perl/bsvf/cmp/git.diff

   1 index b3f9c6a4..3fb63b82
   2 --- a/perl/bsvf/cmp/vfs-2016-08-17.r2/include/ReadPreprocess.pm
   3 +++ b/perl/bsvf/cmp/vfs-2016-08-17.r2/include/ReadPreprocess.pm
   4 @@ -202,7 +202,7 @@ sub dynamic_trim_fastq_tag { #(File_in, phred_scale, desiredQ, emit_threshold)
   5         my $is_gzip_input = DetermineFileType ($file_in);
   6
   7         if ($is_gzip_input) {
   8 -               open ($FH,"-|", "gzip -dc $file_in") or die "Can't open $file_in (gzipped) for reading : $!";
   9 +               open ($FH, "<:gzip", $file_in) or die "Can't open $file_in (gzipped) for reading : $!";
  10         }
  11         else {
  12                 open $FH, '<', $file_in or die "Can't open $file_in for reading : $!";
  13
  14 index 73005d03..30013ace 100644
  15 --- a/perl/bsvf/bin/BSseeker2/bs_utils/utils.py
  16 +++ b/perl/bsvf/bin/BSseeker2/bs_utils/utils.py
  17 @@ -272,7 +272,7 @@ def read_fasta(fasta_file):
  18          print "[Error] Cannot find fasta file : %s !" % fasta_file
  19          exit(-1)
  20      sanitize = re.compile(r'[^ACTGN]')
  21 -    sanitize_seq_id = re.compile(r'[^A-Za-z0-9]')
  22 +    sanitize_seq_id = re.compile(r'[^A-Za-z0-9|]')
  23
  24      chrom_seq = []
  25      chrom_id = None
  26