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fixed #13
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@keiranmraine
keiranmraine committed May 16, 2017
1 parent 32a59f4 commit 166bdae
Showing 1 changed file with 2 additions and 2 deletions.
4 changes: 2 additions & 2 deletions scripts/analysisWGS.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -102,8 +102,8 @@ if [ ! -f $OUTPUT_DIR/pre-exec.done ]; then
fi

## get sample names from BAM headers
NAME_MT=`samtools view -H $BAM_MT | perl -ne 'if($_ =~ m/^\@RG/) {($sm) = $_ =~m/\tSM:([^\t]+)/; print "$sm\n";}' | uniq`
NAME_WT=`samtools view -H $BAM_WT | perl -ne 'if($_ =~ m/^\@RG/) {($sm) = $_ =~m/\tSM:([^\t]+)/; print "$sm\n";}' | uniq`
NAME_MT=`samtools view -H $BAM_MT | perl -ne 'chomp; if($_ =~ m/^\@RG/) {($sm) = $_ =~m/\tSM:([^\t]+)/; print "$sm\n";}' | uniq`
NAME_WT=`samtools view -H $BAM_WT | perl -ne 'chomp; if($_ =~ m/^\@RG/) {($sm) = $_ =~m/\tSM:([^\t]+)/; print "$sm\n";}' | uniq`

echo -e "\tNAME_MT : $NAME_MT"
echo -e "\tNAME_WT : $NAME_WT"
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