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BAC graphs

~/work/potato/scripts/sam-to-R.py -m 1000 -i 99.98 falcon <(samtools view falcon.2.sorted.bam)

Filtering coords

To get the bits of the assemblies that actually overlap the BAC

awk 'BEGIN {lasts=""; lastm=0;} $5 > 4000 && $7 > 94 {if ($12 != lasts || $1 > lastm) {lasts = $12; lastm=$2; print $0;}}' \
    discovar-mp-dt-bn.coords \
    > discovar-mp-dt-bn.fcoords

Make trim files for sequences in the trimmed fasta

sort -n -k3,3 discovar-mp-dt-bn.fcoords \
    | sort -s -k13 \
    | sort -s -k12,12 \
    | awk 'BEG {lastn="";lasts=0;laste=0;} {n=$13;if ($3<$4){s=$3;e=$4}else{s=$4;e=$3} if(lastn=="") {lastn=n;lasts=s;laste=e} else if (lastn!=n) {print lastn,lasts,laste; lastn=n;lasts=s;laste=e;} else if (s > laste+100) {print n,lasts,laste; lasts=s;laste=e} else {laste=e}} END {print lastn,lasts,laste}' \
          > discovar-mp-dt-bn.scaftrim