#  runChicago parameters:
	 
help	FALSE 
print_memory	FALSE 
rda	FALSE 
save_df_only	FALSE 
examples_full_range	FALSE 
en_full_cis_range	FALSE 
en_trans	FALSE 
features_only	FALSE 
opts	NA 
settings_file	NA 
design_dir	/research/work/ilakya/CALCRL_project/PChIC/files/New/ 
cutoff	5 
export_format	interBed,washU_text,washU_track 
export_order	position 
examples_prox_dist	1e+06 
output_dir	<output-prefix> 
en_feat_files	NA 
en_feat_list	NA 
en_feat_folder	NA 
en_min_dist	0 
en_max_dist	1e+06 
en_sample_no	100 
<input_files>	/research/groups/cadgen/PROJECTS/CAD_Enhancer/PChiC-HAEC-3/Romanoski_2_2/Romanoski_2_2.chinput 
<output_prefix>	Romanoski_2_2 

#  chicago pipeline settings (chicagoData@settings):
rmapfile	/research/work/ilakya/CALCRL_project/PChIC/files/New//Digest_Human_HindIII.rmap 
baitmapfile	/research/work/ilakya/CALCRL_project/PChIC/files/New//Digest_Human_HindIII_baits_e75_ID.baitmap 
nperbinfile	/research/work/ilakya/CALCRL_project/PChIC/files/New//Human_HindIII.npb 
nbaitsperbinfile	/research/work/ilakya/CALCRL_project/PChIC/files/New//Human_HindIII.nbpb 
proxOEfile	/research/work/ilakya/CALCRL_project/PChIC/files/New//Human_HindIII.poe 
Ncol	N 
baitmapFragIDcol	4 
baitmapGeneIDcol	5 
maxLBrownEst	1500000 
minFragLen	150 
maxFragLen	40000 
minNPerBait	250 
binsize	20000 
removeAdjacent	TRUE 
adjBait2bait	TRUE 
tlb.filterTopPercent	0.01 
tlb.minProxOEPerBin	50000 
tlb.minProxB2BPerBin	2500 
techNoise.minBaitsPerBin	1000 
brownianNoise.samples	5 
brownianNoise.subset	1000 
brownianNoise.seed	NA 
baitIDcol	baitID 
otherEndIDcol	otherEndID 
otherEndLencol	otherEndLen 
distcol	distSign 
weightAlpha	34.1157346557331 
weightBeta	-2.58688050486759 
weightGamma	-17.1347845819659 
weightDelta	-7.07609245521541 

#  sessionInfo()
R version 3.6.0 (2019-04-26)
Platform: x86_64-redhat-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS/LAPACK: /usr/lib64/R/lib/libRblas.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] Chicago_1.12.0    data.table_1.12.2 argparser_0.4    

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.2          pillar_1.4.2        compiler_3.6.0     
 [4] RColorBrewer_1.1-2  tools_3.6.0         base64enc_0.1-3    
 [7] digest_0.6.20       rpart_4.1-15        tibble_2.1.3       
[10] gtable_0.3.0        htmlTable_1.13.1    checkmate_1.9.4    
[13] lattice_0.20-38     pkgconfig_2.0.2     rlang_0.4.0        
[16] Matrix_1.2-17       rstudioapi_0.10     xfun_0.8           
[19] gridExtra_2.3       stringr_1.4.0       knitr_1.24         
[22] dplyr_0.8.3         cluster_2.1.0       htmlwidgets_1.3    
[25] grid_3.6.0          nnet_7.3-12         tidyselect_0.2.5   
[28] glue_1.3.1          Delaporte_7.0.2     R6_2.4.0           
[31] survival_2.44-1.1   foreign_0.8-72      latticeExtra_0.6-28
[34] Formula_1.2-3       ggplot2_3.2.1       purrr_0.3.2        
[37] magrittr_1.5        MASS_7.3-51.4       htmltools_0.3.6    
[40] backports_1.1.4     Hmisc_4.2-0         scales_1.0.0       
[43] matrixStats_0.54.0  splines_3.6.0       assertthat_0.2.1   
[46] colorspace_1.4-1    stringi_1.4.3       acepack_1.4.1      
[49] lazyeval_0.2.2      munsell_0.5.0       crayon_1.3.4