#!/bin/bash
# env bamset=cg*.bam

echo "# pair insert length n, mean, sd"
for bam in $bamset; do {
 nam=`basename $bam .bam`
 echo -n "$nam	"
 samtools view -f2 -F 0x100 $bam scaffold_5 | grep -v 'XS:A' | cut -f9 | perl -ne\
'chomp; $v=abs($_); if($v<999){ $s+= $v; $ss+= $v*$v; $n++; } 
END { $m=$s/$n; $sd=int(sqrt(($ss - $m*$s)/$n)); $m=int($m); print join("\t",$n,$m,$sd)."\n"; }'

} done