Changed samtools commands in deduplication_script to

FelixKrueger · Aug 20, 2015 · c66e529 · c66e529
1 parent 87270fe
commit c66e529
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Showing 2 changed files with 16 additions and 6 deletions.
diff --git a/RELEASE_NOTES.txt b/RELEASE_NOTES.txt
@@ -1,5 +1,15 @@
+RELEASE NOTES FOR Bismark v0.14.5 (20 08 2015)
+----------------------------------------------
+
+deduplicate_bismark
+===================
+
+Changed all instances of literal calls of 'samtools' calls to '$samtools_path'.
+
+
+
 RELEASE NOTES FOR Bismark v0.14.4 (17 08 2015)
------------------------------------------------
+----------------------------------------------
 
 Bismark
 =======

diff --git a/deduplicate_bismark b/deduplicate_bismark
@@ -29,7 +29,7 @@ use Getopt::Long;
 ### print "--representative\twill browse through all sequences and print out the sequence with the most representative (as in most frequent) methylation call for any given position. Note that this is very likely the most highly amplified PCR product for a given sequence\n\n";
 
 
-my $dedup_version = 'v0.14.4';
+my $dedup_version = 'v0.14.5';
 
 
 my $help;
@@ -204,7 +204,7 @@ foreach my $file (@filenames){
       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";
@@ -266,7 +266,7 @@ foreach my $file (@filenames){
       open (IN,"zcat $file |") or die "Unable to read from gzipped file $file: $!\n";
     }
     elsif ($file =~ /\.bam$/){
-      open (IN,"samtools view -h $file |") or die "Unable to read from BAM file $file: $!\n";
+      open (IN,"$samtools_path view -h $file |") or die "Unable to read from BAM file $file: $!\n";
     }
     else{
       open (IN,$file) or die "Unable to read from $file: $!\n";
@@ -570,7 +570,7 @@ sub deduplicate_barcoded_rrbs{
     open (IN,"zcat $file |") or die "Unable to read from gzipped file $file: $!\n";
   }
   elsif ($file =~ /\.bam$/){
-    open (IN,"samtools view -h $file |") or die "Unable to read from BAM file $file: $!\n";
+    open (IN,"$samtools_path view -h $file |") or die "Unable to read from BAM file $file: $!\n";
   }
   else{
     open (IN,$file) or die "Unable to read from $file: $!\n";
@@ -903,7 +903,7 @@ sub deduplicate_representative {
     open (IN,"zcat $file |") or die "Unable to read from gzipped file $file: $!\n";
   }
   elsif ($file =~ /\.bam$/){
-    open (IN,"samtools view -h $file |") or die "Unable to read from BAM file $file: $!\n";
+    open (IN,"$samtools_path view -h $file |") or die "Unable to read from BAM file $file: $!\n";
   }
   else{
     open (IN,$file) or die "Unable to read from $file: $!\n";