comparison bin/align.pm @ 24:08bbde9d0c9d draft

Uploaded

23:7dd78ad2875f

our @ISA     = qw( Exporter );
our @EXPORT  = qw( &BWA_call &to_build &get_unique &sam_sorted_bam &get_hash_alignment &sam_to_bam_bg &sam_count &sam_count_mis &rpms_rpkm &get_fastq_seq &extract_sam );

sub to_build
{
	my $toBuildHashP  = shift; my $log = shift;

	while ( my ( $k, $v ) = each %{ $toBuildHashP } )
	{
		build_index ( $k, $log ) if $v == 1;
	}
}

sub build_index
{
	my $to_index = shift;

24:08bbde9d0c9d

our @ISA     = qw( Exporter );
our @EXPORT  = qw( &BWA_call &to_build &get_unique &sam_sorted_bam &get_hash_alignment &sam_to_bam_bg &sam_count &sam_count_mis &rpms_rpkm &get_fastq_seq &extract_sam );

sub to_build
{
  my ( $toBuildTabP, $log, $newdir ) = @_;

  foreach my  $pairs ( @{ $toBuildTabP } ) 
  {
    if (  $pairs->[0] == 1 ) 
    {   
      my $sym = $newdir.basename(${$pairs->[1]}).'_symlink.fa';
      symlink( ${$pairs->[1]}, $sym );
      ${$pairs->[1]} = $sym;
      build_index ( ${$pairs->[1]}, $log );
    }   
  }
}

sub build_index
{
	my $to_index = shift;