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Id: 52905
Status: new
Priority: 0/
Queue: Bio-SamTools

Owner: Nobody in particular
Requestors: mab [...]

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Fixed in: (no value)

Subject: Bio::DB::Sam objects crashes threads
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text/plain 868b
While trying to speed up an analysis using multi-threading I realized that the Bio::DB::Sam objects seems to not be thread safe... (Hmm... maybe I am not using the exact perfect semantic here...) Attached is a very simple mock script that will run an analysis using 5 threads. If you don’t provide Bam file(s) as argument, the @bams variable stay undef and the program terminates normally. As soon as you instantiate a bam object by passing the location of a file as arguments, the threads crashes during the joining process. Interestingly enough, the Bio::DB::Bam does not get passed or used by the script, the script only instantiate the object without touching it (or even sending it to the threads...). I have not investigate the objects to find the source of the problem, but I thought it could be important to see if that can be fixed. thanks Marco
text/x-perl 853b
#!/usr/bin/perl use strict; use warnings; use Bio::DB::Sam; use threads; use Thread::Queue; MAIN:{ my $threads = 5; my @bams; @bams = map{ Bio::DB::Sam->new(-bam => $_)} @ARGV if @ARGV; my %chrs = (A => [1..10], B => [30..45], C => [101..123]); for my $chr (keys %chrs){ my @tc = (@{$chrs{$chr}}); my $q = Thread::Queue->new; $q->enqueue(@tc); my $num_workers = @tc < $threads ? @tc : $threads; # no need to be wasteful :) for (1 .. $num_workers) { threads->new(\&worker, $q,$chr,$_); } $_->join for threads->list; print "Done with chromosome $chr\n"; } exit(0); } sub worker { my $q = shift; my $chr = shift; my $th = shift; while(my $feat = $q->dequeue_nb){ print "Analyzing feature $feat from chromosome $chr in thread $th\n"; sleep 2; } }

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