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Use multithread parameter for samtools depth #33

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Use multithread parameter for samtools depth #33

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dff5a09
Update runSR.sh
SAMtoBAM Jan 7, 2026
2d2586b
Update runLR.sh
SAMtoBAM Jan 7, 2026
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2 changes: 1 addition & 1 deletion src/runLR.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -154,7 +154,7 @@ fi


echo -e "[M::worker_pipeline:: Compute effective SMS coverage]"
samtools depth -a LRout/$LRname"_sort.bam" | perl $src/avgdep.pl LRout seq.size - > LRout/$LRname"_sort.depth"
samtools depth -@ $t -a LRout/$LRname"_sort.bam" | perl $src/avgdep.pl LRout seq.size - > LRout/$LRname"_sort.depth"
LRavg_depth=$(cat LRout/Avgcov)
echo -e "[M::SMS mapping coverage: $LRavg_depth]"
rm LRout/Avgcov
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2 changes: 1 addition & 1 deletion src/runSR.sh
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Expand Up @@ -129,7 +129,7 @@ fi
echo -e "[M::worker_pipeline:: Compute effective NGS coverage]"
#-------------------------------------------------------------------------------------------------------------
#samtools depth -a SRout/$SRname"_sort.bam" > SRout/$SRname"_sort.depth"
samtools view -h -@ $t -q $mapquality SRout/$SRname"_sort.bam" |samtools depth -a - | perl $src/avgdep.pl SRout seq.size - >SRout/$SRname"_sort.depth"
samtools view -h -@ $t -q $mapquality SRout/$SRname"_sort.bam" |samtools depth -@ $t -a - | perl $src/avgdep.pl SRout seq.size - >SRout/$SRname"_sort.depth"

SRavg_depth=$(cat SRout/Avgcov)
echo -e "[M::NGS mapping coverage: $SRavg_depth]"
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