Merge branch 'hotfix/v3.3.4'

Author: keiranmraine

docs.tar.gz

@@ -27,7 +27,7 @@ use FindBin qw($Bin);
 use File::Which qw(which);
 # don't use autodie, only core perl in here
 
-our $VERSION = '3.3.3';
+our $VERSION = '3.3.4';
 our @EXPORT = qw($VERSION _which);
 
 const my $LICENSE =>

lib/PCAP.pm

@@ -35,7 +35,7 @@ use File::Copy qw(copy);
 use PCAP::Bwa::Meta;
 
 const my $BWA_ALN => q{ aln%s -t %s -f %s_%s.sai %s %s.%s};
-const my $BAMFASTQ => q{%s view -F 3584 -T %s -u %s| %s exclude=QCFAIL,SECONDARY,SUPPLEMENTARY tryoq=1 gz=1 level=1 outputperreadgroup=1 outputperreadgroupsuffixF=_i.fq outputperreadgroupsuffixF2=_i.fq T=%s outputdir=%s split=%s};
+const my $BAMFASTQ => q{%s view -F 2816 -T %s -u %s| %s exclude=QCFAIL,SECONDARY,SUPPLEMENTARY tryoq=1 gz=1 level=1 outputperreadgroup=1 outputperreadgroupsuffixF=_i.fq outputperreadgroupsuffixF2=_i.fq T=%s outputdir=%s split=%s};
 const my $CRAMFASTQ => q{%s reference=%s inputformat=cram exclude=QCFAIL,SECONDARY,SUPPLEMENTARY tryoq=1 gz=1 level=1 outputperreadgroup=1 outputperreadgroupsuffixF=_i.fq outputperreadgroupsuffixF2=_i.fq T=%s outputdir=%s split=%s filename=%};
 const my $BWA_MEM => q{ mem %s %s -R %s -t %s %s};
 const my $ALN_TO_SORTED => q{ sampe -P -a 1000 -r '%s' %s %s_1.sai %s_2.sai %s.%s %s.%s | %s fixmate=1 inputformat=sam level=1 tmpfile=%s_tmp O=%s_sorted.bam};