feat(htslib): Refactor and move up one dir

Clinical-Genomics · Nov 26, 2019 · 81076dc · 81076dc
1 parent e684435
commit 81076dc
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Showing 13 changed files with 43 additions and 53 deletions.
diff --git a/lib/MIP/Program/Utility/Htslib.pm → lib/MIP/Program/Htslib.pm b/lib/MIP/Program/Utility/Htslib.pm → lib/MIP/Program/Htslib.pm
@@ -1,4 +1,4 @@
-package MIP::Program::Utility::Htslib;
+package MIP::Program::Htslib;
 
 use 5.026;
 use Carp;
@@ -15,6 +15,7 @@ use warnings qw{ FATAL utf8 };
 use Readonly;
 
 ## MIPs lib/
+use MIP::Constants qw{ $SPACE };
 use MIP::Unix::Standard_streams qw{ unix_standard_streams };
 use MIP::Unix::Write_to_file qw{ unix_write_to_file };
 
@@ -23,15 +24,12 @@ BEGIN {
     use base qw{ Exporter };
 
     # Set the version for version checking
-    our $VERSION = 1.01;
+    our $VERSION = 1.02;
 
     # Functions and variables which can be optionally exported
     our @EXPORT_OK = qw{ htslib_bgzip htslib_tabix };
 }
 
-## Constants
-Readonly my $SPACE => q{ };
-
 sub htslib_bgzip {
 
 ## Function : Perl wrapper for writing bgzip recipe to $filehandle or return commands array. Based on htslib 1.3.1.
@@ -101,7 +99,6 @@ sub htslib_bgzip {
     ## Stores commands depending on input parameters
     my @commands = q{bgzip};
 
-    ## Options
     if ($decompress) {
 
         push @commands, q{--decompress};
@@ -116,7 +113,6 @@ sub htslib_bgzip {
         push @commands, q{--stdout};
     }
 
-    ## Infile
     if ($infile_path) {
 
         push @commands, $infile_path;
@@ -134,8 +130,8 @@ sub htslib_bgzip {
     unix_write_to_file(
         {
             commands_ref => \@commands,
-            separator    => $SPACE,
             filehandle   => $filehandle,
+            separator    => $SPACE,
         }
     );
     return @commands;
@@ -244,7 +240,6 @@ sub htslib_tabix {
     ## Stores commands depending on input parameters
     my @commands = q{tabix};
 
-    ## Options
     if ($force) {
 
         push @commands, q{--force};
@@ -279,13 +274,11 @@ sub htslib_tabix {
         push @commands, q{--sequence} . $SPACE . $sequence;
     }
 
-    ## Infile
     if ($infile_path) {
 
         push @commands, $infile_path;
     }
 
-    # Limit output to regions
     if ( @{$regions_ref} ) {
 
         push @commands, join $SPACE, @{$regions_ref};
@@ -303,8 +296,8 @@ sub htslib_tabix {
     unix_write_to_file(
         {
             commands_ref => \@commands,
-            separator    => $SPACE,
             filehandle   => $filehandle,
+            separator    => $SPACE,
         }
     );
     return @commands;

diff --git a/lib/MIP/Recipes/Analysis/Cadd.pm b/lib/MIP/Recipes/Analysis/Cadd.pm
@@ -27,7 +27,7 @@ BEGIN {
     use base qw{ Exporter };
 
     # Set the version for version checking
-    our $VERSION = 1.04;
+    our $VERSION = 1.05;
 
     # Functions and variables which can be optionally exported
     our @EXPORT_OK = qw{ analysis_cadd analysis_cadd_gb_38 };
@@ -36,9 +36,9 @@ BEGIN {
 
