checkExpansions.sh

#!/bin/bash
BAM=$1
MaxRepLength=$2
HG38=$3
for i in {1,2,3,4,5,6,7,8,9,10,12,13,14,16,18,19,20,21,22,X}
do
    ./popSTR computeReadAttributes $BAM . <(cut -d ' ' -f 1-11,14- ./panelMarkerInfo/chr${i}markerInfo) 4 $MaxRepLength chr${i} $HG38 ./markerInfo/longRepeats Y
done

while read -r fileName limit
do
    lineAboveLimit=`awk -v limit="$limit" 'NF==8 && substr($1,1,3) != "chr" && $1>=limit' ./attributes/${fileName} | wc -l`
    motifLength=`echo $fileName | cut -d '_' -f 2 | awk '{print length($1)}'`
    lineAtLengthLimit=`awk -v motifLength="$motifLength" -v maxRepLength="$MaxRepLength" 'NF==8 && substr($1,1,3) != "chr" && $1>=maxRepLength/motifLength' ./attributes/${fileName} | wc -l`
    echo "Marker $fileName has $lineAboveLimit reads supporting a pathogenic expansion and $lineAtLengthLimit reads with repeat longer than $MaxRepLength bases."
done < ./panelMarkerInfo/markersAndLimits