removed breakpoint adjustment using known exon boundaries

Zheng-NGS-Lab · Mar 3, 2023 · 5b1ca52 · 5b1ca52
1 parent de49246
commit 5b1ca52
Showing 1 changed file with 3 additions and 70 deletions.
diff --git a/exec/SplitFusion.2_bam-breakpoint.sh b/exec/SplitFusion.2_bam-breakpoint.sh
@@ -160,76 +160,9 @@ if [ -s _sa.bed ]; then
                                 print $0,$3"_"$4
                         }
                 }' _right | tr ' ' '\t' | sed 1d | sort --parallel=$thread -k1,1b -S $memG | join _lefts.s - | \
-			$awk -v p=${SFpath} -v w=${genomeVer} 'BEGIN{
-	while (getline<sprintf("%s/inst/data/%s_refGene.mostExon.NM",p,w)) {
-		if ($8~/^[0-9]+$/) {
-		for (i=1;i<=$8;i++) {
-                        split($9,b,",");
-                        split($10,c,",");
-                        a[sprintf("%s_%s",$2,b[i]+1)]=1;
-                        a[sprintf("%s_%s",$2,c[i])]=1;
-                }
-		}
-        }
-}
-{
-	if (w=="hg19") {
-	  if ($3!~/^chr/){$3=sprintf("chr%s",$3)}
-	  if ($13!~/^chr/){$13=sprintf("chr%s",$13)}
-	  if ($11!~/^chr/){$11=sprintf("chr%s",$11)}
-	  if ($21!~/^chr/){$21=sprintf("chr%s",$21)}
-	}
-        adj = $10-$9+$20-$19+2 - $2;
-        if ($2 == $12 && adj > 0 && ($8~/[0-9]+M[0-9]+[HS]/ || $8~/[0-9]+[HS][0-9]+M/) && ($18~/[0-9]+M[0-9]+[HS]/ || $18~/[0-9]+[HS][0-9]+M/)) {
-                score=a[$11]+a[$21]; adji = -1; nadj = adj;
-                for (i=0;i<=adj;++i) {
-                        if ($7=="+") {
-                                b1=sprintf("%s_%s",$3,$5-adj+i);
-                        } else {
-                                b1=sprintf("%s_%s",$3,$5+adj-i);
-                        }
-                        if ($17=="+") {
-                                b2=sprintf("%s_%s",$13,$14+i);
-                        } else {
-                                b2=sprintf("%s_%s",$13,$14-i);
-                        }
-                        nscore = a[b1]+a[b2];
-                        if (nscore > score || (nscore == score && nadj > 0)) {
-                                score = a[b1]+a[b2];
-                                adji = i;
-				nadj = 0;
-                        }
-                }
-                if (adji >= 0) {
-                        if ($8~/H/){sh8="H"}else{sh8="S"}
-                        if ($18~/H/){sh18="H"}else{sh18="S"}
-                        if ($7=="+") {
-                                $5-=(adj-adji);
-                                $10-=(adj-adji);
-                                $8=sprintf("%dM%d%s",$10,$2-$10,sh8);
-                        } else {
-                                $5+=(adj-adji);
-                                $10-=(adj-adji);
-                                $8=sprintf("%d%s%dM",$2-$10,sh8,$10);
-                        }
-                        $11=sprintf("%s_%s",$3,$5);
-                        if ($17=="+") {
-                                $14+=adji;
-                                $19+=adji;
-                                $18=sprintf("%d%s%dM",$19-1,sh18,$12-$19+1);
-                        } else {
-                                $14-=adji;
-                                $19+=adji;
-                                $18=sprintf("%dM%d%s",$12-$19+1,$19-1,sh18);
-                        }
-                        $21=sprintf("%s_%s",$13,$14);
-		}
-	}
-		if ($11 < $21){
-			pp=$11"__"$21
-		} else {pp=$21"__"$11
-		}; 
-		print $0,pp
+	$awk '{
+		if ($11 < $21){pp=$11"__"$21} else {pp=$21"__"$11};
+                print $0,pp
 	}' | sort --parallel=$thread -k1,1b -S $memG > _breakpoint.noFilter2
         rm _left _left2 _lefts.s _right _corr.ligat1s _sa.len.bed.mq _sa.bed _sa.len
 else