 ## Constants
 Readonly my $GENOME_BUILD_NR_38 => 38;
-Readonly my $REGION_START       => q{2};
-Readonly my $REGION_END         => q{2};
-Readonly my $SEQUENCE_NAME      => q{1};
+Readonly my $REGION_START       => 2;
+Readonly my $REGION_END         => 2;
+Readonly my $SEQUENCE_NAME      => 1;
 
 sub analysis_cadd {
 
@@ -139,7 +139,7 @@ sub analysis_cadd {
     use MIP::Parse::File qw{ parse_io_outfiles };
     use MIP::Program::Variantcalling::Bcftools qw{ bcftools_annotate bcftools_view };
     use MIP::Program::Cadd qw{ cadd };
-    use MIP::Program::Utility::Htslib qw{ htslib_tabix };
+    use MIP::Program::Htslib qw{ htslib_tabix };
     use MIP::Processmanagement::Processes qw{ submit_recipe };
     use MIP::Sample_info qw{ set_recipe_outfile_in_sample_info };
     use MIP::Recipes::Analysis::Xargs qw{ xargs_command };
@@ -516,7 +516,7 @@ sub analysis_cadd_gb_38 {
     use MIP::Program::Gzip qw{ gzip };
     use MIP::Program::Variantcalling::Bcftools qw{ bcftools_annotate bcftools_view };
     use MIP::Program::Cadd qw{ cadd };
-    use MIP::Program::Utility::Htslib qw{ htslib_bgzip htslib_tabix };
+    use MIP::Program::Htslib qw{ htslib_bgzip htslib_tabix };
     use MIP::Processmanagement::Processes qw{ submit_recipe };
     use MIP::Sample_info qw{ set_recipe_outfile_in_sample_info };
     use MIP::Recipes::Analysis::Xargs qw{ xargs_command };

diff --git a/lib/MIP/Recipes/Analysis/Endvariantannotationblock.pm b/lib/MIP/Recipes/Analysis/Endvariantannotationblock.pm
@@ -25,7 +25,7 @@ BEGIN {
     use base qw{ Exporter };
 
     # Set the version for version checking
-    our $VERSION = 1.07;
+    our $VERSION = 1.08;
 
     # Functions and variables which can be optionally exported
     our @EXPORT_OK = qw{ analysis_endvariantannotationblock };
@@ -155,7 +155,7 @@ sub analysis_endvariantannotationblock {
     use MIP::Gnu::Software::Gnu_grep qw{ gnu_grep };
     use MIP::Parse::File qw{ parse_io_outfiles };
     use MIP::Processmanagement::Processes qw{ submit_recipe };
-    use MIP::Program::Utility::Htslib qw{ htslib_bgzip htslib_tabix };
+    use MIP::Program::Htslib qw{ htslib_bgzip htslib_tabix };
     use MIP::Program::Variantcalling::Gatk qw{ gatk_concatenate_variants };
     use MIP::Sample_info qw{ set_most_complete_vcf set_recipe_metafile_in_sample_info };
     use MIP::Script::Setup_script qw{ setup_script };

diff --git a/lib/MIP/Recipes/Analysis/Prepareforvariantannotationblock.pm b/lib/MIP/Recipes/Analysis/Prepareforvariantannotationblock.pm
@@ -25,7 +25,7 @@ BEGIN {
     use base qw{ Exporter };
 
     # Set the version for version checking
-    our $VERSION = 1.07;
+    our $VERSION = 1.08;
 
     # Functions and variables which can be optionally exported
     our @EXPORT_OK = qw{ analysis_prepareforvariantannotationblock };
@@ -150,7 +150,7 @@ sub analysis_prepareforvariantannotationblock {
     use MIP::Get::Parameter qw{ get_recipe_attributes get_recipe_resources };
     use MIP::Parse::File qw{ parse_io_outfiles };
     use MIP::Processmanagement::Processes qw{ submit_recipe };
-    use MIP::Program::Utility::Htslib qw{ htslib_bgzip htslib_tabix };
+    use MIP::Program::Htslib qw{ htslib_bgzip htslib_tabix };
     use MIP::Recipes::Analysis::Xargs qw{ xargs_command };
     use MIP::Script::Setup_script qw(setup_script);
 

diff --git a/lib/MIP/Recipes/Analysis/Vcf_rerun_reformat.pm b/lib/MIP/Recipes/Analysis/Vcf_rerun_reformat.pm
@@ -26,7 +26,7 @@ BEGIN {
     use base qw{ Exporter };
 
