Merge branch 'hotfix/5.0.5'

cancerit · May 1, 2020 · d0bb91b · d0bb91b
2 parents 6e974f2 + 24c8215
commit d0bb91b
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Showing 5 changed files with 62 additions and 12 deletions.
diff --git a/CHANGES.md b/CHANGES.md
@@ -1,8 +1,12 @@
 # CHANGES
 
+## 5.0.5
+
+* Add `noindex` commandline flag to `merge_or_mark.pl` for bammerge calls. Only permitted alongisde `qnamesort`
+
 ## 5.0.4
 
-* Add `qnamesort` connamdline flag to `merge_or_mark.pl` for bammerge calls (Defaults to `SO=coordinate` without)
+* Add `qnamesort` commandline flag to `merge_or_mark.pl` for bammerge calls (Defaults to `SO=coordinate` without)
 
 ## 5.0.3
 

diff --git a/Dockerfile b/Dockerfile
@@ -58,7 +58,7 @@ FROM  ubuntu:16.04
 
 LABEL maintainer="cgphelp@sanger.ac.uk"\
       uk.ac.sanger.cgp="Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute" \
-      version="5.0.4" \
+      version="5.0.5" \
       description="pcap-core"
 
 ENV OPT /opt/wtsi-cgp

diff --git a/bin/merge_or_mark.pl b/bin/merge_or_mark.pl
@@ -85,6 +85,7 @@ sub setup {
               'n|nomarkdup' => \$opts{'nomarkdup'},
               'p|process=s' => \$opts{'process'},
               'q|querynamesort' => \$opts{'qnamesort'},
+              'i|noindex' => \$opts{'noindex'},
               'csi' => \$opts{'csi'},
               'c|cram' => \$opts{'cram'},
               'sc|scramble=s' => \$opts{'scramble'},
@@ -119,6 +120,9 @@ sub setup {
   if($opts{'qnamesort'} && !$opts{'nomarkdup'}){
       die "ERROR: -qnamesort can only be used in conjunction with -nomarkdups\n";
   }
+  if($opts{'noindex'} && !$opts{'qnamesort'}){
+      die "ERROR: -noindex can only be used in conjunction with -qnamesort\n";
+  }
   $opts{'sortorder'} = $QUERYNAME_SORT_ORDER if($opts{'qnamesort'});
 
   if($opts{'threads'} > 4) {
@@ -168,6 +172,8 @@ =head1 SYNOPSIS
     -nomarkdup   -n   Don't mark duplicates [flag]
     -qnamesort   -q   Use queryname sorting flag in bammerge rather than coordinate. [flag].
                       To be used in conjunction with -nomarkdup only
+    -noindex     -i   Don't attempt to index the merged file. Only available in conjunction with 
+                      -qnamesort.
     -csi              Use CSI index instead of BAI for BAM files [flag].
     -cram        -c   Output cram, see '-sc' [flag]
     -scramble    -sc  Single quoted string of parameters to pass to Scramble when '-c' used
@@ -243,6 +249,11 @@ =head2 OPTIONAL parameters
 Use queryname sorting in bammerge calls rather than the default coordinate.
 Can only be used in combination with B<-nomarkdup>
 
+=item B<-noindex>
+
+Don't attempt to generate an index for the merged file.
+Can only be used in combination with B<-qnamesort>
+
 =item B<-cram>
 
 Final output file will be a CRAM file instead of BAM.  To tune the the compression methods see then

diff --git a/lib/PCAP.pm b/lib/PCAP.pm
@@ -28,7 +28,7 @@ use FindBin qw($Bin);
 use File::Which qw(which);
 # don't use autodie, only core perl in here
 
