Linkage_pull.pl code

[Avramis]

The source code for Linkage_pull.pl in the dpclust3p/R/preprocessing.R file is deprecated and should be removed.

Adjust the commands

cmd=paste(LINKAGEPULL, " ", nearbyMuts_file, " ", bam_file, " ", bai_file, " ", zoomed_phase_file, " Mut", sep="")

in line 181 within the run_linkage_pull_mut function, and

cmd=paste(LINKAGEPULL, " ", linkedFile, " ", bam_file, " ", bai_file, " ", outfile, " SNP", sep="")

in line 276 within the run_linkage_pull_mut function to call the currently used function.