Merge 3715665 into 3ac75d9

.gitignore

@@ -5,4 +5,5 @@
 !mip_install_perl.sh
 mip_log/
 **/.idea
+_Deparsed_XSubs.pm
 .gitignore

CHANGELOG.md

@@ -2,6 +2,10 @@
 All notable changes to this project will be documented in this file.
 This project adheres to [Semantic Versioning](http://semver.org/).
 
+## [9.0.5]
+- Predicted gender from wgs samples are now used in the generated fam files.
+- Restrict plink analysis to intersected target capture kits for mixed wgs/wes cases
+
 ## [9.0.4]
 - Increased memory allocation for samtools_subsample_mt
 - Check that vep plugin paths exists prior to executing mip

definitions/rd_dna_parameters.yaml

@@ -1433,7 +1433,7 @@ gatk_combinevariantcallsets:
   data_type: SCALAR
   default: 1
   file_tag: _gatkcomb
-  outfile_suffix: ".vcf"
+  outfile_suffix: ".vcf.gz"
   type: recipe
 gatk_combinevariantcallsets_bcf_file:
   associated_recipe:

lib/MIP/Constants.pm

@@ -20,7 +20,7 @@ BEGIN {
     use base qw{ Exporter };
 
     # Set the version for version checking
-    our $VERSION = 1.25;
+    our $VERSION = 1.26;
 
     # Functions and variables which can be optionally exported
 
@@ -80,7 +80,7 @@ Readonly our %ANALYSIS => (
 );
 
 ## Set MIP version
-Readonly our $MIP_VERSION => q{v9.0.4};
+Readonly our $MIP_VERSION => q{v9.0.5};
 
 ## Cli
 Readonly our $MOOSEX_APP_SCEEN_WIDTH => 160;

lib/MIP/Get/File.pm

@@ -25,32 +25,30 @@ BEGIN {
     use base qw{ Exporter };
 
     # Set the version for version checking
-    our $VERSION = 1.14;
+    our $VERSION = 1.15;
 
     # Functions and variables which can be optionally exported
     our @EXPORT_OK = qw{
-      get_exom_target_bed_file
+      get_exome_target_bed_file
       get_io_files
       get_merged_infile_prefix
       get_path_entries
     };
 }
 
-sub get_exom_target_bed_file {
+sub get_exome_target_bed_file {
 
 ## Function : Get exome_target_bed file for specfic sample_id and add file_ending from file_info hash if supplied
 ## Returns  : $exome_target_bed_file
 ## Arguments: $exome_target_bed_href => Exome target bed files lnked to sample ids
 ##          : $file_ending           => File ending to add to file
-##          : $log                   => Log object
 ##          : $sample_id             => Sample id
 
     my ($arg_href) = @_;
 
     ## Flatten argument(s)
     my $exome_target_bed_href;
     my $file_ending;
-    my $log;
     my $sample_id;
 
     my $tmpl = {
@@ -62,12 +60,7 @@ sub get_exom_target_bed_file {
             store       => \$exome_target_bed_href,
         },
         file_ending => { store => \$file_ending },
-        log         => {
-            required => 1,
-            defined  => 1,
-            store    => \$log
-        },
-        sample_id => {
+        sample_id   => {
             required    => 1,
             defined     => 1,
             strict_type => 1,
@@ -77,6 +70,11 @@ sub get_exom_target_bed_file {
 
     check( $tmpl, $arg_href, 1 ) or croak q{Could not parse arguments!};
 
+    ### PREPROCESSING:
+
+    ## Retrieve logger object
+    my $log = Log::Log4perl->get_logger($LOG_NAME);
+
     ## To track sample_ids with capture kits
     my %seen;
 
@@ -111,7 +109,7 @@ sub get_exom_target_bed_file {
     $log->fatal(
         q{Could not detect }
           . $sample_id
-          . q{ in '-exome_target_bed' associated files in sub routine get_exom_target_bed_file},
+          . q{ in '-exome_target_bed' associated files in sub routine get_exome_target_bed_file},
         $NEWLINE
     );
     exit 1;
@@ -506,7 +504,7 @@ sub _collect_outfile {
             strict_type => 1,
         },
         value => { defined => 1, required => 1, store => \$value, },
-        key => { defined => 1, store => \$key, required => 1, strict_type => 1, },
+        key   => { defined => 1, store => \$key, required => 1, strict_type => 1, },
     };
 
     check( $tmpl, $arg_href, 1 ) or croak q{Could not parse arguments!};

lib/MIP/Get/Parameter.pm

@@ -20,7 +20,7 @@ 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{
@@ -115,19 +115,18 @@ sub get_gatk_intervals {
 
     check( $tmpl, $arg_href, 1 ) or croak q{Could not parse arguments!};
 
-    use MIP::Get::File qw{ get_exom_target_bed_file };
+    use MIP::Get::File qw{ get_exome_target_bed_file };
     use MIP::File::Interval qw{ generate_contig_interval_file };
 
     ## Store gatk interval
     my %gatk_intervals;
 
     if ( $analysis_type eq q{wes} ) {
 
-        my $exome_target_bed_file = get_exom_target_bed_file(
+        my $exome_target_bed_file = get_exome_target_bed_file(
             {
                 exome_target_bed_href => $exome_target_bed_href,
                 file_ending           => $file_ending,
-                log                   => $log,
                 sample_id             => $sample_id,
             }
         );

lib/MIP/Main/Analyse.pm

@@ -77,7 +77,7 @@ BEGIN {
     require Exporter;
 
