Use of uninitialized value

[riasc]

Hello Tim,

on a recent run with the original LIGR-seq dataset I'm getting the following messages when calling Aligater detect:

Use of uninitialized value $name in pattern match (m//) at /data/richard/LIGR-seq/Aligater/bin/detect.pl line 572, <> line 1087686070.
Use of uninitialized value $name in pattern match (m//) at /data/richard/LIGR-seq/Aligater/bin/detect.pl line 571, <> line 1087686070.
Use of uninitialized value $name in pattern match (m//) at /data/richard/LIGR-seq/Aligater/bin/detect.pl line 572, <> line 1087686070.
Use of uninitialized value $biotype in string eq at /data/richard/LIGR-seq/Aligater/bin/detect.pl line 560, <> line 1087686070.

So I called ./Aligater/aligater detect -p 40 --gtf GCF_000001405.39_GRCh38.p13_all.gtf --rmsk repeatMasker.hg19.slim.bed --gfam Homo_sapiens.gene_families.txt < input.sam > outputlig

So the lines refer to:

# rank biotype by..
sub biorank {
  my $biotype = shift;
  return 6 if ($biotype eq "misc-RNA");
  return 5 if ($biotype =~ /RNA/);
  return 3 if ($biotype =~ /intron/);
  return 2 if ($biotype !~ /protein-coding/);
  return 4;
}

So this is just for sorting and can be neglected? Thanks