changed output format to contain FPKM etc. ; fixed a bug for paired-end reads

[rsem.git] / rsem-form-counts-matrix

diff --git a/rsem-form-counts-matrix b/rsem-form-counts-matrix
index b5324a525b3045c5898d22d3e1fc66291a7f8597..d275d6e3e07bf94bea346028a4654b98bb9ae0ea 100755 (executable)
--- a/rsem-form-counts-matrix
+++ b/rsem-form-counts-matrix
@@ -8,6 +8,8 @@ if (scalar(@ARGV) == 0) {
     exit(-1);
 }
 
+my $offsite = 4; # for new file formats
+
 my $line;
 my $n = scalar(@ARGV);
 my $M = -1;
@@ -19,7 +21,7 @@ for (my $i = 0; $i < $n; $i++) {
     while ($line = <INPUT>) {
        chomp($line); 
        my @fields = split(/\t/, $line);
-       push(@sample, $fields[1]);
+       push(@sample, $fields[$offsite]);
     }
     close(INPUT);
     if (scalar(@sample) == 0) {