     # Set the version for version checking
-    our $VERSION = 1.06;
+    our $VERSION = 1.07;
 
     # Functions and variables which can be optionally exported
     our @EXPORT_OK = qw{ analysis_vcf_rerun_reformat_sv analysis_vcf_rerun_reformat };
@@ -137,7 +137,7 @@ sub analysis_vcf_rerun_reformat_sv {
     use MIP::Parse::File qw{ parse_io_outfiles };
     use MIP::Processmanagement::Processes qw{ submit_recipe };
     use MIP::Program::Variantcalling::Bcftools qw{ bcftools_view };
-    use MIP::Program::Utility::Htslib qw{ htslib_bgzip htslib_tabix };
+    use MIP::Program::Htslib qw{ htslib_bgzip htslib_tabix };
     use MIP::Script::Setup_script qw{ setup_script };
     use MIP::Set::File qw{ set_io_files };
 
@@ -372,7 +372,7 @@ sub analysis_vcf_rerun_reformat {
     use MIP::Parse::File qw{ parse_io_outfiles };
     use MIP::Processmanagement::Processes qw{ submit_recipe };
     use MIP::Program::Variantcalling::Bcftools qw{ bcftools_view };
-    use MIP::Program::Utility::Htslib qw{ htslib_bgzip htslib_tabix };
+    use MIP::Program::Htslib qw{ htslib_bgzip htslib_tabix };
     use MIP::Script::Setup_script qw{ setup_script };
 
     ### PREPROCESSING:

diff --git a/lib/MIP/Recipes/Analysis/Vep.pm b/lib/MIP/Recipes/Analysis/Vep.pm
@@ -29,7 +29,7 @@ BEGIN {
     use base qw{ Exporter };
 
     # Set the version for version checking
-    our $VERSION = 1.23;
+    our $VERSION = 1.24;
 
     # Functions and variables which can be optionally exported
     our @EXPORT_OK =
@@ -1682,7 +1682,7 @@ sub _subset_vcf {
 
     check( $tmpl, $arg_href, 1 ) or croak q{Could not parse arguments!};
 
-    use MIP::Program::Utility::Htslib qw{ htslib_bgzip };
+    use MIP::Program::Htslib qw{ htslib_bgzip };
     use MIP::Program::Variantcalling::Bcftools qw{ bcftools_index bcftools_view };
 
     ## Prepare for bcftools_view

diff --git a/lib/MIP/Recipes/Analysis/Vt_core.pm b/lib/MIP/Recipes/Analysis/Vt_core.pm
@@ -24,7 +24,7 @@ BEGIN {
     use base qw{ Exporter };
 
     # Set the version for version checking
-    our $VERSION = 1.07;
+    our $VERSION = 1.08;
 
     # Functions and variables which can be optionally exported
     our @EXPORT_OK = qw{ analysis_vt_core analysis_vt_core_rio };
@@ -203,7 +203,7 @@ sub analysis_vt_core {
     use MIP::Gnu::Coreutils qw{ gnu_mv };
     use MIP::Gnu::Software::Gnu_sed qw{ gnu_sed };
     use MIP::Processmanagement::Processes qw{ submit_recipe };
-    use MIP::Program::Utility::Htslib qw{ htslib_bgzip htslib_tabix };
+    use MIP::Program::Htslib qw{ htslib_bgzip htslib_tabix };
     use MIP::Program::Variantcalling::Allele_frequency qw{ calculate_af max_af };
     use MIP::Program::Variantcalling::Bcftools qw{ bcftools_view bcftools_index };
     use MIP::Program::Variantcalling::Vt qw{ vt_decompose vt_normalize vt_uniq };
@@ -578,7 +578,7 @@ sub analysis_vt_core_rio {
     use MIP::Gnu::Software::Gnu_sed qw{ gnu_sed };
     use MIP::Processmanagement::Slurm_processes
       qw{ slurm_submit_job_no_dependency_add_to_samples };
-    use MIP::Program::Utility::Htslib qw{ htslib_bgzip htslib_tabix };
+    use MIP::Program::Htslib qw{ htslib_bgzip htslib_tabix };
     use MIP::Program::Variantcalling::Allele_frequency qw{ calculate_af max_af };
     use MIP::Program::Variantcalling::Bcftools qw{ bcftools_view bcftools_index };
     use MIP::Program::Variantcalling::Vt qw{ vt_decompose vt_normalize vt_uniq };

