Fix RNEXT output

tsnorri · tsnorri · commit bce7ba4c2d10 · 2023-04-25T18:57:48.000+03:00
diff --git a/xa2multi.pl b/xa2multi.pl
@@ -9,7 +9,9 @@
 		print;
 		my @t = split("\t");
 		while ($l =~ /([^,;]+),([-+]\d+),([^,]+),(\d+);/g) {
-			my $mchr = ($t[6] eq $1)? '=' : $t[6]; # FIXME: TLEN/ISIZE is not calculated!
+			my $mchr = ($t[6] eq '=') ? $t[2] : $t[6];
+			my $mchr_ = ($mchr eq $1) ? '=' : $mchr;
+			# FIXME: TLEN/ISIZE is not calculated!
 			my $seq = $t[9];
 			my $phred = $t[10];
 			# if alternative alignment has other orientation than primary, 
@@ -19,7 +21,7 @@
 				$seq =~ tr/ACGTacgt/TGCAtgca/;
 				$phred = reverse $phred;
 			}
-			print(join("\t", $t[0], 0x100|($t[1]&0x6e9)|($2<0?0x10:0), $1, abs($2), 0, $3, @t[6..7], 0, $seq, $phred, "NM:i:$4"), "\n");
+			print(join("\t", $t[0], 0x100|($t[1]&0x6e9)|($2<0?0x10:0), $1, abs($2), 0, $3, $mchr_, $t[7], 0, $seq, $phred, "NM:i:$4"), "\n");
 		}
 	} else { print; }
 }

Original file line number	Diff line number	Diff line change
`@@ -9,7 +9,9 @@`
`9`	`9`	`print;`
`10`	`10`	`my @t = split("\t");`
`11`	`11`	`while ($l =~ /([^,;]+),([-+]\d+),([^,]+),(\d+);/g) {`
`12`		`- my $mchr = ($t[6] eq $1)? '=' : $t[6]; # FIXME: TLEN/ISIZE is not calculated!`
	`12`	`+ my $mchr = ($t[6] eq '=') ? $t[2] : $t[6];`
	`13`	`+ my $mchr_ = ($mchr eq $1) ? '=' : $mchr;`
	`14`	`+ # FIXME: TLEN/ISIZE is not calculated!`
`13`	`15`	`my $seq = $t[9];`
`14`	`16`	`my $phred = $t[10];`
`15`	`17`	`# if alternative alignment has other orientation than primary,`
`@@ -19,7 +21,7 @@`
`19`	`21`	`$seq =~ tr/ACGTacgt/TGCAtgca/;`
`20`	`22`	`$phred = reverse $phred;`
`21`	`23`	`}`
`22`		`- print(join("\t", $t[0], 0x100\|($t[1]&0x6e9)\|($2<0?0x10:0), $1, abs($2), 0, $3, @t[6..7], 0, $seq, $phred, "NM:i:$4"), "\n");`
	`24`	`+ print(join("\t", $t[0], 0x100\|($t[1]&0x6e9)\|($2<0?0x10:0), $1, abs($2), 0, $3, $mchr_, $t[7], 0, $seq, $phred, "NM:i:$4"), "\n");`
`23`	`25`	`}`
`24`	`26`	`} else { print; }`
`25`	`27`	`}`