BWA seems to ignore bz2 files
Issue #11
resolved
it does not accept bz2 files and we dont descpmpress them
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- changed status to resolved
Fixing Issue
#11. BWA now reads compressed files→ <<cset 9a37d0f96d75>>
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Solved using a very smart solution (from google) :
sub system_bash { my @args = ( "bash", "-c", shift ); system(@args); }
$command="bwa mem ".$bwapardef." ".$bwaindex." <(bunzip2 -c $file) <(bunzip2 -c $mate_file)>".$real_name;
system_bash($command)