Merge pull request #3 from khillion/master

modified help page and samtools_path usage

SNPsplit

@@ -192,7 +192,7 @@ sub process_masked_BAM_file{
 
   my ($file) = @_;
 
-  open (IN,"samtools view -h $file |") or die "Failed to read from BAM file $file: $!\n";
+  open (IN,"$samtools_path view -h $file |") or die "Failed to read from BAM file $file: $!\n";
   warn "Reading from sorted mapping file '$file'\n";
   ### READING FROM MAPPING BAM FILE
 
@@ -1078,7 +1078,7 @@ sub sam2bam_convert{
   warn "Now converting '$file' to '$bamfile' ...\n";
   sleep (3);
 
-  system ("samtools view -bS $file > $bamfile");
+  system ("$samtools_path view -bS $file > $bamfile");
 
   warn "BAM conversion finished\n\n";
   sleep (3);
@@ -1094,7 +1094,7 @@ sub sort_by_name_paired_end{
   $sorted =~ s/bam$/sortedByName.bam/;
 
   warn "Sorting paired-end BAM file '$file' by read IDs ...\n";
-  system ("samtools sort -n $file -o $sorted");
+  system ("$samtools_path sort -n $file -o $sorted");
 
   $file = $sorted; # setting sorted BAM file as new $file
   warn "Finished sorting BAM file into new file '$file'\n\n";
@@ -1281,7 +1281,7 @@ sub check_for_bs{
     open (DETERMINE,"zcat $file |") or die "Unable to read from gzipped file $file: $!\n";
   }
   elsif ($file =~ /\.bam$/ ){
-    open (DETERMINE,"samtools view -h $file |") or die "Unable to read from BAM file $file: $!\n";
+    open (DETERMINE,"$samtools_path view -h $file |") or die "Unable to read from BAM file $file: $!\n";
   }
   else{
     open (DETERMINE,$file) or die "Unable to read from $file: $!\n";
@@ -1604,7 +1604,7 @@ The SNPsplit-sort module reads in the tagged BAM file and sorts the reads (or re
 tag (or the combination of tags for paired-end or Hi-C reads) into subfiles.
 
 
-  USAGE:      SNPsplit_genome_preparation  [options] --vcf_file <VCF.file> --genome /path/to/genome/ [input file(s)]
+  USAGE:      SNPsplit  [options] --snp_file <SNP.file.gz> [input file(s)]
 
 
 input file(s)          Mapping output file in SAM or BAM format. SAM files (ending in .sam) will first be
@@ -1641,7 +1641,7 @@ input file(s)          Mapping output file in SAM or BAM format. SAM files (endi
                        automatically. In addition it will perform a quick check to see if a paired-end file appears
                        to have been positionally sorted, and if not will set the --no_sort flag.
 
---samtools-path        The path to your Samtools installation, e.g. /home/user/samtools/. Does not need to
+--samtools_path        The path to your Samtools installation, e.g. /home/user/samtools/. Does not need to
                        be specified explicitly if Samtools is in the PATH already.
 
 --verbose              Verbose output (for debugging).