Issue with readme and problem of setting working directory

[tahuh]

Hi @dinhdiep

Thanks for sharing this nice software to the community.

I have reviewed the README file and found that there is a wrong instruction at Identifying the methylation haplotype blocks

cghap2mhbs.sh [haplotype file] [target bed] [minimum LD R2 cutoff] [output name prefix]

This should be changed into cghap2mhbs.sh [haplotype file] [target bed] [minimum LD R2 cutoff] [snp files] [output name prefix]

The source code scripts/cghap2mhbs.sh says

if [ -z "$4" ]
then
        echo "usage: $0 [haplotype file] [target bed] [minimum LD R2 cutoff] [snp file] [output name prefix]"
        exit 0
fi

In addition to above readme suggestion, there are problems regarding to global or local PATH settings in some scripts or code.

For example, the perl script bin/cgHap2MHBs_parallel.pl wants to run bin/hapInfo_maskSNPs2mld_block.pl as shown below

sub run_process{
#  my $hap_info_file = 
#  my $bin_file = 
#  my $min_r2 = 
#  my $cg_snp_bed_file =
  my $file = shift;
  my $cmd = "bin/hapInfo_maskSNPs2mld_block.pl hapinfo_$file.tmp $minR2 $snpBedFile > $outNamePrefix.$file";
  system($cmd);
  unlink("hapinfo_$file.tmp");
}

But when I execute bin/cgHap2MHBs_parallel.pl perl cannot find bin/hapInfo_maskSNPs2mld_block.pl.

Below is how my system complains about above problem.

sh: 1: bin/hapInfo_maskSNPs2mld_block.pl: not found
sh: 1: bin/hapInfo_maskSNPs2mld_block.pl: not found
sh: 1: bin/hapInfo_maskSNPs2mld_block.pl: not found
sh: 1: bin/hapInfo_maskSNPs2mld_block.pl: not found
sh: 1: bin/hapInfo_maskSNPs2mld_block.pl: not found
sh: 1: bin/hapInfo_maskSNPs2mld_block.pl: not found
sh: 1: bin/hapInfo_maskSNPs2mld_block.pl: not found
sh: 1: bin/hapInfo_maskSNPs2mld_block.pl: not found
sh: 1: bin/hapInfo_maskSNPs2mld_block.pl: not found
sh: 1: bin/hapInfo_maskSNPs2mld_block.pl: not found
sh: 1: bin/hapInfo_maskSNPs2mld_block.pl: not found
sh: 1: bin/hapInfo_maskSNPs2mld_block.pl: not found

This happens not only this perl script but some other shell scripts.

It would be great if you make a comment about path settings or fix those issue.

Thanks for reading this long comment.

[Flower9618]

Hello, I meet the same problem. Do you know what this snp file means? @tahuh .Thank you very much.