join _2 to _1 and shift SAM alignment

# SUPER_1_1 is 1085289420bp
# SUPER_1_2 joins and both become SUPER_1
samtools view -h split_1.mapped.bam |perl -pne 's/SUPER_1_1/SUPER_1/g' |perl -ne 'chomp;@F=split(/\t/,$_);next if $F[1] eq "SN:SUPER_1";if(/SN:SUPER_1_2/){$F[1]="SN:SUPER_1";$F[2]="LN:2170579067"};if($F[2] eq "SUPER_1_2"){$F[2]="SUPER_1";$F[3]+=1085289420;$F[7]+=1085289420 if $F[6] eq "="};if($F[6] eq "SUPER_1_2"){$F[6]="SUPER_1";$F[7]+=1085289420};print join "\t", @F;print "\n"' | /software/grit/conda/envs/snake_env/bin/PretextMap --sortby nosort --mapq 0 -o fixed.pretext --highRes

join_and_shift.pl

#/usr/bin/env perl
# background:
#  SUPER_1 was split at 1085289420 into SUPER_1_1 and SUPER_1_2, to allow aligning
#  we now want to convert the alignments back into a joined SUPER_1 and need to rename
#  SUPER_1_1 and SUPER_1_2 -> SUPER_1
#  if they were SUPER_1_2 coordinates, they need shifting by 1085289420
#  we might have to calculate TLEN for cases where both are on SUPER_1
#  the header needs fixing


# in theory all SUPER_1_1 coordinates should be the same as SUPER_1
s/SUPER_1_1/SUPER_1/g;

chomp;
@F=split(/\t/,$_);

# header
next if $F[1] eq "SN:SUPER_1";
if(/SN:SUPER_1_2/){
	$F[1]="SN:SUPER_1";
	$F[2]="LN:2170579067"
}

# shift SUPER_1_2 coordinates
if($F[2] eq "SUPER_1_2"){
	$F[2]="SUPER_1";
	$F[3]+=1085289420
}
if($F[6] eq "SUPER_1_2"){
	$F[6]="SUPER_1";
	$F[7]+=1085289420
}

# fix TLEN
# is an approximation, as I don't have the second cigar at that point
if ($F[2] eq 'SUPER_1' && $F[6] eq 'SUPER_1'){
	$F[8]=$F[7]-$F[3]+1
}

print join "\t", @F;
print "\n"'