From b0dd62230f914a1b5bee4482cfa14532a568f999 Mon Sep 17 00:00:00 2001
From: raysloks <raysloks@gmail.com>
Date: Fri, 5 May 2023 09:56:31 +0200
Subject: [PATCH] Fixes the shared baf.tmp issue

---
 utils/generate_gens_data.pl | 133 ++++++++++++++++++------------------
 1 file changed, 67 insertions(+), 66 deletions(-)

diff --git a/utils/generate_gens_data.pl b/utils/generate_gens_data.pl
index 309202e8..7f439499 100755
--- a/utils/generate_gens_data.pl
+++ b/utils/generate_gens_data.pl
@@ -23,7 +23,7 @@
 # Calculate coverage data
 open( COVOUT, ">".$COV_OUTPUT );
 for my $i (0..$#COV_WINDOW_SIZES) {
-    generate_cov_bed($cov_fn, $COV_WINDOW_SIZES[$i], $PREFIXES[$i]);
+	generate_cov_bed($cov_fn, $COV_WINDOW_SIZES[$i], $PREFIXES[$i]);
 }
 close COVOUT;
 
@@ -31,13 +31,14 @@
 print STDERR "Calculating BAFs from gvcf...\n";
 # Calculate BAFs
 system( 
-    $SCRIPT_ROOT."/gvcfvaf.pl ".
-    "$gvcf_fn $GNOMAD > baf.tmp"
-    );
+	$SCRIPT_ROOT."/gvcfvaf.pl ".
+	"$gvcf_fn $GNOMAD > ".$SAMPLE_ID.".baf.tmp"
+	);
+
 open( BAFOUT, ">".$BAF_OUTPUT );
 for my $i (0..$#BAF_SKIP_N) {
-    print STDERR "Outputting BAF $PREFIXES[$i]...\n";
-    generate_baf_bed("baf.tmp", $BAF_SKIP_N[$i], $PREFIXES[$i]);
+	print STDERR "Outputting BAF $PREFIXES[$i]...\n";
+	generate_baf_bed($SAMPLE_ID.".baf.tmp", $BAF_SKIP_N[$i], $PREFIXES[$i]);
 }
 close BAFOUT;
 
@@ -46,76 +47,76 @@
 system("tabix -f -p bed $BAF_OUTPUT.gz");
 system("bgzip -f -\@10 $COV_OUTPUT");
 system("tabix -f -p bed $COV_OUTPUT.gz");
-unlink("baf.tmp");
+unlink($SAMPLE_ID.".baf.tmp");
 
 sub generate_baf_bed {
-    my( $fn, $skip, $prefix ) = @_;
-    open( my $fh, $fn );
-    my $i = 0;
-    while(<$fh>) {
-	if( $i++ % $skip == 0 ) {
-	    chomp;
-	    my @a = split /\t/;
-	    print BAFOUT $prefix."_".$a[0]."\t".($a[1]-1)."\t".$a[1]."\t".$a[2]."\n";
+	my( $fn, $skip, $prefix ) = @_;
+	open( my $fh, $fn );
+	my $i = 0;
+	while(<$fh>) {
+		if( $i++ % $skip == 0 ) {
+			chomp;
+			my @a = split /\t/;
+			next if $#a != 2;
+			print BAFOUT $prefix."_".$a[0]."\t".($a[1]-1)."\t".$a[1]."\t".$a[2]."\n";
+		}
 	}
-    }
-    close $fn;
+	close $fn;
 }
 
 sub generate_cov_bed {
 
-    my( $fn, $win_size, $prefix ) = @_;
-    
-    open(my $fh, $fn);
-    my( $reg_start, $reg_end, $reg_chr, $force_end );
-    my @reg_ratios;
-    while(<$fh>) {
-	next if /^@/ or /^CONTIG/;
-	chomp;
-	my ($chr, $start, $end, $ratio ) = split /\t/;
-	my $orig_end = $end;
-	unless( $reg_start ) {
-	    $reg_start = $start;
-	    $reg_end = $end;
-	    $reg_chr = $chr;
-	}
-
-	if( $chr eq $reg_chr ) {
-	    if( $start - $reg_end < $win_size ) {
-		push @reg_ratios, $ratio;
-		$reg_end = $end;
-	    }
+	my( $fn, $win_size, $prefix ) = @_;
+	
+	open(my $fh, $fn);
+	my( $reg_start, $reg_end, $reg_chr, $force_end );
+	my @reg_ratios;
+	while(<$fh>) {
+		next if /^@/ or /^CONTIG/;
+		chomp;
+		my ($chr, $start, $end, $ratio ) = split /\t/;
+		my $orig_end = $end;
+		unless( $reg_start ) {
+			$reg_start = $start;
+			$reg_end = $end;
+			$reg_chr = $chr;
+		}
 
-	    # If there is a large gap to the next region, prematurely end region
-	    else {
-		$force_end = 1;
-		$end = $reg_end;
-	    }
-	}
-	else {
-	    $force_end = 1;
-	    $end = $reg_end;
-	}
-	if( $end - $reg_start + 1 >= $win_size or $force_end ) {
-	    my $mid_point = $reg_start + int(($end - $reg_start)/2);
-	    print COVOUT $prefix."_".$reg_chr."\t".($mid_point-1)."\t".$mid_point."\t".mean(@reg_ratios)."\n";
-	    undef $reg_start;
-	    undef $reg_end;
-	    undef $reg_chr;
-	    undef @reg_ratios;
-	}
+		if( $chr eq $reg_chr ) {
+			if( $start - $reg_end < $win_size ) {
+				push @reg_ratios, $ratio;
+				$reg_end = $end;
+			}
+			# If there is a large gap to the next region, prematurely end region
+			else {
+				$force_end = 1;
+				$end = $reg_end;
+			}
+		}
+		else {
+			$force_end = 1;
+			$end = $reg_end;
+		}
+		if( $end - $reg_start + 1 >= $win_size or $force_end ) {
+			my $mid_point = $reg_start + int(($end - $reg_start)/2);
+			print COVOUT $prefix."_".$reg_chr."\t".($mid_point-1)."\t".$mid_point."\t".mean(@reg_ratios)."\n";
+			undef $reg_start;
+			undef $reg_end;
+			undef $reg_chr;
+			undef @reg_ratios;
+		}
 
-	if( $force_end ) {
-	    $reg_start = $start;
-	    $reg_end = $orig_end;
-	    $reg_chr = $chr;
-	    push @reg_ratios, $ratio;
-	    undef $force_end;
+		if( $force_end ) {
+			$reg_start = $start;
+			$reg_end = $orig_end;
+			$reg_chr = $chr;
+			push @reg_ratios, $ratio;
+			undef $force_end;
+		}
 	}
-    }
-    close $fh;
+	close $fh;
 }
-    
+	
 sub mean {
-    return sum(@_)/@_;
+	return sum(@_)/@_;
 }