feat(bwamem2): Remove samtools view

Clinical-Genomics · Aug 21, 2020 · e4147b7 · e4147b7
1 parent c8aed46
commit e4147b7
Showing 1 changed file with 14 additions and 21 deletions.
diff --git a/lib/MIP/Recipes/Analysis/Bwa_mem.pm b/lib/MIP/Recipes/Analysis/Bwa_mem.pm
@@ -25,7 +25,7 @@ BEGIN {
     use base qw{ Exporter };
 
     # Set the version for version checking
-    our $VERSION = 1.26;
+    our $VERSION = 1.27;
 
     # Functions and variables which can be optionally exported
     our @EXPORT_OK = qw{ analysis_bwa_mem analysis_bwa_mem2 analysis_run_bwa_mem };
@@ -573,6 +573,7 @@ sub analysis_bwa_mem2 {
     use MIP::Parse::File qw{ parse_io_outfiles };
     use MIP::Processmanagement::Processes qw{ submit_recipe };
     use MIP::Program::Bwa qw{ bwa_mem2_mem };
+    use MIP::Program::Gnu::Coreutils qw{ gnu_rm };
     use MIP::Program::Samtools
       qw{ samtools_index samtools_stats samtools_sort samtools_view };
     use MIP::Sample_info qw{
@@ -735,8 +736,8 @@ sub analysis_bwa_mem2 {
         ## Add missing "@RG"
         $rg_header_line =
           $DOUBLE_QUOTE . q{@RG} . q{\t} . $rg_header_line . $DOUBLE_QUOTE;
-        my $samtools_view_outfile_path =
-          $outfile_path_prefix . $UNDERSCORE . q{mem} . $outfile_suffix;
+        my $bwa_mem_outfile_path =
+          $outfile_path_prefix . $UNDERSCORE . q{mem} . $DOT . q{sam};
 
         # Prior to ALTs in reference genome
         bwa_mem2_mem(
@@ -749,37 +750,21 @@ sub analysis_bwa_mem2 {
                 read_group_header       => $rg_header_line,
                 soft_clip_sup_align => $active_parameter_href->{bwa_soft_clip_sup_align},
                 second_infile_path  => $second_fastq_file_path,
+                stdoutfile_path     => $bwa_mem_outfile_path,
                 thread_number       => $recipe_resource{core_number},
             }
         );
 
-        # Pipe SAM to BAM conversion of aligned reads
-        print {$filehandle} $PIPE . $SPACE;
-
-        samtools_view(
-            {
-                auto_detect_input_format => 1,
-                filehandle               => $filehandle,
-                infile_path              => q{-},
-                outfile_path             => $samtools_view_outfile_path,
-                thread_number            => $recipe_resource{core_number},
-                uncompressed_bam_output  => $uncompressed_bam_output,
-                with_header              => 1,
-            }
-        );
         say {$filehandle} $NEWLINE;
 
-        ## Set samtools sort input; Pipe from samtools view
-        my $samtools_sort_infile = $samtools_view_outfile_path;
-
         ## Increment paired end tracker
         $paired_end_tracker++;
 
         ## Sort the output from bwa mem
         samtools_sort(
             {
                 filehandle    => $filehandle,
-                infile_path   => $samtools_sort_infile,
+                infile_path   => $bwa_mem_outfile_path,
                 outfile_path  => $outfile_path,
                 output_format => $output_format,
                 temp_file_path_prefix =>
@@ -817,6 +802,14 @@ sub analysis_bwa_mem2 {
                 }
             );
             say {$filehandle} $AMPERSAND . $NEWLINE;
+
+            gnu_rm(
+                {
+                    filehandle  => $filehandle,
+                    infile_path => $bwa_mem_outfile_path,
+                }
+            );
+            say {$filehandle} $AMPERSAND . $NEWLINE;
         }
         say {$filehandle} q{wait} . $NEWLINE;