diff --git a/lib/MIP/Recipes/Download/Clinvar.pm b/lib/MIP/Recipes/Download/Clinvar.pm
@@ -27,7 +27,7 @@ BEGIN {
     use base qw{ Exporter };
 
     # Set the version for version checking
-    our $VERSION = 1.02;
+    our $VERSION = 1.03;
 
     # Functions and variables which can be optionally exported
     our @EXPORT_OK = qw{ download_clinvar };
@@ -124,7 +124,7 @@ sub download_clinvar {
 
     use MIP::Get::Parameter qw{ get_recipe_resources };
     use MIP::Gnu::Coreutils qw{ gnu_rm };
-    use MIP::Program::Utility::Htslib qw{ htslib_bgzip htslib_tabix };
+    use MIP::Program::Htslib qw{ htslib_bgzip htslib_tabix };
     use MIP::Program::Variantcalling::Bcftools qw{ bcftools_annotate };
     use MIP::Recipes::Download::Get_reference qw{ get_reference };
     use MIP::Script::Setup_script qw{ setup_script };

diff --git a/lib/MIP/Recipes/Download/Dbnsfp.pm b/lib/MIP/Recipes/Download/Dbnsfp.pm
@@ -27,7 +27,7 @@ BEGIN {
     use base qw{ Exporter };
 
     # Set the version for version checking
-    our $VERSION = 1.02;
+    our $VERSION = 1.03;
 
     # Functions and variables which can be optionally exported
     our @EXPORT_OK = qw{ download_dbnsfp };
@@ -132,7 +132,7 @@ sub download_dbnsfp {
     use MIP::Gnu::Coreutils qw{ gnu_cat gnu_head gnu_sort };
     use MIP::Gnu::Software::Gnu_grep qw{ gnu_grep };
     use MIP::Language::Awk qw{ awk };
-    use MIP::Program::Utility::Htslib qw{ htslib_bgzip htslib_tabix };
+    use MIP::Program::Htslib qw{ htslib_bgzip htslib_tabix };
     use MIP::Recipes::Download::Get_reference qw{ get_reference };
     use MIP::Script::Setup_script qw{ setup_script };
     use MIP::Processmanagement::Slurm_processes

diff --git a/lib/MIP/Recipes/Download/Genomic_superdups.pm b/lib/MIP/Recipes/Download/Genomic_superdups.pm
@@ -27,7 +27,7 @@ BEGIN {
     use base qw{ Exporter };
 
     # Set the version for version checking
-    our $VERSION = 1.03;
+    our $VERSION = 1.04;
 
     # Functions and variables which can be optionally exported
     our @EXPORT_OK = qw{ download_genomic_superdups };
@@ -129,7 +129,7 @@ sub download_genomic_superdups {
     use MIP::Gnu::Coreutils qw{ gnu_cut gnu_sort gnu_uniq };
     use MIP::Gnu::Software::Gnu_grep qw{ gnu_grep };
     use MIP::Parse::File qw{ parse_file_suffix };
-    use MIP::Program::Utility::Htslib qw{ htslib_bgzip htslib_tabix };
+    use MIP::Program::Htslib qw{ htslib_bgzip htslib_tabix };
     use MIP::Recipes::Download::Get_reference qw{ get_reference };
     use MIP::Script::Setup_script qw{ setup_script };
     use MIP::Processmanagement::Slurm_processes

diff --git a/lib/MIP/Recipes/Download/Gnomad.pm b/lib/MIP/Recipes/Download/Gnomad.pm
@@ -26,7 +26,7 @@ BEGIN {
     use base qw{ Exporter };
 