-our $VERSION = '5.0.4';
+our $VERSION = '5.0.5';
 our @EXPORT = qw($VERSION _which);
 
 const my $LICENSE =>

diff --git a/lib/PCAP/Bam.pm b/lib/PCAP/Bam.pm
@@ -44,6 +44,9 @@ const my $BAMBAM_MERGE_CRAM => q{%s %s tmpfile=%s level=0 %s| %s -r %s -t %d -I
 
 const my $LANE_BAMBAM_MERGE => q{%s SO=%s %s tmpfile=%s level=0 | pee '%s tmpfile=%s index=1 md5=1 numthreads=%d md5filename=%s.md5 indexfilename=%s.%s > %s' '%s -o %s.bas -@ %d'};
 const my $LANE_BAMBAM_MERGE_CRAM => q{%s SO=%s %s tmpfile=%s level=0 | %s -r %s -t %d -I bam -O cram %s | tee %s | %s index - %s.crai};
+const my $LANE_BAMBAM_MERGE_NOIDX => q{%s SO=%s %s tmpfile=%s level=0 | pee '%s tmpfile=%s md5=1 numthreads=%d md5filename=%s.md5 > %s' '%s -o %s.bas -@ %d'};
+const my $LANE_BAMBAM_MERGE_CRAM_NOIDX => q{%s SO=%s %s tmpfile=%s level=0 | %s -r %s -t %d -I bam -O cram %s %s};
+
 const my $LANE_BAMBAM_DUP => q{%s level=0 %s | %s -l 0 -m | %s tmpfile=%s level=0 markthreads=%d M=%s.met | %s -l 0 -p | pee '%s tmpfile=%s index=1 md5=1 numthreads=%d md5filename=%s.md5 indexfilename=%s.%s > %s' '%s -o %s.bas -@ %d'};
 const my $LANE_BAMBAM_DUP_CRAM => q{%s level=0 %s | %s -l 0 -m | %s tmpfile=%s level=0 markthreads=%d M=%s.met | %s -l 0 -p | %s -r %s -t %d -I bam -O cram %s | tee %s | %s index - %s.crai};
 
@@ -131,9 +134,10 @@ sub merge_or_mark_lanes {
 
   # subtly different, as need to strip mmQc before dup-rem, and then reapply
   if(defined $options->{'nomarkdup'} && $options->{'nomarkdup'} == 1) {
-    if($options->{'cram'}) {
-      my $add_sc = $options->{'scramble'} || q{};
-      $commands[0] = sprintf $LANE_BAMBAM_MERGE_CRAM,
+      if(defined $options->{'noindex'} && $options->{'noindex'} == 1){
+        if($options->{'cram'}) {
+            my $add_sc = $options->{'scramble'} || q{};
+            $commands[0] = sprintf $LANE_BAMBAM_MERGE_CRAM_NOIDX,
                               $tools{'bammerge'},
                               $options->{'sortorder'},
                               $input_str,
@@ -142,12 +146,10 @@ sub merge_or_mark_lanes {
                               $options->{'reference'},
                               $helper_threads,
                               $add_sc,
-                              $marked,
-                              $tools{'samtools'},
                               $marked;
-    }
-    else {
-      $commands[0] = sprintf $LANE_BAMBAM_MERGE,
+        }
+        else {
+            $commands[0] = sprintf $LANE_BAMBAM_MERGE_NOIDX,
                               $tools{'bammerge'},
                               $options->{'sortorder'},
                               $input_str,
@@ -156,11 +158,44 @@ sub merge_or_mark_lanes {
                               $brc_tmp,
                               $helper_threads,
                               $marked,
-                              $marked, $idx_type,
                               $marked,
                               $tools{'bam_stats'},
                               $marked,
                               $helper_threads;
+        }
+      }
+      else{
+        if($options->{'cram'}) {
+            my $add_sc = $options->{'scramble'} || q{};
+            $commands[0] = sprintf $LANE_BAMBAM_MERGE_CRAM,
+                                $tools{'bammerge'},
+                                $options->{'sortorder'},
+                                $input_str,
+                                $bbb_tmp,
+                                $tools{'scramble'},
+                                $options->{'reference'},
+                                $helper_threads,
+                                $add_sc,
+                                $marked,
+                                $tools{'samtools'},
+                                $marked;
+        }
+        else {
+            $commands[0] = sprintf $LANE_BAMBAM_MERGE,
+                                $tools{'bammerge'},
+                                $options->{'sortorder'},
+                                $input_str,
+                                $bbb_tmp,
+                                $tools{'bamrecompress'},
+                                $brc_tmp,
+                                $helper_threads,
+                                $marked,
+                                $marked, $idx_type,
+                                $marked,
+                                $tools{'bam_stats'},
+                                $marked,
+                                $helper_threads;
+        }
     }
   }
   else {