Merge commit 'refs/pull/111/head' of github.com:wtsi-npg/p4 into HEAD

Changes

@@ -1,6 +1,13 @@
 CHANGES LOG
 -----------
 
+release 0.17
+ - human split with no target align (secondary stage) template introduced
+ - initial work for stage one (bcl, adapter, phiX and spatial filter to split processing) using templates
+ - bammarkduplicates reintroduced for unaligned file because downstream qc processing relies on presence of markdups_metrics file
+ - library cram merging: merge_aligned.json and merge_final_output_prep.json
+ - remove potential deadlock by using non-blocking open of STDIN
+
 release 0.16.4
  - add extra branch to teepot command in to stream seqchksum output downstream (instead of using a file as an internal node)
 

bin/viv.pl

@@ -6,6 +6,7 @@
 use File::Slurp;
 use JSON;
 use POSIX;
+use Fcntl;
 use File::Temp qw/ tempdir /;
 use Getopt::Std;
 use Readonly;
@@ -303,18 +304,21 @@ sub _fork_off {
 			$0 .= q{ (pending }.$node->{'id'}.qq{: $cmd)}; #rename process so fork can be easily identified whilst open waits on fifo
 			open STDERR, q(>), $node->{'id'}.q(.).$$.q(.err) or croak "Failed to reset STDERR, pid $$ with cmd: $cmd";
 			select(STDERR);$|=1;
+			print STDERR "Process $$ for cmd $cmd:\n";
+			print STDERR ' fileno(STDERR,'.(fileno STDERR).")\n";
 			if(not $node->{use_STDIN}) { $node->{'STDIN'} ||= '/dev/null'; }
 			if($node->{'STDIN'}) {
-				open STDIN,  q(<), $node->{'STDIN'} or croak "Failed to reset STDIN, pid $$ with cmd: $cmd";
+				sysopen STDIN, $node->{'STDIN'}, O_RDONLY|O_NONBLOCK or croak "Failed to reset STDIN, pid $$ with cmd: $cmd\n$!";
+				fcntl STDIN, F_SETFL, (fcntl STDIN,F_GETFL,0 or croak "fcntl F_GETFL fail $!")&~O_NONBLOCK or croak "fcntl F_SETFL fail $!" ;
 			}
+			print STDERR ' fileno(STDIN,'.(fileno STDIN).') reading from '.($node->{'STDIN'}?$node->{'STDIN'}:'stdin') ."\n";
 			if(not $node->{use_STDOUT}) { $node->{'STDOUT'} ||= '/dev/null'; }
 			if($node->{'STDOUT'}) {
 				open STDOUT, q(>), $node->{'STDOUT'} or croak "Failed to reset STDOUT, pid $$ with cmd: $cmd";
 			}
-			print STDERR "Process $$ for cmd $cmd:\n";
-			print STDERR ' fileno(STDIN,'.(fileno STDIN).') reading from '.($node->{'STDIN'}?$node->{'STDIN'}:'stdin') ."\n";
 			print STDERR ' fileno(STDOUT,'.(fileno STDOUT).') writing to '.($node->{'STDOUT'}?$node->{'STDOUT'}:'stdout') ."\n";
-			print STDERR ' fileno(STDERR,'.(fileno STDERR).")\n";
+			print STDERR ' select waiting on STDIN' ."\n";
+			my$rin="";vec($rin,fileno(STDIN),1)=1; select($rin,undef,undef,undef);
 			print STDERR " execing....\n";
 			exec @cmd or croak qq[Failed to exec cmd: ], join " ", @cmd;
 		}

bin/vtfp.pl

@@ -380,7 +380,7 @@ sub subst_walk {
 		}
 	}
 	elsif(ref $elem eq q[ARRAY]) {
-		for my $i (0 .. $#{$elem}) {
+		for my $i (reverse (0 .. $#{$elem})) {
 			# if one of the elements is a subst_param hash,
 			if(ref $elem->[$i] eq q[HASH] and my $param_name = $elem->[$i]->{subst}) {
 				# value for a "subst" key must always be the name of a parameter
@@ -476,7 +476,7 @@ sub fetch_subst_value {
 			$logger->($VLFATAL, q[subst_constructor vals attribute must be array, param_name: ], $param_name);
 		}
 
-		for my $i (0..$#$vals) {
+		for my $i (reverse (0..$#$vals)) {
 			if(ref $vals->[$i] eq q[HASH] and $vals->[$i]->{subst}) {
 				$vals->[$i] = fetch_subst_value($vals->[$i]->{subst}, $param_store, $subst_requests);
 				if(ref $vals->[$i] eq q[ARRAY]) {