,float incval,char myread[512],char myref[512]);
-int usage(FILE *fp,int val);
 std::map<int, mydataD> load_bdamage_full(const char* fname,int &printlength);
 std::map<int, mydata2> load_lcastat(const char* fname);
 void  reconstructRefWithPosHTS(const bam1_t   * b,std::pair< kstring_t *, std::vector<int> > &pp,char *reconstructedTemp);