root@max:/data/images/proton/DKlab/mr/parclip/bmix/nlopt-2.4.2# ./configure --enable-shared
reczko@max:/data/images/proton/DKlab/mr/parclip/bmix$ LD_LIBRARY_PATH=/usr/local/lib
reczko@max:/data/images/proton/DKlab/mr/parclip/bmix$ export LD_LIBRARY_PATH
reczko@max:/data/images/proton/DKlab/mr/parclip/bmix$ R CMD INSTALL nloptr_1.0.4.tar.gz 
reczko@max:/data/images/proton/DKlab/mr/parclip/bmix/BMix-master/source_R$ ./BMix ../test/CONFIG.txt 
../test/BMix_output/  created
Constructing mpileup file ...
Extracting mismatch information ...
../test/BMix_output/MismSummaries/  created
Output mismatch summary files opened in ../test/BMix_output/MismSummaries/
Classifying mismatches
../test/BMix_output/TC_Results/  created
Executing Rscript
[1] "../test/BMix_output/MismSummaries/" "../test/BMix_output/TC_Results/"   
[3] "5"                                  "0.95"                              
[5] "1"                                 
[1] "Estimated parameters:"
[1] "epsilon 0.001"
[1] "gamma 0.106025018001361"
[1] "nu 0.0080474838480915"
[1] "psi 0.422296623309176"
[1] "Estimated parameters:"
[1] "epsilon 0.0029154908599324"
[1] "gamma 0.145269909966978"
[1] "nu 0.00804172058596477"
[1] "psi 0.291050863933724"
Forming read groups ...
Reporting binding sites ...
../test/BMix_output/BindingSites/  created

/data/results/tools/samtools/samtools-1.3/misc/bowtie2sam.pl IL4-k-v3.bowtie |samtools view -Sb -t /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/WholeGenomeFasta/genome.fa.fai - | samtools sort -o - - > IL4-k-v3.bam


Interpret results in
/data/images/proton/DKlab/mr/parclip/bmix/BMix-master/test/IL4TC_Results/TC_f.results
Chr	Position	X	Y	MLE_ClassI	MLE_pC
chr10	3012878	0	12	2	0.99578562243382

using:
/data/images/proton/DKlab/mr/parclip/bmix/BMix-master/source_R/BMix.R
plot_classification = function (figure_file_name, classified_data, PosteriorTHR){ 
  # plot the classified points
  pdf(width=5, height=5, figure_file_name, useDingbats=F)
  F1 = (classified_data$MLE_ClassI==1)
  F2 = (classified_data$MLE_ClassI==2)
  F3 = (classified_data$MLE_ClassI==3)
  F4 = (classified_data$MLE_pC<PosteriorTHR)
  xl = range(c(classified_data$Y[F1],classified_data$Y[F2],classified_data$Y[F3]))
  yl = c(0,1)
  plot(classified_data$Y[F1],classified_data$X[F1]/classified_data$Y[F1], 
       log="x", xlim=xl, ylim=yl, pch=20, col = "darkorange", xaxt = 'n', yaxt='n',
       xlab="",ylab="")
  par(new=TRUE)
  plot(classified_data$Y[F2],classified_data$X[F2]/classified_data$Y[F2], 
       log="x", xlim=xl, ylim=yl, pch=20, col = "darkred", xaxt = 'n', yaxt='n',
       xlab="",ylab="")
  par(new=TRUE)
  plot(classified_data$Y[F3],classified_data$X[F3]/classified_data$Y[F3], 
       log="x", xlim=xl, ylim=yl, pch=20, col = "navy", xaxt = 'n', yaxt='n',
       xlab="",ylab="")
  par(new=TRUE)
  plot(classified_data$Y[F4],classified_data$X[F4]/classified_data$Y[F4], 
       log="x", xlim=xl, ylim=yl, pch=20, col = "darkgrey",
       xlab="coverage",ylab="mismatch frequency", cex.axis=1.5, cex.lab=1.5)
  legend("topright", cex = 0.5, legend = c("variant", "background", "cross-link loci", "not classified"), bty = "n", lty = 1, lwd=4, col = c("darkorange","darkred","navy","darkgrey"))
  par(new=FALSE)
  dev.off()
}

# using shrimp aln
]0;/data/images/proton/DKlab/mr/parclip/bmix/BMix-master/source_Rreczko@max:/data/images/proton/DKlab/mr/parclip/bmix/BMix-master/source_R$ time ./BMix ../test/CONFIG.IFN.txt 
/data/images/proton/DKlab/mr/parclip/bmix/BMix-master/test/IFN  created
Constructing mpileup file ...
Extracting mismatch information ...
/data/images/proton/DKlab/mr/parclip/bmix/BMix-master/test/IFNMismSummaries/  created
Output mismatch summary files opened in /data/images/proton/DKlab/mr/parclip/bmix/BMix-master/test/IFNMismSummaries/
Classifying mismatches
/data/images/proton/DKlab/mr/parclip/bmix/BMix-master/test/IFNTC_Results/  created
Executing Rscript
[1] "/data/images/proton/DKlab/mr/parclip/bmix/BMix-master/test/IFNMismSummaries/"
[2] "/data/images/proton/DKlab/mr/parclip/bmix/BMix-master/test/IFNTC_Results/"   
[3] "5"                                                                           
[4] "0.95"                                                                        
[5] "0"                                                                           
[1] "Estimated parameters:"
[1] "epsilon 0.00246994179223742"
[1] "gamma 0.151192196408611"
[1] "nu 0.000391802427667106"
[1] "psi 0.0112615783369127"
Forming read groups ...
Reporting binding sites ...
/data/images/proton/DKlab/mr/parclip/bmix/BMix-master/test/IFNBindingSites/  created

real	74m6.109s

#correlation with PARalyzer1_1b
/data/images/proton/DKlab/mr/parclip/paralyzer/PARalyzer_v1_1b/res/per_sample_plus/sh-clusters-IFN.txt3.csv.bed.flt.noIGG.plus.anno.csv
Wnt3	120	1185	ENSMUST00000000127	299	335	G24.1_AATTACATCGAGATCATGCCCAGCGTAGCAGAAGGTG_34_326_1_3_12	0.9485459890922588	+
Ncs1	357	927	ENSMUST00000000199	3830	3855	G93.1_ACGCCCCCTGGTGGTGATGAGCCGCA_10_3834_2_3_12	0.9185308021486109	+
/data/images/proton/DKlab/mr/parclip/bmix/BMix-master/test/IFNBindingSites/Sites_sorted.bed
ENSMUST00000000127	300	336	0	0	+
ENSMUST00000000199	3831	3852	0	0	+