     # Set the version for version checking
-    our $VERSION = 1.04;
+    our $VERSION = 1.05;
 
     # Functions and variables which can be optionally exported
     our @EXPORT_OK = qw{ download_gnomad };
@@ -123,7 +123,7 @@ sub download_gnomad {
 
     use MIP::Get::Parameter qw{ get_recipe_resources };
     use MIP::Program::Rtg qw{ rtg_vcfsubset };
-    use MIP::Program::Utility::Htslib qw{ htslib_tabix };
+    use MIP::Program::Htslib qw{ htslib_tabix };
     use MIP::Recipes::Download::Get_reference qw{ get_reference };
     use MIP::Script::Setup_script qw{ setup_script };
     use MIP::Processmanagement::Slurm_processes

diff --git a/t/htslib_bgzip.t b/t/htslib_bgzip.t
@@ -20,10 +20,12 @@ use Readonly;
 
 ## MIPs lib/
 use lib catdir( dirname($Bin), q{lib} );
+use MIP::Constants qw{ $COMMA $SPACE };
+use MIP::Test::Commands qw{ test_function };
 use MIP::Test::Fixtures qw{ test_standard_cli };
 
 my $VERBOSE = 1;
-our $VERSION = 1.00;
+our $VERSION = 1.01;
 
 $VERBOSE = test_standard_cli(
     {
@@ -32,29 +34,24 @@ $VERBOSE = test_standard_cli(
     }
 );
 
-## Constants
-Readonly my $COMMA => q{,};
-Readonly my $SPACE => q{ };
-
 BEGIN {
 
     use MIP::Test::Fixtures qw{ test_import };
 
 ### Check all internal dependency modules and imports
 ## Modules with import
     my %perl_module = (
-        q{MIP::Program::Utility::Htslib} => [qw{ htslib_bgzip }],
-        q{MIP::Test::Fixtures}           => [qw{ test_standard_cli }],
+        q{MIP::Program::Htslib} => [qw{ htslib_bgzip }],
+        q{MIP::Test::Fixtures}  => [qw{ test_standard_cli }],
     );
 
     test_import( { perl_module_href => \%perl_module, } );
 }
 
-use MIP::Program::Utility::Htslib qw{ htslib_bgzip };
-use MIP::Test::Commands qw{ test_function };
+use MIP::Program::Htslib qw{ htslib_bgzip };
 
 diag(   q{Test htslib_bgzip from Htslib.pm v}
-      . $MIP::Program::Utility::Htslib::VERSION
+      . $MIP::Program::Htslib::VERSION
       . $COMMA
       . $SPACE . q{Perl}
       . $SPACE

diff --git a/t/htslib_tabix.t b/t/htslib_tabix.t
@@ -25,7 +25,7 @@ use MIP::Test::Commands qw{ test_function };
 use MIP::Test::Fixtures qw{ test_standard_cli };
 
 my $VERBOSE = 1;
-our $VERSION = 1.01;
+our $VERSION = 1.02;
 
 $VERBOSE = test_standard_cli(
     {
@@ -41,18 +41,18 @@ BEGIN {
 ### Check all internal dependency modules and imports
 ## Modules with import
     my %perl_module = (
-        q{MIP::Program::Utility::Htslib} => [qw{ htslib_tabix }],
-        q{MIP::Test::Fixtures}           => [qw{ test_standard_cli }],
+        q{MIP::Program::Htslib} => [qw{ htslib_tabix }],
+        q{MIP::Test::Fixtures}  => [qw{ test_standard_cli }],
     );
 
     test_import( { perl_module_href => \%perl_module, } );
 }
 
-use MIP::Program::Utility::Htslib qw{ htslib_tabix };
+use MIP::Program::Htslib qw{ htslib_tabix };
 use MIP::Test::Commands qw{ test_function };
 
 diag(   q{Test htslib_tabix from Htslib.pm v}
-      . $MIP::Program::Utility::Htslib::VERSION
+      . $MIP::Program::Htslib::VERSION
       . $COMMA
       . $SPACE . q{Perl}
       . $SPACE