     # Set the version for version checking
-    our $VERSION = 1.59;
+    our $VERSION = 1.60;
 
     # Functions and variables which can be optionally exported
     our @EXPORT_OK = qw{ mip_analyse };
@@ -461,7 +461,6 @@ sub mip_analyse {
             case_id          => $active_parameter_href->{case_id},
             execution_mode   => q{system},
             fam_file_path    => $active_parameter_href->{pedigree_fam_file},
-            parameter_href   => $parameter_href,
             sample_ids_ref   => $active_parameter_href->{sample_ids},
             sample_info_href => \%sample_info,
         }
@@ -505,9 +504,12 @@ sub mip_analyse {
 
     write_job_ids_to_file(
         {
-            case_id         => $active_parameter_href->{case_id},
-            job_id_href     => \%job_id,
-            job_ids_file_path => catfile($active_parameter_href->{outdata_dir}, q{slurm_job_ids} . $DOT . q{yaml}),
+            case_id           => $active_parameter_href->{case_id},
+            job_id_href       => \%job_id,
+            job_ids_file_path => catfile(
+                $active_parameter_href->{outdata_dir},
+                q{slurm_job_ids} . $DOT . q{yaml}
+            ),
         }
     );
 

lib/MIP/Parse/Gender.pm

@@ -36,7 +36,7 @@ BEGIN {
     use base qw{ Exporter };
 
     # Set the version for version checking
-    our $VERSION = 1.10;
+    our $VERSION = 1.11;
 
     # Functions and variables which can be optionally exported
     our @EXPORT_OK = qw{ build_stream_file_cmd
@@ -240,13 +240,15 @@ sub parse_fastq_for_gender {
 ## Arguments: $active_parameter_href   => Active parameters for this analysis hash {REF}
 ##          : $consensus_analysis_type => Consensus analysis_type
 ##          : $file_info_href          => File info hash {REF}
+##          : $sample_info_href        => Sample info hash {REF}
 
     my ($arg_href) = @_;
 
     ## Flatten argument(s)
     my $active_parameter_href;
     my $consensus_analysis_type;
     my $file_info_href;
+    my $sample_info_href;
 
     my $tmpl = {
         active_parameter_href => {
@@ -269,6 +271,13 @@ sub parse_fastq_for_gender {
             store       => \$file_info_href,
             strict_type => 1,
         },
+        sample_info_href => {
+            default     => {},
+            defined     => 1,
+            required    => 1,
+            store       => \$sample_info_href,
+            strict_type => 1,
+        },
     };
 
     check( $tmpl, $arg_href, 1 ) or croak q{Could not parse arguments!};
@@ -371,6 +380,7 @@ sub parse_fastq_for_gender {
                 consensus_analysis_type => $consensus_analysis_type,
                 file_info_href          => $file_info_href,
                 sample_id               => $sample_id,
+                sample_info_href        => $sample_info_href,
                 y_read_count            => $y_read_count,
             }
         );
@@ -386,6 +396,7 @@ sub update_gender_info {
 ##          : $consensus_analysis_type => Consensus analysis_type
 ##          : $file_info_href          => File info hash {REF}
 ##          : $sample_id               => Sample id
+##          : $sample_info_href        => File info hash {REF}
 ##          : $y_read_count            => Y read count
 
     my ($arg_href) = @_;
@@ -395,6 +406,7 @@ sub update_gender_info {
     my $consensus_analysis_type;
     my $file_info_href;
     my $sample_id;
+    my $sample_info_href;
     my $y_read_count;
 
     my $tmpl = {
@@ -424,6 +436,13 @@ sub update_gender_info {
             store       => \$sample_id,
             strict_type => 1,
         },
+        sample_info_href => {
+            default     => {},
+            defined     => 1,
+            required    => 1,
+            store       => \$sample_info_href,
+            strict_type => 1,
+        },
         y_read_count => {
             required => 1,
             store    => \$y_read_count,
@@ -435,6 +454,7 @@ sub update_gender_info {
     use MIP::Active_parameter
       qw{ add_gender remove_sample_id_from_gender set_gender_estimation set_include_y };
     use MIP::Contigs qw{ update_contigs_for_run };
+    use MIP::Sample_info qw{ set_sample_gender };
 
     my $log = Log::Log4perl->get_logger($LOG_NAME);
 
@@ -445,6 +465,7 @@ sub update_gender_info {
     my $genders = $gender . q{s};
     $log->info(qq{Found $gender according to fastq reads});
 
+    ## Update in active parameter hash
     add_gender(
         {
             active_parameter_href => $active_parameter_href,
@@ -476,6 +497,17 @@ sub update_gender_info {
         }
     );
 
+    ## Update gender in sample info hash
+    set_sample_gender(
+        {
+            gender           => $gender,
+            sample_id        => $sample_id,
+            sample_info_href => $sample_info_href,
+        }
+    );
+
+    ## Update cache
+
     ## Update contigs depending on settings in run (wes or if only male samples)
     update_contigs_for_run(
         {